AgrO is an ontlogy for representing agronomic practices, techniques, variables and related entities
Agronomy Ontology
The Agronomy Ontology by CGIAR is licensed under CC BY 4.0 (https://creativecommons.org/licenses/by/4.0/).
Relates an entity in the ontology to the name of the variable that is used to represent it in the code that generates the BFO OWL file from the lispy specification.
Really of interest to developers only
BFO OWL specification label
Relates an entity in the ontology to the term that is used to represent it in the the CLIF specification of BFO2
BFO CLIF specification label
editor preferred term
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 term should be used and/or a citation to a work which uses it. May also include other kinds of examples that facilitate immediate understanding, such as widely know prototypes or instances of a class, or cases where a relation is said to hold.
in branch
An annotation property indicating which module the terms belong to. This is currently experimental and not implemented yet.
has curation status
PERSON:Alan Ruttenberg
PERSON:Bill Bug
PERSON:Melanie Courtot
definition
The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.
2012-04-05: Barry Smith The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible. Can you fix to something like: A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property. Alan Ruttenberg Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. On the specifics of the proposed definition: We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with.
editor note
An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology.
term editor
Name of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several people
20110707, MC: label update to term editor and definition modified accordingly. See https://github.com/information-artifact-ontology/IAO/issues/115.
alternative term
An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent)
definition source
Formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007
Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w
has obsolescence reason
Relates an annotation property to an obsolescence reason. The values of obsolescence reasons come from a list of predefined terms, instances of the class obsolescence reason specification.
curator note
An administrative note of use for a curator but of no use for a user
term tracker item
the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/
An IRI or similar locator for a request or discussion of an ontology term.
Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg
The 'tracker item' can associate a tracker with a specific ontology term.
ontology term requester
The name of the person, project, or organization that motivated inclusion of an ontology term by requesting its addition.
The 'term requester' can credit the person, organization or project who request the ontology term.
is denotator type
Relates an class defined in an ontology, to the type of it's denotator
In OWL 2 add AnnotationPropertyRange('is denotator type' 'denotator type')
Alan Ruttenberg
imported from
For external terms/classes, the ontology from which the term was imported
expand expression to
ObjectProperty: RO_0002104 Label: has plasma membrane part Annotations: IAO_0000424 "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.org/obo/owl/GO#GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)"
A macro expansion tag applied to an object property (or possibly a data property) which can be used by a macro-expansion engine to generate more complex expressions from simpler ones
Chris Mungall
expand assertion to
ObjectProperty: RO??? Label: spatially disjoint from Annotations: expand_assertion_to "DisjointClasses: (http://purl.obolibrary.org/obo/BFO_0000051 some ?X) (http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)"
A macro expansion tag applied to an annotation property which can be expanded into a more detailed axiom.
first order logic expression
antisymmetric property
part_of antisymmetric property xsd:true
Use boolean value xsd:true to indicate that the property is an antisymmetric property
OBO foundry unique label
An alternative name for a class or property which is unique across the OBO Foundry.
The intended usage of that property is as follow: OBO foundry unique labels are automatically generated based on regular expressions provided by each ontology, so that SO could specify unique label = 'sequence ' + [label], etc. , MA could specify 'mouse + [label]' etc. Upon importing terms, ontology developers can choose to use the 'OBO foundry unique label' for an imported term or not. The same applies to tools .
PERSON:Bjoern Peters
PERSON:Chris Mungall
GROUP:OBO Foundry <http://obofoundry.org/>
has ID digit count
Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> Annotations: 'has ID prefix': "http://purl.obolibrary.org/obo/RO_" 'has ID digit count' : 7, rdfs:label "RO id policy" 'has ID policy for': "RO"
Relates an ontology used to record id policy to the number of digits in the URI. The URI is: the 'has ID prefix" annotation property value concatenated with an integer in the id range (left padded with "0"s to make this many digits)
Person:Alan Ruttenberg
has ID range allocated
Datatype: idrange:1 Annotations: 'has ID range allocated to': "Chris Mungall" EquivalentTo: xsd:integer[> 2151 , <= 2300]
Relates a datatype that encodes a range of integers to the name of the person or organization who can use those ids constructed in that range to define new terms
has ID range allocated to
has ID policy for
Relating an ontology used to record id policy to the ontology namespace whose policy it manages
has ID prefix
Relates an ontology used to record id policy to a prefix concatenated with an integer in the id range (left padded with "0"s to make this many digits) to construct an ID for a term being created.
elucidation
person:Alan Ruttenberg
Person:Barry Smith
Primitive terms in a highest-level ontology such as BFO are terms which are so basic to our understanding of reality that there is no way of defining them in a non-circular fashion. For these, therefore, we can provide only elucidations, supplemented by examples and by axioms
has associated axiom(nl)
An axiom associated with a term expressed using natural language
has associated axiom(fol)
An axiom expressed in first order logic using CLIF syntax
is allocated id range
Relates an ontology IRI to an (inclusive) range of IRIs in an OBO name space. The range is give as, e.g. "IAO_0020000-IAO_0020999"
Add as annotation triples in the granting ontology
retired from use as of
relates a class of CRID to the date after which further instances should not be made, according to the central authority
In OWL 2 add AnnotationPropertyRange xsd:dateTimeStamp
has ontology root term
Ontology annotation property. Relates an ontology to a term that is a designated root term of the ontology. Display tools like OLS can use terms annotated with this property as the starting point for rendering the ontology class hierarchy. There can be more than one root.
Nicolas Matentzoglu
may be identical to
A annotation relationship between two terms in an ontology that may refer to the same (natural) type but where more evidence is required before terms are merged.
David Osumi-Sutherland
VFB
Edges asserting this should be annotated with to record evidence supporting the assertion and its provenance.
scheduled for obsoletion on or after
Used when the class or object is scheduled for obsoletion/deprecation on or after a particular date.
Chris Mungall, Jie Zheng
GO ontology
has axiom id
A URI that is intended to be unique label for an axiom used for tracking change to the ontology. For an axiom expressed in different languages, each expression is given the same URI
has axiom label
term replaced by
Use on obsolete terms, relating the term to another term that can be used as a substitute
An assertion that holds between an OWL Object Property and a temporal interpretation that elucidates how OWL Class Axioms that use this property are to be interpreted in a temporal context.
temporal interpretation
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
is part of
my brain is part of my body (continuant parthood, two material entities)
my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)
this day is part of this year (occurrent parthood)
a core relation that holds between a part and its whole
Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other.
Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/
Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime
Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.) A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'.
part_of
part of
has part
my body has part my brain (continuant parthood, two material entities)
my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)
this year has part this day (occurrent parthood)
a core relation that holds between a whole and its part
Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part.
Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.) A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'.
has_part
realized in
this disease is realized in this disease course
this fragility is realized in this shattering
this investigator role is realized in this investigation
is realized by
realized_in
[copied from inverse property 'realizes'] to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003])
Paraphrase of elucidation: a relation between a realizable entity and a process, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process
realizes
this disease course realizes this disease
this investigation realizes this investigator role
this shattering realizes this fragility
to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003])
Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process
preceded by
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.
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
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.
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
has measurement unit label
The process of creation is, for example, writing down on paper the name of a friend by deliberately creating a certain pattern using ink. Here the ink + paper is the independent continuant and the carrier is the pattern in the ink. c = pattern in the ink b = paper + ink r = friend
c specifically denotes r =def r is a portion of reality & c is a particular quality & c depends specifically on some independent continuant b & b acquired c as the result of the achievement of an objective to enable pointing to r repeatedly. Marked means there is a changed or additional quality of the bearer - the quality is the information carrier. Case 1 Memory trace as mark created when reading some description of some friend. The trace can denote. Case 2 Pattern of ink arrayed on paper as mark when writing down a friend's name Case 3 Pattern of magnetic domains on scattered pieces of a hard disk platter as mark when saving a file.
8/6/2009 Alan Ruttenberg: The suggestions is to deprecate specific and generically denotes in favor of a single denote relationship that corresponds to the generic sense
see https://github.com/information-artifact-ontology/IAO/issues/25&q=denote
Smith, Ceusters, Ruttenberg, 2000 years of philosophy
This document is about information artifacts and their representations
A (currently) primitive relation that relates an information artifact to an entity.
7/6/2009 Alan Ruttenberg. Following discussion with Jonathan Rees, and introduction of "mentions" relation. Weaken the is_about relationship to be primitive. We will try to build it back up by elaborating the various subproperties that are more precisely defined. Some currently missing phenomena that should be considered "about" are predications - "The only person who knows the answer is sitting beside me" , Allegory, Satire, and other literary forms that can be topical without explicitly mentioning the topic.
is about
An information artifact IA mentions an entity E exactly when it has a component/part that denotes E
7/6/2009 Alan Ruttenberg. P4 RC1 munges our GCI so remove it for now: mentions some entity equivalentTo has_part some ('generically denotes' some entity)
7/6/2009 Alan Ruttenberg: Add this relation following conversation with Jonathan Rees that N&S GCI for is_about was too strong. Really it was simply sufficient. To effect this change we introduce this relation, which is subproperty of is_about, and have previous GCI use this relation "mentions" in it's (logical) definition
PERSON: Jonathan Rees
Person: Alan Ruttenberg
mentions
A person's name denotes the person. A variable name in a computer program denotes some piece of memory. Lexically equivalent strings can denote different things, for instance "Alan" can denote different people. In each case of use, there is a case of the denotation relation obtaining, between "Alan" and the person that is being named.
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
2009-11-10 Alan Ruttenberg. Old definition said the following to emphasize the generic nature of this relation. We no longer have 'specifically denotes', which would have been primitive, so make this relation primitive. g denotes r =def r is a portion of reality there is some c that is a concretization of g every c that is a concretization of g specifically denotes r
Conversations with Barry Smith, Werner Ceusters, Bjoern Peters, Michel Dumontier, Melanie Courtot, James Malone, Bill Hogan
denotes
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.
is quality measurement of
inverse of the relation 'denotes'
Person: Jie Zheng, Chris Stoeckert, Mike Conlon
denoted by
relating a cartesian spatial coordinate datum to a unit label that together with the values represent a point
has coordinate unit label
relates a process to a time-measurement-datum that represents the duration of the process
is duration 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
is quality measured as
A relation between a data item and a quality of a material entity where the material entity is the specified output of a material transformation which achieves an objective specification that indicates the intended value of the specified quality.
Person:Bjoern Peters
is quality specification of
inverse of the relation of is quality specification of
quality is specified as
relates a time stamped measurement datum to the time measurement datum that denotes the time when the measurement was taken
has time stamp
relates a time stamped measurement datum to the measurement datum that was measured
has measurement datum
has_specified_input
see is_input_of example_of_usage
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.
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
is_specified_input_of
has_specified_output
A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of.
is_specified_output_of
inheres in
this fragility inheres in this vase
this fragility is a characteristic of this vase
this red color inheres in this apple
this red color is a characteristic of this apple
a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence.
a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence
A dependent inheres in its bearer at all times for which the dependent exists.
inheres_in
Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing.
characteristic of
bearer of
this apple is bearer of this red color
this vase is bearer of this fragility
Inverse of characteristic_of
a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence
A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist.
bearer_of
is bearer of
has characteristic
participates in
this blood clot participates in this blood coagulation
this input material (or this output material) participates in this process
this investigator participates in this investigation
a relation between a continuant and a process, in which the continuant is somehow involved in the process
participates_in
has participant
this blood coagulation has participant this blood clot
this investigation has participant this investigator
this process has participant this input material (or this output material)
a relation between a process and a continuant, in which the continuant is somehow involved in the process
Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time.
has_participant
A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The journal article (a generically dependent continuant) is concretized as the quality (a specifically dependent continuant), and both depend on that copy of the printed journal (an independent continuant).
An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process).
A relationship between a generically dependent continuant and a specifically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants.
is concretized as
A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The quality (a specifically dependent continuant) concretizes the journal article (a generically dependent continuant), and both depend on that copy of the printed journal (an independent continuant).
A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant.
concretizes
this catalysis function is a function of this enzyme
a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence
A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists.
function_of
is function of
This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.
function of
this red color is a quality of this apple
a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence
A quality inheres in its bearer at all times for which the quality exists.
is quality of
quality_of
quality of
this investigator role is a role of this person
a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence
A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists.
is role of
role_of
role of
this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function)
a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence
A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists.
has_function
has function
this apple has quality this red color
a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence
A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist.
has_quality
has quality
this person has role this investigator role (more colloquially: this person has this role of investigator)
a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence
A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists.
has_role
has role
a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence
has disposition
disposition of
this cell derives from this parent cell (cell division)
this nucleus derives from this parent nucleus (nuclear division)
a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity
This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'.
derives_from
derives from
this parent cell derives into this cell (cell division)
this parent nucleus derives into this nucleus (nuclear division)
a relation between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity
This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops into'. To avoid making statements about a future that may not come to pass, it is often better to use the backward-looking 'derives from' rather than the forward-looking 'derives into'.
derives_into
derives into
is location of
my head is the location of my brain
this cage is the location of this rat
a relation between two independent continuants, the location and the target, in which the target is entirely within the location
Most location relations will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime
location_of
location of
located in
my brain is located in my head
this rat is located in this cage
a relation between two independent continuants, the target and the location, in which the target is entirely within the location
Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus
located_in
This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation.
the surface of my skin is a 2D boundary of my body
a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity
A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts.
Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape.
2D_boundary_of
boundary of
is 2D boundary of
is boundary of
2D boundary of
my body has 2D boundary the surface of my skin
a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity
has boundary
has_2D_boundary
has 2D boundary
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.
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.
has positive regulatory component activity
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 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.
X ends_after Y iff: end(Y) before_or_simultaneous_with end(X)
ends after
X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y)
immediately preceded by
X immediately_precedes_Y iff: end(X) simultaneous_with start(Y)
immediately precedes
x overlaps y if and only if there exists some z such that x has part z and z part of y
overlaps
x only in taxon y if and only if x is in taxon y, and there is no other organism z such that y!=z a and x is in taxon z.
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.
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.
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
develops from
develops into
process(P1) regulates process(P2) iff: P1 results in the initiation or termination of P2 OR affects the frequency of its initiation or termination OR affects the magnitude or rate of output of P2.
regulates
Process(P1) negatively regulates process(P2) iff: P1 terminates P2, or P1 descreases the the frequency of initiation of P2 or the magnitude or rate of output of P2.
negatively regulates
Process(P1) postively regulates process(P2) iff: P1 initiates P2, or P1 increases the the frequency of initiation of P2 or the magnitude or rate of output of P2.
positively regulates
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.
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
A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations.
temporally related to
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
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
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.
developmentally preceded by
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.
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
A relationship that holds via some environmental process
evolutionarily related to
A mereological relationship or a topological relationship
mereotopologically related to
A relationship that holds between entities participating in some developmental process (GO:0032502)
developmentally related to
enables
A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities.
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
has member is a mereological relation between a collection and an item.
has member
input of
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
This relation groups causal relations between material entities and causal relations between processes
causally related to
p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain
causally upstream of
p is immediately causally upstream of q iff both (a) p immediately precedes q and (b) p is causally upstream of q. In addition, the output of p must be an input of q.
immediately causally upstream of
p 'causally upstream or within' q iff (1) the end of p is before the end of q and (2) the execution of p exerts some causal influence over the outputs of q; i.e. if p was abolished or the outputs of p were to be modified, this would necessarily affect q.
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
involved in or involved in regulation of
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.
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.
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
helper property (not for use in curation)
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.
A relationship between a material entity and a process where the material entity has some causal role that influences the process
p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one of direct activation or direct inhibition. p may be upstream, downstream, part of or a container of q.
molecular interaction relation helper property
The entity or characteristic A is causally upstream of the entity or characteristic B, A having an effect on B. An entity corresponds to any biological type of entity as long as a mass is measurable. A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size).
Process(P1) directly regulates process(P2) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2.
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.
Holds between c and p if and only if c is capable of some activity a, and a positively regulates p.
Process(P1) directly postively regulates process(P2) 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 P1 directly positively regulates P2.
Process(P1) directly negatively regulates process(P2) 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 P1 directly negatively regulates P2.
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
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.
has measurement value
has x coordinate value
has z coordinate value
has y coordinate value
A planned process in which soil is mechanicaly mixed, stirred or overturned.
incorporation process
tillage
tillage process
A planned process in which the agricultural field surface is shaped for ensuring that the depths and discharge variations over the agricultural field are relatively uniform.
land levelling
land levelling process
A planned process in which the thickness of crop residue on the surface of an agricultural field is managed.
crop residue management
residue management
crop residue management process
A planned process in which water is artificially supplied to plant or soil to sustain plants.
irrigation
irrigation process
A pruning process in which one or more suckers are removed.
desuckering process
Which suckers are removed depends on the criteria set by the agent of the desuckering process.
desuckering
A role that inheres in a water body that is realised in an irrigation process where water is transported from that water body to the target of the irrigation process.
irrigation water source role
A water body from which water is taken during an irrigation process and transported to the target of the irrigation process.
irrigation source
Volume of water applied during an irrigation process.
irrigation depth
quantity of irrigation water
volume of irrigation water
A tillage process in which, approximately, less than 15 percent of the soil surface is covered by crop residue after planting.
conventional tillage
intensive tillage
tillage_technique
conventional tillage process
A tillage process in which between, approximately, 15 to 30 percent of the soil surface is covered by plant residue after planting.
reduced tillage
reduced tillage process
A tillage process in which a proportion of plant residue, left over after a harvesting process, is left relatively undisturbed on the tilled land; this is done in order to accomplish several conservation objectives including the maintenance of soil moisture content, the reduction of soil erosion and soil compaction, and/or the reduction of labour intensity and fuel consumption.
conservation tillage
Usually 30 percent of soil surface covered by plant residue is neccessary to achieved conservation tillage.
conservation tillage process
A land levelling process in which a laser guided equipement is used to shape land surface.
laser land levelling
laser land levelling process
A pest control process in which physical means such as barriers, traps and handpicking, or physical conditions like high temperature, are used to control unwanted organisms.
mechanical pest control
mechanical pest control process
A pest control process in which organisms are employed to manage unwanted organisms.
biological control
biological pest control
biological pest control process
A planned process in which unwanted organisms are controlled.
pest control
pest control process
A pest control process in which chemical is used to manage unwanted organisms.
chemical pest control
chemical pest control process
A planned process in which the useful part or parts of the plant are gathered.
harvest
harvesting
The usefulness of the part or parts of the plant depends on the criteria set by the agent of the harvesting process.
harvest process
A planned process in which the soil is left undisturbed apart from where the seeds or planting material are placed.
zero tillage
No-till is often considered as being a conservation tillage process.
no-till
A planned process in which selected parts of the plant are removed. The practice entails targeted removal of diseased, damaged, dead, non-productive, structurally unsound, or otherwise unwanted tissue from plants. This is done in order to shape the plant or tree, improve plant or tree health, reduce the risk from falling branches, prepare nursery specimens for transplanting, and increase the yield or quality of harvested products.
pruning
thinning process
thinning
A tillage process in which saturated or near-saturated soil are worked into soft structureless mud, mainly for paddy rice production.
puddling
puddling process
A conservation tillage process in which non-inversion tillage tools that partially incorporate surface organic material are used on the entire surface of the field.
mulch tillage
mulch-till
A conservation tillage process in which, in a land with permanent ridges, previous crop's residue is cleared off ridge-tops into adjacent furrows to make way for the new crop being planted on ridges.
ridge tillage
ridge-till
A conservation tillage process in which narrow strips are tilled where seeds will be planted, leaving the soil in between the rows untilled.
zone tillage
strip-till
A plant anatomical entity that is defined to mean plants or parts of plant capable of and intended for producing or reproducing entire plants.
plant reproductive material
planting material
A fertilizer that is derived from animal or vegetable matter, and contains a carbon-hydrogen linkage.
Organic fertilizer is sometime defined as being derived from natural sources including non-living organism sources like rock.
organic fertilizer role
A role that inheres in an organism that is realized in an agricultural process where the organism is unwanted.
pest role
A plan specification which describes how a material entity is applied to another material entity.
fertilizer application technique
pesticide application technique
fertilizer application method
application method
An application method in which a liquid material entity is applied by aircraft to an area.
aerial topdressing
crop dusting
aerial application
An application method in which a material entity is applied in bands below, above, on one side, or on both sides of seeds or seedlings at planting.
banding
band application
A band application in which the material entity is applied after seeding or planting.
sidedress application
side dressing
An application method which specifies how a material entity is to be uniformly applied to an area.
broadcasting
broadcast application method
A broadcast application in which fertilizer is applied to an area before planting or before seedling emergence.
fertilizer basal application
A broadcast application in which a material entity is applied to an area after seedling emergence and establishment of plants.
topdress application
top dressing
An application method in which a chemical entity is applied to the lower portions of plant stems or tree trunks just above the soil line.
chemical basal application
An application method in which a water-soluble chemical is injected into water flowing through an irrigation system.
chemigation
An application method in which a material entity is applied at the time of sowing, and placed in contact with seeds.
combined drilling
drill placement
on the seed application
placed with seed application
pop-up application
seed placement
contact placement
An application method in which the material entity is placed in the reduced soil layer.
subsurface placement
The material entity is often compacted into pellet or briquette before being placed into the soil.
The reduction soil layer is usually localized around 5 to 10 cm under the soil surface.
This application method is often used in paddy field.
deep placement
An application method in which a water-soluble fertilizer is injected into water flowing through an irrigation system.
fertigation
An application method in which a liquid material entity is sprayed to the leafy portions of a plant.
foliar spray
foliar application
An application method in which the material entity is placed in a continuous band on the bottom of the furrow during the process of ploughing. Each band is covered as the next furrow is turned. The aim is to place the material entity in moist soil where it can become more available to growing plants.
plough sole placement
An application method in which a liquid material entity is conveyed from a reservoir to a rope or wick that is wiped into unwanted plants.
rope-wick treatment
wiper treatment
rope-wick application
An application method in which a material entity is appplied directly on seeds before seeding.
seed treatment
seed dressing
An application method in which a material entity is injected under pressure beneath the soil surface.
soil injection
An application method in which a material entity is injected under the bark of trees.
tree injection
A plan specification which describes how water is applied to plants or soil.
irrigation method
An irrigation process in which water is distributed under low pressure through a piped network, and is applied as a small discharge to each plant or adjacent to it.
localized irrigation
localized irrigation process
A localized irrigation process in which water is conveyed under pressure through a pipe system where it drips slowly onto the soil close to the plants.
drip irrigation
micro irrigation
trickle irrigation
drip irrigation process
A localized irrigation process in which water is distributed by diffusion and capillary action through the wall of buried unglazed clay pot.
pitcher irrigation
pitcher irrigation process
A localized irrigation process in which water is conveyed under pressure through a buried pipe system where it drips slowly below the soil surface close to plants' roots.
SDI
subsurface drip irrigation
subsurface drip irrigation process
An irrigation process in which water is distributed through a buried piped network with a layer of geotextile on top. Geotextiles absorb the water from the drippers of the piped network and transport that water under the soil surface via mass flow and capillary action.
SSTI
subsurface textile irrigation
subsurface textile irrigation process
An irrigation process in which water is distributed through a system of pipes, and is sprayed into the air through sprinklers so that it breaks up into small water drops which fall to the ground.
irrigation with sprinkler
sprinkler irrigation process
A sprinkler irrigation process in which water is dispersed through a long, segmented arm that revolves around a pivot point and covers a circular area.
center-pivot irrigation
central pivot irrigation
circle irrigation
waterwheel irrigation
center-pivot irrigation process
An irrigation process in which water is delivered to the plant root zone from below the soil surface.
seepage irrigation
sub-irrigation
subground irrigation process
subsurface irrigation
sub-irrigation process
An irrigation process in which water is applied and distributed over the soil surface by gravity.
surface irrigation
surface irrigation process
A surface irrigation process in which water is applied into basins. Basins are flat areas of land surronded by low bunds.
bassin irrigation
Basin irrigation is suitable for crops that are unaffected by standing in water for long periods (e.g. 12-24 hours) like rice or some trees.
bassin irrigation process
A bassin irrigation process in which basins are flooded during the entire growing season of plants.
coutinuous flooding
paddy irrigation
continuous flood process
A surface irrigation process in which water is distributed to an area divided into borders. Borders are long, sloping strips of land separated by bunds. Water is applied to the top end of borders.
bay irrigation
border check irrigation
border irrigation
border strip irrigation
Borders are typically longer and narrower compared to basin irrigation.
border irrigation process
A surface irrigation process in which water is carried into small channels called furrows down the land slope between the plant rows. Water is applied to the top end of each furrow and infiltrates into the soil as it moves along the slope channel.
furrow irrigation
furrow irrigation process
A surface irrigation process in which water is spread over a flat area without control over water flow or prior preparation.
uncontrolled flooding
wild flooding
uncontrolled flooding process
A role that inheres in an organism that is realised in a pest control process where that organism is used to suppress unwanted organisms.
biological pest control agent role
A role that inheres in an environmental material that is realised in a land preparation process where that environmental material is applied to soil in order to neutralize soil acidity.
liming role
Plants that are grown to be tilled, or cut down to lay on top of the ground for the purpose of adding organic matter and nutrients to the soil.
green manure
Animal manure that contains plant material, which has been used as bedding for animals and has absorbed the feces and urine.
FYM
barnyard manure
farmyard manure
An animal manure made of animal feces and urine with no or very little material used for animal bedding.
slurry manure
farm slurry
An animal manure made of animal urine and sometimes waste water.
liquid manure
Organic matter mostly derived from animal feces which can be used as organic fertilizer in agriculture.
The excreta of animals, with or without an admixture of bedding or litter, fresh or at various stages of further decomposition or composting.
animal manure
An animal manure that contains poultry excreta, spilled feed, feathers, and material used as bedding in poultry operations.
broiler litter
chicken litter
poultry litter
An animal manure that contains solid waste from fishes often originateing from aquaculture operations.
fish manure
An animal manure that is produced from ground-up whole fish or by-products mixed with water, and heated to remove oils and proteins.
fish emulsion
An animal manure obtained by drying and grinding or otherwise treating fish or fish waste to which no other matter has been added.
fish meal
An animal manure made from whole fish or by-products put into water and cold-ground up.
fish hydrolysate
The biomass remaining after pressing oil seeds to extract oil.
oil cake
Dry, inert powder made from blood. Blood usually comes from cattle or hogs as a slaughterhouse by-product.
blood meal
The biomass remaining after sugarcane stalks are crushed to extract their juice.
obsolete bagasse
An agricultural environmental material that contains ground-biomass remaining after pressing oil seeds.
ground oil cake
oil meal
An oil meal that contains crushed cotton seeds from which oil has been removed.
cottonseed meal
An agricultural environmental material that contains ground dry alfalfa.
alfalfa meal
A compost that contains the residual compost waste generated by mushroom production. It generally consists of a combination of wheat straw, dried blood, horse manure and ground chalk, composted together.
spent mushroom compost
Layer of material applied to the soil surface to conserve moisture, improve soil fertility, reduce weed growth, or enhance the visual appeal of the area.
mulch
A mulch where plastic sheet is used to cover soil surface. Plants grow through slits or holes in thin plastic sheeting.
plastic mulch
A mulch where textile material is used to covert the soil surface. The fabric itself can be made from synthetic or organic materials, sometimes from recycled sources.
landscape fabric
A mulch where shredded or entire piece of paper or newspaper cover the soil surface.
newspaper mulch
paper mulch
A mulch where lawn waste resulting from mowing are used to cover the soil surface.
grass clippings mulch
A mulch where pine needles are used to cover soil surface.
pine straw mulch
pine needles mulch
A mulch where straw is used to cover soil surface.
straw mulch
A mulch where foil is used to cover soil surface.
aluminum mulch
A mulch where stones are used to cover soil surface.
stone mulch
A mulch where tree leaves are used to cover soil surface.
leave mulch
A mulch where compost is used to cover soil surface.
compost mulch
A mulch where wood chips are used to cover soil surface. Wood chips are a byproduct of the pruning of trees.
wood chips mulch
A mulch where the outer corky bark layer of timber trees, shredded or not, are used to cover soil surface.
bark mulch
A biological pest control process in which organisms that will help to manage pests are introduced to a new locale where they do not occur naturally.
classical biological pest control
importation
organisms importation process
A biological pest control process in which organisms that help to manage pests are released to boost the naturally occurring population.
augmentation
organisms augmentation process
A biological pest control process in which suitable habitat or food are provided to the naturally occurring population of organisms that help to manage pests.
conservation
organisms conservation process
A mechanical pest control process in which pests are killed.
destruction technique
mechanical pest destruction process
A mechanical pest control process in which pests are kept away.
exclusion technique
mechanical pest exclusion process
A mechanical pest control process in which pests are removed without being killed.
removal technique
mechanical pest removal process
A planned process in which a layer of material is apply to the soil surface to conserve moisture, improve soil fertility, reduce pests population and enhance the visual appeal of the area.
mulch management
mulching
mulching process
A planned process in which a liming material is applied to soil to reduce acidity.
liming
liming process
Seed soaked in water until the physical process of germination, the penetration of the root though the seed coat, has occurred.
wet seed
pregerminated seed
Piece of a plant, often piece of the stem or root, that is used for vegetative propagation.
plant cutting
A shoot of a perennial plant.
ratoon
Organism used to pull agricultural implements.
draught animal
working animal
draft animal
obsolete horse
obsolete donkey
steer
obsolete bull
obsolete camel
obsolete mule
obsolete buffalo
obsolete elephant
A mobile machine specifically designed to deliver a high tractive effort at slow speeds, and mainly used for the purposes of hauling a trailer or machinery used in agriculture or construction.
tractor
A tractor with one axle, self-powered and self-propelled. The operator usually walks behind it or rides the implement being towed.
two-wheel tractor
walking tractor
single-axle tractor
A tractor with two axles. Agricultural implements may be towed behind or mounted on the tractor, and the tractor may also provide a source of power if the implement is mechanized.
four-wheel tractor
two-axle tractor
A roller armed with blunt spikes for dragging over newly plowed land to break the clods and render it fit for seeding.
clod crusher
An implement that consists of many carbon steel or boron discs, which have many varying concavities and disc blade sizes and spacing and which are arranged into two or four sections. It is used to till the soil where crops are to be planted. It is also used to chop up unwanted weeds or crop remainders.
bladed harrow
disc plough
disc harrow
An implement that cut, lift and reverse soil with a cutting depth of approximately 15 cm.
frame-plough
moldboard plow
mouldboard
turnplough
mouldboard plough
An implement that typically has only one thin blade with a sharpened tip, and is used to loosen and break up soil at depths about 30 cm.
flat lifter
mole plough
subsoiler
An implement that loosen and aerate soil without inverting or turning it.
chisel plough
An implement that is used for plants, such as potatoes or scallions, which are grown buried in ridges of soil. A ridging plough has two mouldboards facing away from each other, cutting a deep furrow on each pass, with high ridges either side.
ridging plough
An implement that is designed to cut the soil and turn it on its side, minimizing the damage to the earthworms, soil microorganism, and fungi.
need a more precise definition
spade plough
Board used in field with a total water coverage to shape field surface. Weight can be added to the board.
leveling board
levelling board
Bucket dragged by animal or tractor to shape soil surface. Bucket dimensions and capacity vary according to the available power source and field conditions.
drag bucket
drag scraper
leveling bucket
levelling bucket
A bucket tracted by a tractor and controlled by a laser to shape soil surface. A laser transmitter transmits a laser beam, which is intercepted by the laser receiver mounted on the leveling bucket. The control panel mounted on the tractor interprets the signal from the receiver and raises or lowers the bucket.
laser-controlled bucket
An implement consisting of a heavy framework having high numbers of steel tines on an harrow mat.
drag harrow
harrow
chain harrow
An implement consisting of a heavy framework having several spikes or tines, and dragged by an animal or a tractor.
tine harrow
An implement used to distribute manure over a field. It usually consists of a trailer towed behind a tractor with a rotating mechanism driven by the tractor's power take off.
honey wagon
muck spreader
manure spreader
An implement designed to inject slurry into the soil.
slurry injector
An implement that consists of a hopper, a metering unit, and a distribution device that uses centrifugal force to spread material like seeds, fertilizer granules, liming material, onto the soil surface.
broadcast seeder
centrifugal fertilizer spreader
broadcast spreader
A planned process in which seeds are applied on or into the soil.
crop establishement
direct seeding
seeding
sowing
sowing process
seeding process
An implement that is used to spray liquid and that is fitted with a harness on the operator back.
knapsack sprayer
backpack sprayer
An implement that is used to spray liquid and is held in the hand. It usually has an air pump which compresses air into the tanks and pressurizes the liquid to spray.
hand sprayer
An implement that uses a combination of air and liquid to deliver liquid material to the target. It includes include nozzles that deliver spray droplets directly into a high-speed airstream. The air blast shatters the drops of liquid material into fine droplets and transports them to the target.
airblast sprayer
An implement which is used to create well-defined grooves in the soil where some material like seeds or fertilizer can be placed at a proper depth.
furrow opener
An area density quality which inheres in liming material by virtue of some influence exerted by the mass of liming material applied on a given surface area.
liming material area density
Plant material remaining on the field ground after harvesting, including leaves, stalks, roots.
crop residue description
crop residue
Two or more crop plants planted in a line.
row
A site which is located between two rows of crop plants.
interrow
An area density quality which inheres in nitrogen by virtue of some influence exerted by the mass of nitrogen applied in a given surface area.
amount of N applied per area
amount of nitrogen applied
Generated equivalence by pattern 'agro/patterns/chemical_area_density', using dosdp-tools and ROBOT tool
nitrogen area density
An area density quality which inheres in phosphorus by virtue of some influence exerted by the mass of phosphorus applied in a given surface area.
amount of P applied per area
phosphorus total amount
quantity of phosphorus applied
phosphorus area density
Object with a tube shape used to carry irrigation water through the field
irrigation tube
An area density quality which inheres in sulfur by virtue of some influence exerted by the mass of sulfur applied in a given surface area.
amount of sulfur applied on a surface
sulfur area density
An area density quality which inheres in chemical pest control material by virtue of some influence exerted by the mass of chemical pest control material applied in a given surface area.
chemical pest control material area density
pesticide application rate
pesticide area density
An area density quality which inheres in nitrate by virtue of some influence exerted by the mass of nitrate applied in a given surface area.
amont of nitrate applied
nitrate area density
An area density quality which inheres in ammonium by virtue of some influence exerted by the mass of ammonium applied in a given surface area.
amount of ammonium applied
ammonium area density
An area density quality which inheres in calcium by virtue of some influence exerted by the mass of calcium applied in a given surface area.
amount of Ca applied per area
amount of calcium applied
calcium area density
An area density quality which inheres in magnesium by virtue of some influence exerted by the mass of magnesium applied in a given surface area.
amount of magnesium applied
magnesium area density
An area density quality which inheres in iron by virtue of some influence exerted by the mass of iron applied in a given surface area.
amount of iron applied
iron area density
An area density quality which inheres in zinc by virtue of some influence exerted by the mass of zinc applied in a given surface area.
amount of Zn applied per area
amount of zinc applied on a surface
zinc area density
An area density quality which inheres in copper by virtue of some influence exerted by the mass of copper applied in a given surface area.
copper area density
An area density quality which inheres in boron by virtue of some influence exerted by the mass of boron applied in a given surface area.
boron area density
An area density quality which inheres in molybdenum by virtue of some influence exerted by the mass of molybdenum applied in a given surface area.
molybdenum area density
An area density quality which inheres in manganese by virtue of some influence exerted by the mass of manganese applied in a given surface area.
manganese area density
An area density quality which inheres in chlorine by virtue of some influence exerted by the mass of chlorine applied in a given surface area.
amount of chlorine applied on a surface
chlorine area density
A length quality which is equal to the length of the tillage tool that penetrate into the soil.
tillage depth
tillage tool blade length
A thickness quality which is equal to the distance betwenn the top of the mulch layer to the top of the soil layer.
mulch thickness
Small earth embankment which contain irrigation water within basins.
dyke
levee
ridge
bund
An environmental material containing calcium and/or magnesium compounds and applied to soil in order to neutralize soil acidity.
liming material
Form of overhead sprinkler irrigation consisting of several segments of pipe joined together and supported by trusses, mounted on wheeled towers with sprinklers positioned along its length. The machine moves in a circular pattern and is fed with water from the pivot point at the center of the circle.
central pivot irrigation machine
circle irrigation machine
waterwheel irrigation machine
center pivot irrigation machine
Hydrological process in which water move through soil and permeable rocks.
percolation process in soil
Mass of fertilizer applied on a given surface area.
fertilizer amount
amount of fertilizer applied
fertilizer application rate
fertilizer quantity applied
fertilizer area density
An area density quality which inheres in potassium by virtue of some influence exerted by the mass of potassium applied in a given surface area.
amount of K applied per area
amount of potassium applied on a surface
potassium area density
amount of seeds used
seeding area density
sowing rate
Mass of the seeds sown on a given surface area.
A pest control process in wich extremely hot temperature are used to kill pest.
heat treatment
An area density quality which inheres in plant reproductive material by virtue of some influence exerted by the mass of plant reproductive material planted in a given surface area.
plant reproductive material area density
planting rate
A pest control process in which extremely cold temperature are used to kill pest.
cold treatment
A mechanical pest control process in which the area being treated against pest is saturated with water at a depth of 15 to 30 cm for a period of 3 to 8 weeks.
flood treatment
A mulchin process in which the soil is covered with a layer of clear or black plastic. The plastic that is covering the ground traps heat energy from the sun and raises the temperature of the soil preventing the growth of or killing the plants.
soil solarization treatment
A mechanical pest control process in which pest or area with pest are directly burned and flamed.
fire treatment
A mechanical pest control process in which steam is used to kill pest.
steam treatment
A mechanical pest process in which diatomaceous earth is used to kill pest. Diatomaceous earth is composed of finely ground skeletons of fossil diatoms. Sharp edges of the ground diatoms scratch the waxy or oily outer layer of soft-bodied insects, which die eventually from dehydration.
diatomaceous earth spreading
A crop residue management process in which crop residues are burned in the field.
crop residue burning process
A crop residue management process in which crop residues are spread across the field.
obsolete crop residue spreading process
A land levelling process which uses animal drawn or tractor-drawn levelers.
traditional land levelling
traditional land levelling process
A mechanical pest removal process in which pests are physically caught.
trapping
trapping process
A mechanical pest exclusion process in which barriers are used to prevent pest from getting into the area to be protected.
using barrier process
A pest removal process in which unwanted organisms are removed by hands.
hand picking
hand pulling
hand roguing
hand picking process
A mechanical pest removal process in which a forceful stream of water is used to dislodge pests.
water pressure spraying process
A mechanical pest removal process in which a field vacuum is used to suck insects from plants.
insect vaccuming
insect vacuuming process
A cutting process in which the above ground of the plants are cut or shred.
mowing
topping
topping process
mowing process
An implement that is used during a tillage process.
tillage implement
An implement that is used during a land levelling process.
land levelling implement
An implement that is used during a residue management process.
residue management implement
An implement that is used during a fertilization process.
agronomic fertilization implement
fertilization equipment
fertilization implement
An implement that is used during a transplanting process.
transplanting implement
A planned process in which a plant is moved from one location to be planted in another one.
replanting
transplanting
transplanting process
plant transplanting process
An implement that is used in a planting process.
planting implement
A planned process in which a plant reproductive material is set into the soil.
planting process
An implement that is used during a sowing process.
seeding implement
sowing implement
An implement that is used during a chemical pest control process.
pesticide implement
chemical pest control implement
An implement that is used in an harvest process.
plant harvest implement
An implement that is used during a puddling process.
puddling implement
An implement that is used during a mulch process.
mulch implement
Source of energy used to pulled an implement.
obsolete implement traction source
A traction that uses only human power to use an implement.
obsolete human power
A traction that uses motorized power to pulled an implement.
obsolete motorized traction
A traction that uses animal power to pulled an implement.
obsolete animal traction
An equipment that is used during an irrigation process.
irrigation equipment
Protocol used to measure the area density of a material.
material area density mesurement protocol
Protocol in which the material is weighed with a scale. The weight of the material is then divided by the surface area over which the material is applied to obtain the area density of the material.
material weight per area measurement protocol
Protocol in which the volume of a material is mesured with a graduated container. The volume of the material is then divided by the surface area over which the material is applied to obtain the area density of the material.
material volume per area measurement protocol
Protocol in which the weight or the volume of the material is recorded from the packaging of the material. This value is then divided by the surface area over which the material is applied to obtain the area density of the material.
material area density recording
With a ruler measure the distance between the soil surface and the top of the mulch layer.
mulch thickness measurement protocol
With a ruler measure the distance between the center of two rows. The center of the rows is where the plant reproductive material has been planted.
interrow width measurement protocol
Measure the length of sprout with a steel tape.
sprout lenght measurement protocol
Measure the shortest distance between the water source and the entrance of the field with a measuring wheel.
water source distance measurement protocol
A protocol defined as follow: 1.Weight a sample of the material. 2.Dry this sample. 3.Weight the dry sample. Moisture concentration = ((Ww-Wd)/Ww) x 100 in which : WW = wet weight of the sample, and Wd = weight of the sample after drying.
moisture concentration measurement protocol
Measure the distance between the soil surface and the top of a bund. Repeat this operation on multiple bunds, and average the results.
bund height measurement protocol
Measurement protocol in which the depth into the soil of an agricultural process is measured.
agricultural operation depth measurement protocol
agricultural process depth measurement protocol
Use of a penometer to measure the depth of the agricultural process.
agricultural process depth measurement protocol using a penometer
Measure the length of the implement that goes into the soil to realize the agricultural process to knoe the depth of the agricultural process. For exemple, measure the length of the tool blade used for tillage to evaluate tillage depth.
implement lenght measurement protocol
Record the concentration of the chemical element of interest in the fertilizer used indicated on the fertilizer container.
chemical concentration in fertilizer recording protocol
Count the number of row that have been harvested.
harvested row counting protocol
How to count a row that have been partially harvested?
Count the number of plants using a quadrat. A quadrat is a frame of a know area. Set the quadrat on the soil and count the number of plants inside it. Repeat this observation as often as mentioned in your sampling protocol. Total number of plants= [(total number of plants counted inside the quadrat during all the observations)/ (quadrat area)/(number of observation)]x field size.
plant population measurement protocol using quadrat
plant density measurement protocol using quadrat
Count the number of plants in a defined area. Plant density= Total number of plants/ defined area
plant population simple measurement protocol
plant density simple measurement protocol
Protocol that describes how to count the number of plants in a known area.
plant population measurement protocol
plant density measurement protocol
Measure the distance between the beginning and the end of the row.
row length mesurement protocol
Protocol in which the lignin concentration of an environmental material is measured.
lignin concentration measurement protocol
Measure the lignin concentration following the acetylbromide method.
lignin concentration measurement protocol using acetylbromide
Measure the lignin concentration following the acid detergent fiber method
ADF method
lignin concentration measurement protocol using acid detergent fiber
Measure the lignin concentration with the thioglycolic acid method.
lignin concentration measurement protocol using thioglycolic acid
Measure the lignin concentration with the Klason method.
lignin concentration measurement Klason protocol
Measure the lignin concentration with the permanganate method.
lignin concentration measurement protocol using permanganate
Measure the lignin concentration with the acid detergent lignin method.
ADL method
lignin concentration measurement protocol using acid detergent lignin
A determination of organic carbon protocol that uses chromic acid to measure the oxidizable organic carbon in an environmental material.
wet oxidation method
walkley-black acid digestion method
walkley-black method
Method for the quantitative determination of organic nitrogen in chemical substance.
TKN method
total kjeldahl nitrogen
kjeldahl digestion
kjeldahl method
Protocol used to determine organic carbon content in environmental material according to the amount of CO2 released during combustion of the material.
dry combustion method
Protocol used to determine the content of organic nitrogen in environmental material.
determination of organic nitrogen in environmental material protocol
Protocol used to determine the content of organic carbon in environmental material.
determination of organic carbon protocol
Protocol used to measure soil organic matter and soil organic carbon. The method is based upon measuring the weight loss from a dry soil sample when exposed to high temperatures (between 350°C and 600°C). The weight loss that occurs at this temperature is then correlated to oxidizable organic carbon.
LOI method
weight loss on ignition method
Record the speed of the tractor in the field.
Need to add a standard protocol to measure tractor speed, if it exists.
tractor speed recording protocol
Record the color of the mulch applied.
Need to add a standard protocol to measure the color of the mulch, if it exists.
mulch color recording protocol
Protocol in which the age of the transplant is determined by counting the number of days between the seeding date and the transplanting date.
transplant age counting protocol
Measure the distance between the soil surface and the top of the irrigation equipment buried in soil.
irrigation equipment depth measurement protocol
Tie a small but heavy weight to the end of a piece of string. Lower the weight into the well until it reaches the bottom. Take up the slack and mark the string at ground level. Pull the weight out of the well and measure from the bottom of the weight to the ground level mark. This is the depth of the well.
well depth measurement protocol
Measure the lenght of the pivot.
pivot lenght measurement protocol
Record the number of pest control agent released per surface area.
pest control agent released density recording protocol
Record the quantity of water used for irrigation.
irrigation water quantity recording protocol
Protocol in which the rapidity at which water moves through soil is measured.
percolation test protocol
Protocol that describes how to measure a field area.
area measurement protocol
Measure the field area in the field.
area direct measurement
GIS
Measure the field area using a map (paper or electronic format).
area measurement using cartography
Record the information giving by a person that knows the field area (farmer, field owner).
area recording protocol
Protocol that describes how to measure the percentage of soil coverage by environmental material like mulch or crop residue.
soil coverage by environmental material measurement protocol
Assess visually the percentage of soil covered by environmental material.
soil coverage visual assessment protocol
Measure the percentage of soil covered by environmental material by counting the environmental material using quadrat, rope with knots or other devices.
soil coverage manual measurement protocol
Use GIS to measure the percentage of soil covered by environmental material.
soil coverage measurement using GIS
Add all the quantities of the environmental material of interest applied over a specified period.
total quantity of environmental material used compute protocol
Protocol that describes how to measure the percentage of incorporation in soil of an environmental material.
environmental material incorporation percentage measurement protocol
Assess visually the percentage of environmental material that has been buried into soil during the incorporation process.
incorporation percentage visual assessment
Use GIS to measure the percentage of environmental material that has been buried into soil during the incorporation process.
incorporation percentage measurement using GIS
Measure the percentage of environmental material that has been buried into soil by counting the environmental material using quadrat, rope with knots or other devices befor and after the incorporation process.
incorporation percentage manual measurement
An area quality inhering in a farm.
farm area
An area quality inhering in a field.
field area
A site within which an agricultural experimental process is conducted
This should be harmonized with statistical plot designs, perhaps with STATO
gross plot
plot
agricultural experimental plot
An area quality inhering in a plot.
plot size
agricultural experimental plot area
gross plot area
parcel area
plot area
A block is a relatively large area or several identical units receiving all or most of the treatments. A collection of plots is called a block.
block
Number of block used for an experiment.
number of blocks
Number of plot used during an experiment.
number of plots
A length quality that inheres in the smallest unit of an experiment.
plot length
A width entity that inheres in the smallest unit of an experiment.
plot width
A rounded container used to cultivate plant.
pot
Number of pot used during an experiment.
number of pots
Distance between the top and the bottom of a pot.
pot height
A width entity that inheres in some row.
row width
A length quality that is the distance between the beginning and the end of a row.
row length
Distance quality that represents the distance between two plots.
plot spacing
space between plants
Distance between two hills.
hill spacing
inter-row spacing
Orientation of the rows in a field.
row orientation
Orientation of the plots in a field.
plot orientation
Replication is the repetition of the set of all the treatment combinations used in an experiment.
replication
A process during which some material is applied to a subject
treatment
Number of treatments tested during an experiment.
number of treatments
Number of replications in an experiment.
number of replicates
number of replications
A crop is any cultivated plant, fungus, or alga that is harvested for food, clothing, livestock,fodder, biofuel, medicine, or other uses
crop
Number of different crop used in an experiment.
number of crops
Number of crops cultivated at the same time during the previous year in the field where the experiment is done.
number of crops previously cultivated
Orientation of the slope.
slope aspect
slope orientation
An experimental design that enables an additional factor or treatment to be included at more than one level; each plot is split into two or more parts.
split plot design
http://www.fao.org/wairdocs/ilri/x5546e/x5546e0a.htm#7.5.4 split plot arrangement
An experimental design in which the desired precision for measuring the interaction effect between the two factors is higher than that for measuring the main effect of either one of the two factors. This is accomplished with the use of three plot sizes : 1. Vertical strip plot for the first factor – vertical factor 2. Horizontal strip plot for the second factor – horizontal factor 3. Interaction plot for the interaction between 2 factors
split block design
strip plot design
An experimental design in which two or more factors, each with discrete possible values or "levels", and whose experimental units take on all possible combinations of these levels across all such factors. That is, the design provides information on the average effect of the individual factors as well as the interaction between these two factors.
factorial design
An experimental design in which the treatments are assigned completely at random so that each experimental unit has the same chance of receiving any one treatment. Any difference among experimental units receiving the same treatment is considered as experimental error. Hence, it is appropriate only for experiments with homogeneous experimental units, such as laboratory experiments, where environmental effects are relatively easy to control.
CRD
completely randomized design
An experimental design in which the blocks should be composed of plots that are as homogeneous as possible. Further, blocks in the same replication should be as near as possible to maximize the variation among replication. These incomplete blocks are combined into groups that form separate, complete replications.
lattice design
An experimental design in which each treatment is included only once and is near to a control treatment. A control treatment is usually either a common practice or no practice.
replicated control design
An experimental design in which basic farming practices are compared using demonstration strips on a farm field. Usually the comparison is between two to four treatments, up to a maximum of 10 and each treatment is included only once.
demonstration strip design
A lattice design in which the number of treatment must be a perfect square. Blocks per replicate and plots per block are equal, and are the square root of the number of treatments.
square lattice design
A lattice design that is a resolvable incomplete block design where the number of treatments or block size does not meet the strict requirements for one of the lattice designs. Also the number of entries is a multiple of block size.
alpha lattice design
Shape of the land surface surronding an area.
higher-level landform
Description of the geomorphology of the immediate surroundings of the experimental site.
agronomic land element
The grade of a physical feature, landform or constructed line refers to the tangent of the angle of that surface to the horizontal.
environmental feature gradient
environmental feature slope
slope inclination
environmental feature grade
A factor of an experiment is a controlled independent variable; a variable whose levels are set by the experimenter. A factor is a general type or category of treatments. Different treatments constitute different levels of a factor.
experimental factor
Constraint known to affect the experiment or the crop performances.
experimental constraint
A plan specification that states how treatments are allocated to the experimental units during an agronomic trial. It refers to the conceptual framework within which the experiment is conducted.
agronomic experimental design
Unexpected event arrived during the experiment.
complication during the experiment
A complication with the equipement used during the experiment.
equipement complication
A complication with a person or a group of people working on the experiement.
complication caused by a personel
Percentage of the area of the experiment damaged due to a complication during the experiment.
percent of experiment area damaged
A planned process in which an analysis of soil is performed to determine soil characteristics.
soil analysis
soil test
soil analysis process
planting distribution
Planting is done on flat-top circular mounds.
hill distribution
Planting is done in lines.
row distribution
Planting distribution where the crop zone and the traffic lanes (wheel tracks or furrows) are distinctly and permanently separated. Soil is moved from the traffic lanes and added to the crop zone, slightly raising the surface level of the crop zone
raised bed planting
row on bed distribution
Planting is done on all the field surface.
uniform distribution
Shape quality that refers to the general shape of a slope in both vertical and horizontal directions.
curvature as the direction of the bend
slope curvature
slope form
slope shape
Maximum length of an agromical field.
field maximum length
An observation post where weather conditions and meteorological data are observed and recorded and reported.
weather station
Distance between the ground and the temperature sensor.
temperature sensor siting height
Distance between the ground and the wind speed sensor.
wind speed sensor siting height
Location where the experiment is implemented.
experimental site
Experimental site in which the experiment is implemented on the field of a farmer.
farmer field
Experimental site in which the experiment is done in a the field of a research station.
experimental station field
research station field
An experimental site in which the experiment is performed in a structure with walls and roof made chiefly of transparent material, such as glass, with the possibility to regulate climatic conditions.
hothouse
screenhouse
glasshouse
greenhouse
Experimental site where the experiment is done in a forest owned by a government.
governmental forest
Experimental site where the experiment is done in a private forest.
private forest
Elevation above the sea level of the experimental site.
experimental site elevation
experimental site altitude
Elevation above sea level of the weather station.
weather station altitude
A planned process in which a procedure is carried out to support, refute, or validate a hypothesis.
This class is relevant to more than the agronomy domain. It should be replaced by a class in a more general ontology of experiments
trial
experiment
An experiment in which a scientific method is implemented for testing certain agricultural phenomena.
agronomic experiment
type of study
agricultural experiment
A person engaged in agriculture, raising living organisms for food or raw materials.
farmer
A person who conducts research.
scientist
researcher
A person that is enrolled or attends classes at a school, college, or university.
intern
student
A person that works in a research station.
research station employee
A person that is employed by the government to assist people in rural areas with methods of farming and home economics.
extension agent
A person that is an educator who works at a college or university.
faculty member
Roled performed by a person during an experiment.
person role within the experiment
A person that has a role of collecting data related to the experiment.
data collector
A person that is the holder of an independent grant and the lead researcher for the grant project.
principal investigator
A person that has a role of managing the experiment.
Need a better definiton that highlights the differences with the principal investigator.
experiment manager
A person that has a role of performing the operations required to run the experiment in the field.
field laborer
An object to be used by hand to plough soil.
hand plough
Vegetation maintained in purpose on and at the border of an agronomic experimental field.
obsolete Vegetation maintained on an experimental field
Strip of flowers established at the edge of the field.
obsolete flower strip
Type of vegetation surrounding an agronomic experimental site
obsolete vegetation surronding an experimental site
Slope on which terraces have been build.
terraced
Slope shape irregular.
irregular shape
An agricultural field that is set aside for a period of time before it is cultivated again; or an agricultral field that is under permanent crops, meadows or pastures and that is not being used for such purposes for a period of at least one year.
fallow land
Strips of land along the borders of crop fields. It also include vegetative strips adjacent to roads, paths, railways, hedgerows and forest boundaries.
field margin
Tool for loosening compacted soil layers 12 to 16 inches (30 to 40 cm) deep and still maintain high surface residue levels.
paraplow
paraplough
Tillage tool that stirs and pulverizes the soil, either before planting (to aerate the soil and prepare a smooth, loose seedbed) or after the crop has begun growing (to kill weeds—controlled disturbance of the topsoil close to the crop plants kills the surrounding weeds by uprooting them, burying their leaves to disrupt their photosynthesis, or a combination of both). Cultivator is designed to disturb the soil in careful patterns, sparing the crop plants but disrupting the weeds. Cultivator teeth work near the surface.
cultivator
A disk harrow with disc blades arranged into four sections.
tandem disc harrow
A disk harrow with disc blades arranged into two sections.
offset disc harrow
A sowing device that positions seeds in the soil and then covers them. The seed drill sows the seeds at equal distances and proper depth, ensuring that the seeds get covered with soil.
drill seeder
seed drill
A seeding implement that consists of a seed drum, main shaft, ground wheel, floats, and handle. Joining smaller ends of frustum of cones makes the seed drum.
paddy drum seeder
drum seeder
An agricultural hand tool ade of a blade set to an handle and used to shape the soil, control weeds, clear soil, and harvest root crops.
hoe
A seed drill that consists of a seed box attached to the mainframe of a hand wheel hoe. A fluted roller assembly is provided at the bottom of the seed box. Fluted roller is rotated with the help of chain and sprockets from the ground wheel.
manual oilseed drill
A curved metal bar used to open the soil before putting the seed into the soil.
tyne opener planter
Manually operated device for creating a conical cavity in the soil for sowing of seeds. It consists of a wooden round stick with one end having a sheet metal cone. The other end is provided with a handgrip.
dibbling stick
Manually operated hand tool which consists of a seed hopper, cell roller for metering of seeds, spring actuated jaws for penetration in the soil, pipe and handle.
naveen dibbler
An tool made of mild steel flat or leaf spring by forging operation. The working end is flattened and edge made sharp for easy penetration in the soil.
hand dibbler
Manually operated push device for dibbling of medium and bold size seeds. It consists of a rotating dibbling head with penetrating jaws, covering-cum-transport wheel, seed hopper with cell wooden roller and a handle.
rotary dibbler
Manually operated hand tool that consists of cutter head having semicircular blades connected to pipe with the help of clamp and flange. The connecting pipe is further connected to a handle.
earth auger
A flat and circular piece of metal used to open the soil before putting the seed into the soil.
single disc opener planter
Double flat and circular piece of metal used to open the soil before putting the seed into the soil.
double disck opener planter
Irrigation method based on manual intervention.
manual irrigation
Irrigation method with no or just a minimum of manual intervention beside the surveillance. Almost every system can be automated with help of timers, sensors or computers or mechanical appliances.
automatic irrigation
An application method in which a material entity is placed into the soil in holes made with a pointed implement.
precision seeding
dibbling
An application method in which seeds are uniformlyplaced into shallow furrows before closing the furrows.
line sowing
drilling
An object used to perform an agricultural process.
agricultural implement
Vertical arrangement of plants in a field.
column
Total quantity of fertilizer applied in a given surface area during a cropping season.
fertilizer amount over a season
fertilizer area density over a cropping season
Elevation above the sea level of the soil profile.
soil profile altitude
A planned process in which grazing animals on pasture are managed by humans.
regulation of grazing
Grazing management system developped by Allan Savory. The system is based on a rotational grazing system but doing so at high densities for short intervals. Livestock is used as a tool to increase soil fertility and plant life. Incorporating plant organic matter and manure into the soil promotes the recycling of nutrients.
holistic grazing
holistic planned grazing
A grazing management method that involves moving livestock at least daily between small paddocks, sized to match the number of grazing animals, and split by fence. The goal is for every plant in the grazing cell to be either eaten or walked on and trampled. Grass in each paddock then rests for 60-120 days or more.
ultra-high density grazing
mob grazing
A grazing management system in which the land is subdivided or sectioned off into smaller areas, sometimes called paddocks. The livestock are moved from one paddock to another in order to best promote plant health and growth.
rotational grazing
A grazing management system in which livestock have unrestricted access to the pasture area throughout the grazing season.
continuous grazing
A system of grazing which confined animals to a strip or small part of the field for rapid grazing in a short time period.. The rest of the field is protected by a temporary fence, usually electric.
strip grazing
A rotational grazing management system that implies many paddocks are utilized and livestock are moved on a frequent basis. It provides more stable production during poor growing conditions, greater yield, higher quality, decreased weed and erosion, and uniform soil fertility levels.
MIG
Voisin grazing management
management intensive grazing
intensive rotational grazing
An intensive rotational grazing system in which livestock is allowed to graze for a limited time, leaving a leafy stubble, and then is moved to another area.
controlled grazing
Intensive grazing system in which the field is divided into many small plots of equal size. Grasses are raised with application of large quantities of nitrogenous fertilizers. The livestock are divided into three groups : high, medium and low yeilders. They are let into the paddock by rotation so that the opportunity for grazing most nutritious immature grasses goes to the high yielders followed by medium producers and lastly low yielders.
hohenheim grazing system
A grazzing management system that allows young farm animals to graze part of the pasture before the adults. It employs a gate through which young animals, but not adults, can pass to get first choice of fresh feed in the next door paddock.
creep grazing
A gazing management system in which two or more groups of animal, usually with different nutritional needs, graze the same paddock but at different time.
first-last grazing
Area of field that have been harvested.
harvested surface area
soil mulch coverage
Area of soil surfae covered with mulch.
Area of soil covered by organic fertilizer.
soil organic fertilizer coverage
Height of the small earth embankments which contain irrigation water within basins.
bund height
Tractor speed in the field.
tractor speed
An area density quality which inheres in micronutrients by virtue of some influence exerted by the mass of micronutrients applied in a given surface area. Micronutrients for plants are Boron, Chlorine, Iron, Zinc, Manganese, Molybdenum, Copper, Nikel.
micronutrients area density
An area density quality which inheres in above-ground crop residue by virtue of some influence exerted by the mass of above-ground crop residue applied in a given surface area.
crop residue amount
crop residue area density
Length of the pivot used during the irrigation process.
center pivot irrigation equipment length
Distance between the bottom of the well and the soil surface.
well depth
An area density quality which inheres in rhizobium by virtue of some influence exerted by the mass of rhizobium inoculated into the soil.
quantity of rhizobium
rhizobium area density
Amount of nutrient in the crop as a ratio of the amount applied or available.
NRE
nitrogen recovery efficiency
Calculate the amount of nitrogen in the crop as a ratio of the amount of nitrogen applied or available.
nitrogen recovery efficiency measurement protocol
Ratio between the amount of nitrogen fertilizer removed from the field by the crop and the amount of nitrogen fertilizer applied. It provides information about the relative utilization of additional nitrogen applied to a agricultural production system.
nitrogen use efficiency
Calculate the ratio between the amount of nitrogen fertilizer removed with the crop and the amount of nitrogen fertilizer applied.
nitrogen use efficiency measurement protocol
Carbon-to-nitrogen ratio is a ratio of the mass of carbon to the mass of nitrogen in an organic fertilizer.
organic fertilizer carbon to nitrogen ratio
Agricultural tool that is hand-held and composed of a curved blade with a sharp inside and a handle. It is used for harvesting, or reaping, grain crops or cutting succulent forage chiefly for feeding livestock, either freshly cut or dried as hay.
bagging hook
brishing hook
grasshook
reaping hook
rip-hook
slash-hook
swap hook
sickle
Planned process is which the edible part of the cereal grain is loosen from the scaly, inedible chaff that surrounds it. It is the step in grain preparation after harvesting and before winnowing, which separates the loosened chaff from the grain. Threshing does not remove the bran from the grain.
threshing process
Agricultural tool made from two or more large sticks attached by a short chain; one stick is held and swung, causing the other to strike a pile of grain, loosening the husks.
flail
Agricultural tool that consists of a shaft about 170 centimetres (67 in) long made of wood or metal. The shaft has either one or two short handles at right angles to it, usually one near the upper end and always another roughly in the middle. A curved, steel blade between 60 to 90 centimetres (24 to 35 in) long is mounted at the lower end at 90°, or less, to the shaft. It is hand powered.
scythe
A planned process in which the grain is separated from chaff. It is also used to remove weevils or other pests from stored grain. It is done after threshing, the loosening of grain or seeds from the husks and straw.
winnowing process
A pruning process in which whole tops of trees or large branches and/or trunks from the tops of trees are removed, leaving stubs or lateral branches that are too small to assume the role of a terminal leader.
hat-racking
heading
rounding
tipping
étêtage
tree topping process
A pruning process in which dried, yellowish green, bottom leaves in the sugarcane crop are removed at regular intervals.
detrashing process
detrashing
A pruning process in which branches from either standing or downed trees are removed.
limbing process
limbing
A planned process in which a rigid support is used to support, or to prevent from falling a crop or a tree.
staking process
Need a better definition to know if staking and propping are exactly the same process, or have differences.
propping process
An harvest process that involves a multiple step process to turns green, perishable, forage into a product that can be safely stored and easily transported without danger of spoilage.
haymaking process
An harvest process in which the cut herbage is putting into rows for further handling and collection, and sometimes also for protection at night.
swathing
windrowing
An harvesting process in which dry forage is bound by ropes into a bale.
baling process
An harvest process in which herbage is put into cocks (small heaps). It is an intermediate stage of herbage drying used in some manual systems.
trussing process
A planned process in which the harvest is stored.
storage process
agricultural product storage process
An harvest process in which the mature part of the crop is cut.
cutting process
Maximum width of an agronomical field.
field maximum width
An cropping system in which a definite cycle of crops or crop types is grown in succession on the same land.
crop rotation process
rotation
rotation process
crop rotation
Yates (1954) notes the agricultural definition is looser than an experimental one, i.e. substitution of crops or change to the length of the cycle. This definition must regard changes to the period of a rotation cycle as a different rotation, but should allow a rotation to be defined either using either named crops or a combination of named crops and crop types, for example an Oats, Legumes, Wheat rotation.
A process in which a definite cycle of management interventions is done on the same land.
sequence
sequence process
An agricultural implement that uses moving forks to aerate or "wuffle" the hay and thus speed up the process of hay-making. It is used after cutting and before windrowing.
hay tedder
tedder
An harvest implement that reaps, threshes, and cleans a crop in one operation.
combine harvester
An harvesting process in which root crop are removed from the soil
lifting process
A planned process in which an herbicide is applied to a crop shortly before harvest. The purpose is to reduce green crop foliage or assit crop drying.
Pre-harvest crop desiccation
siccation
dessication process
An agricultural experiment running over decadal time periods.
long-term experiment
An agricultural experiment running over less than decadal time periods.
short-term experiment
An agricultural experiment having one or more definite sequences.
sequence experiment
Richard Ostler
An agricultural experiment having more than one definite rotations or a comparison between rotation and mono-cropping.
rotation experiment
crop rotation experiment
An agricultural experiment involving the prolonged growing of a single crop.
continuous crop experiment
continuous mono-cropping experiment
monoculture experiment
mono-cropping experiment
An cropping system in which a single crop is cultivated in an area at a time.
continuous crop
continuous mono-cropping
mono-cropping
monocropping
monoculture
An agricultural experiment in which a sequence of crops is grown without repetition
short-term rotation experiment
crop-sequence experiment
single cycle experiment
An agronomic experimental design set for rotation experiments
rotation experimental design
rotation layout
A rotation layoutan using series.
serial layout
A rotation layout that does not use series. Therefore, plots carrying different phases of a rotation are intermixed across the experimental land.
non-serial layout
A block in which the plots carry the same phase of a rotation. A series is defined to answer management constraints rather than statistical constraints.
series
A planned process which is a distinguishable part of a rotation process
rotation phase
A duration inhering in a crop rotation process
rotation duration
crop rotation duration
An area density unit which is equal to the number of seeds per meters squared.
seed/m2
seed per meter square
An area density unit which is equal to the number of seeds per acre.
seed/ac
seed per acre
An area density unit which is equal to the number of rows per plot.
row/plot
row per plot
An area density unit which is equal to the number of rows per meters squared.
row/m2
row per meter square
An area density unit which is equal to the number of rows per feet squared.
row/ft2
row per foot square
An area density unit which is equal to the number of rows per acre.
row/ac
row per acre
An area density unit which is equal to the number of rows per hectare.
row/ha
row per hectare
An area density unit which is equal to the number of plants per hill.
plants/hill
plants per hill
Number of plants per row.
plants/row
plants per row
Number of plants per square meter.
plants/m2
plants per square meter
An area density unit which is equal to the number of plants per hectare.
plants/ha
plants per hectare
Number of plants per pot.
plants/pot
plants per pot
A planned process in which ridges are created.
Ridging, hilling, earthing up
ridging process
A planned process in which trees, stumps, brush, stones and other obstacles are removed from an area with the intention of creating a potential use for agricultural purposes.
land clearing process
An area density quality which inheres in animal manure by virtue of some influence exerted by the mass of animal manure applied in a given surface area.
amount of animal manure applied
animal manure area density
An agricultural process using processes that are non-polluting, conserve non-renewable energy and natural resources, are economically efficient, are safe for workers, communities and consumers, and do not compromise the needs of future generations
sustainable agriculture process
An cropping system in which two or more crops are cultivated in the same space at the same time.
intercropping
An agricultural process in which two or more plant species are cultivated on the same area, totally mixed without arrangement in distinct rows.
mixed intercropping
An agricultural process in which two or more plant species are cultivated in separate alternate row.
row intercropping
An agricultural process in which two or more plant species are planted simultaneously within the same row in varying seeding ratios.
within row intercropping
An agricultural process in which two or more plant species are cultivated on the same area and where the second crop is sown during the growth, often near the onset of reproductive development or fruiting of the first crop, so that the first crop is harvested to make room for the full development of the second crop
relay cropping
An agricultural process in which a fast-growing crop is seeded simultaneously with a slow-growing crop, so that the first crop is harvested before the second crop starts to mature.
temporal intercropping
sequential intercropping
An agricultural process in which two or more plant species are cultivated simultaneously on the same area in different strips wide enough to permit independent cultivation but narrow enough for the crops to interact agronomically.
strip intercropping
The date of a land clearing process
land clearing date
A process in which vegetation is cut down and burned as a method of clearing the land for cultivation.
S&B
fire-fallow cultivation
slash-and-burn
slash-and-burn process
A process in which vegetation is cut down and removed from the land.
slash-and-remove process
A process in which rocks are crushed to clear the land.
rock crushing process
A process in which vegetation is cut down, grinded and mulched on the cleared land.
cut and grind process
A process in which slashed vegetation is piled together and burned.
pile and burn process
A process in which vegetation is burned as a method of clearing the land.
burn technique
land burning process
A process in which rocks are removed to clear the land.
rock removal process
A process in which roots are crushed to clear the land.
roots crushing process
ridging date
A device used to create ridges.
ridging device
ridging implement
A device used to create ridges at the same time than planting.
ridging device mounted on planting implement
The concentration of crop residue when measured in liquid water.
Concentration of water in crop residue.
crop residue moisture
A device that applys the spray liquid through nozzles, which are attached to a horizontal structure (boom) and which are normally directed towards the ground.
A device used to spray a liquid.
sprayer
An implement which is a pipe for distributing spray using attached nozzles. It has a list of system components that work together to deliver the spray fluid.
boom sprayer
An agricultural implement that harvests forage plants to make silage.
chopper
forager
silage harvester
forage harvester
An agricultural implement that cuts and often also gathers crops when they are ripe.
reapper
An agricultural implement, resembling a plow, that pulls up harvestable parts of plants growing underground.
digger
A width entity that inheres in some ridge.
ridge width
Distance between the top and the bottom of a ridge.
A height entity that inheres in some ridge.
ridge height
Distance between two ridges.
distance between ridges
All living biomass above the soil including stem, stump, branches, bark, seeds and foliage.
aboveground organic material
aboveground biomass
All living biomass of live roots. Fine roots of less than (suggested) 2mm diameter are sometimes excluded because these often cannot be distinguished empirically from soil organic matter or litter.
below-ground biomass
Young sporophyte developing out of a plant embryo from a seed.
seedling
A proccess in which water inputs rely only on rainfall.
no irrigation
rainfed
zero irrigation
rainfed process
A manual tool used to sow large seeds in rows or in bunches on plastic mulch films or in the earth. This device is used to sow seeds manually, while standing in a natural position.
jab planter
A moistness quality inhering in a bearer by virtue of the bearer being partially covered in liquid.
moist
A crop residue removal process in which crop residues are removed from the field.
crop residue removal process
Use more defined class with better reasoning
mm/plot
obsolete_millimeter per plot
Number of plant per feet squared.
plants/ft2
plants per foot square
in/plot
obsolete_inch per plot
Number of plants per plot.
plants/plot
plants per plot
Number of square meters of agricultural field or plot harvested.
number of m2 harvested
number of m2 units harvested
number of square meter harvested
Distance between the ground and the point where the plant is cut for harvest.
harvest cut height
The amount of a pesticide
obsolete pesticide amount
Number of pesticide process
number of pesticide application
The time of a pesticide application process
timing of pesticide application
pesticide application date
The amount of a weeding chemical
obsolete weeding chemical amount
Distance between water source and field.
source distance
distance between the water source and the field
A planned process which confines all machinery loads to the least possible area of permanent traffic lanes. The permanent traffic lanes are normally parallel to each other.
CTF
controlled traffic
controlled traffic farming
Process which involves the selective removal of certain parts of a plant or a tree, such as branches, buds, or roots.
pruning method
pruning process
Process which involves cutting the plants back 6 to 12 inches above ground level.
renewal pruning process
renewal pruning
An agricultural experimental plot from which unwanted areas have been removed, most often the outside rows.
net plot
Huelsen, W. A. (1943). Stand irregularity and its relation to the yields of sweet corn. Journal of Agricultural Research, 67(5), 211–224. https://naldc.nal.usda.gov/download/IND43969864/PDF
Agricultural experimental plot area, where the quantity measure inheres in area size, covering the field trial.
obsolete_gross plot
A measurement datum that is a unique identifier of a precise geographic location on the earth, usually expressed in alphanumeric characters
geographic coordinate system
GPS coordinates measurement datum
geo-location
geolocation
GPS coordinates
A unique identifier of the postion a field on earth, usually expressed in alphanumeric characters.
field location
field geolocation
geo-location of a field
GPS coordinates of a field
Latitude coordinate of a field.
field latitude coordinate measurement datum
field latitude coordinate
Longitude coordinate of a field.
field longitude coordinate measurement datum
field longitude coordinate
An agricultural process in which rows of trees and/or shrubs are planted to create alleys within which agricultural or horticultural crops are produced.
alleycropping
hedgerow intercropping
A cropping system that involves growing crops in a wide strip, typically 6 meters in width, between lines of closely planted, fast-growing trees or shrubs.
These woody species are usually leguminous and are pruned frequently to provide a mulching material and nutrients to the crop in the alley.
alley cropping
An agricultural process in which the integration of trees or shurbs, pasture and grazing livestock operations on the same land is deliberate.
silvopastoral system
silvopasture
A perennial cropping system featuring multiple layers or strata occupied by different trees and other perennial crops.
CMSAFs
Complex multistrata agroforestry systems
multistrata agroforestry
Prunings from trees (leaves, branches,...)
tree prunings
Woody species planted and left to grow during fallow.
improved fallow
A land-use systems and technologies where woody perennials (trees, shrubs, palms, bamboos, etc.) are deliberately used on the same land-management units as agricultural crops and/or animals, in some form of spatial arrangement or temporal sequence
agroforestry practice
agroforestry process
agroforestry technique
agroforestry
A combination of crops and trees on the same land at the same time.
agrisilvicultural system
agrisilviculture
Application of water below full crop requirements compared to a control of conventional irrigation.
deficit irrigation
deficit irrigation process
An irrigation process in which part of the root is exposed to drying soil and the remaining is irrigated in accordance with crop requirements and soil drying rate.
APRI
PRD
alternate partial rootzone irrigation
partial root zone drying
alternate partial rootzone irrigation process
An irrigation process in which small amounts of water are added to essentially rainfed crops during times when rainfall fails to provide sufficient moisture for normal plant growth.
supplemental irrigation
The active collection and storage of water runoff.
rainwater harvesting
water harvesting process
water harvesting
A manufactured container within which water is stored.
water tank
A vegetated area which includes strips of grass within a field or farm created for erosion control, typically they are placed along contour lines.
grass strip
A crop cultivated on a same location before the current crop.
cultivo anterior
former crop
previous crop
this class is a duplicte of the calss: agronomic fertilization process date
obsolete fertilizer application date
An band application in which a material entity is applied in bands on surface.
band application on surface
An band application in which a material entity is applied in bands below surface.
band application beneath surface
An broadcast application method in which a material entity is uniformly incorportated to an area.
broadcast incorporated
An broadcast application method in which a material entity is uniformly applied to the surface of an area.
broadcast on surface
Application of input into the soil close to the seed or plant.
localized application
An area density unit which is equal to the mass of an object in kilograms divided by the surface area representing a plot.
kg/plot
kilogram per plot
Agricultural experiment performed on a farm.
on farm experiment
Agricultural experiment performed on a research station.
on station experiment
Incorporation of crop residue into soil.
crop residue incorporation process
A process in which crop residue are mulched
crop residue spreading process
crop residue mulching process
A crop residue management process in which crop residue are left in the field.
crop residue retained
crop residue retention process
A crop residue removal process in which crop residue are grazed
crop residue grazing process
A crop residue removal process in which crop residue are harvested and removed from the field.
crop residue harvest process
An plot area quality inhering in a net plot. It corresponds to the plot area minus the unwanted area removed, most often the outside rows.
net plot area
Intercropping in which several rows of crops are interspersed with hedges of fast growing shrubs that are coppiced every few weeks to provide a nitrogen-rich mulch for the crop.
Sinclair, F.L., 1999. A general classification of agroforestry practice. Agroforestry systems, 46(2), pp.161-180.
Elevation above the sea level of a field.
agricultural field altitude
farmer's field altitude
field altitude
Distance between two plants in a same row.
distance between plants in a row
intrarow spacing
intra-row spacing
Type of seed variety used
seed type
seed variety type
Seed variety locally selected.
local seed variety
improved seed variety
Seed variety produced by cross-pollinated plants.
hybrid seed variety
Latitude coordinate of a weather station
weather station latitude
Longitude coordinate of a weather station.
weather station longitude
A unique identifier of the postion a weather station on earth, usually expressed in alphanumeric characters.
geo-location of a weather station
weather station GPS coordinates
GPS coordinates of a weather station
Distance between the weather station and the field.
distance between a weather station and the field
Maximum temperature of air.
temperature of air maximum
Minimum temperature of air.
temperature of air minimum
Average temperature of air.
temperature of air average
Average temperature of air over a day.
temperature of air average daily
Average temperature of air over a year.
average annual temperature
temperature of air average yearly
Average temperature of air over a month.
temperature of air average monthly
Minimum temperature of air reached in a day.
temperature of air minimum daily
Minimum temperature of air reached in a year.
temperature of air minimum yearly
Maximum temperature of air reached in a day.
temperature of air maximum daily
Maximum temperature of air reached in a year.
temperature of air maximum yearly
Humidity that correspond to moisture content of the atmosphere, expressed as a percentage of the amount of moisture that can be retained by the atmosphere at a given temperature and pressure without condensation.
relative humidity
An agricultural process in which crops are cultivated following crop sequences and management techniques.
farming system
cropping system
An agricultural implement that is a small hand-propelled vehicle, usually with just one wheel, designed to be pushed and guided by a single person using two handles at the rear.
brouette
carretilla
wheelbarrow
An agricultural implement consisting of a tank and a spraying system attached to wheels.
carretilla de aspersión
wheelbarrow tank sprayers
wheeled sprayer
wheelbarrow sprayer
An implement that is a mechanical device, used to move the liquids or gases from one place to another by using mechanical action.
motobomba
motor pump
An implement consisting of a broad blade fixed to a medium-length handle.
palas
pelle
shovel
Sprinkler able to move by its own power.
self-propelled sprinkler
An agricultural process in which furrow are build in the field.
contruction de sillons
formación de surcos
furrow design process
furrow construction process
An agricultural implement that consists of a long stick ending in a point or embedded in a metal tip that can have the shape of a shovel or spatula, or a straight part and a curved part. It is used to open holes in the ground in South America.
coa
An agricultural implement that consist of a broad blade typically 30 to 45 centimetres long and usually under 3 millimetres thick.
machete
machette
An agricultural implement that is a traditional wooden plough.
Arado Egipcio
egyptian plow
egyptian plough
Agricultural implement consisting of either of a series of toothed wheels on one or more horizontal axles or a single large toothed wheel on a vertical axle.
herce rotative
rotary harrow
Agricultural implement that consist of a motorized cultivator that works the soil by means of rotating tines or blades.
power tiller
rotary hoe
rotary plough
rotary plow
rotavator
rototiller
rotary tiller
The depth at which a seed is deposited during a seeding process.
sowing depth
planting depth
seeding depth
a trench that is long, narrow, shallow and made in the ground with an agricultural implement.
furrow
A lenght quality that inheres in a furrow
furrow lenght
A planned process that aims to prevent soil erosion.
prévention de l'érosion du sol
soil conservation
soil erosion prevention process
area of soil surface covered by stones.
soil surface stoniness
area of soil surface covered by gravels.
soil surface gravelliness
The number of seasons
number of seasons
The distance between a field and the house of a farmer.
distance between field and farmer house
Fertility quality inhering in soil. Soil fertility is the ability of a soil to sustain plant growth.
soil fertility
A person that own an agricultural field.
field owner
Number of diseased plants in a plant population expressed as a number or a proportion.
disease incidence
Area or proportion of plant tissue that is symptomatic.
disease severity
Amount of herbicide applied on a surface.
herbicide amount
herbicide application rate
herbicide quantity applied
herbicide area density
Amount of insecticide applied on a surface.
insecticide amount
insecticide aplication rate
insecticide quantity applied
insecticide area density
An agricultural process in which water is managed on an agricultural field.
hydric regime
regimen hidrico
régime hydrique
water management process
Amount of rock in an agricultural field.
field stone content
level of rocks in the field
field rockiness
An plot area quality inhering in a net plot. It corresponds to the plot area harvested minus the unwanted area removed, most often the outside rows.
net plot area harvested
Equipment used to harvest an animal or its production which is meant for consumption.
animal harvesting equipment
A part of the plucking machine that moves the birds through the stages of plucking within the plucking apparatus
plucking belt
A conveyor belt used to collect eggs in an industrial egg production environment.
egg collection belt
egg belt
An equipment used in the transportation of an animal.
animal transportation equipment
The lining of a box or crate used to transport chicks (juvenile chickens).
chick pad
A truck used to haul dead animal from an abattoir.
dead haul truck
A truck used to haul live animals.
live haul truck
An equipment used to feed and water livestock animals.
animal feeding equipment
A bowl or pan which is used to feed livestock.
feed pan
A bowl from which animals can drink.
watering bowl
The box which is used to transport chick (juvenile chicken).
chick box
An animal feeding equipment that has a food storage unit and which enables livestock to obtain their own food.
animal feeder
An animal feeding equipment that has a water storage unit which enables livestock to obtain their own water.
animal drinker
An agricultural process in which the intentional movement of an animal by transport occurs.
animal transport
animal transportation
transportation of animals
animal transportation process
An agricultural process in which an animal is harvested for consumption.
animal harvesting process
A carefully designed and maintained ecosystem of useful plants modelled on the structure of young natural woodland, utilising plants of direct and indirect benefit to people – often edible plants. Forest garden can be cultivated on any scale.
forest garden
Crawford, Martin (2010). Creating a Forest Garden. Green Books. https://www.agroforestry.co.uk/wp-content/uploads/product/creating-a-forest-garden-2/Creating_a_forest_garden.pdf
Start date of an experiment.
experiment start date
End date of an experiment.
experiment end date
An application method in which a material entity is applied manually.
manual application
Plant resulting from the union of scion and stock.
budded plant
grafted plant
graft
Waste material produced when an animal is processed for consumption.
animal processing waste material
Waste material produced when poultry is processed for consumption.
poultry processing waste material
A fluid that leaks from a bag containing an animal carcass, and can include water, chemicals and anatomical fluids.
weep fluid
A type of water obtained from rinsing poultry carcasses during the feather plucking process.
poultry plucking water
Narrow and shallow channels which are eroded into unprotected soil by hillslope runoff.
rill seedbed
A ridge seedbed with ridges that follow the contour at a spacing of usually 1 to 2 metres.
coutour ridge seedbed
A process in which plant disease is treated.
disease control process
An area density unit which is equal to the number of seeds per hectacre.
seed/ha
seed per hectare
A woody piece or part of a tree used during an agricultural process.
stick
A planned process in which a sample of soil is taken.
soil sample
soil sampling process
Date of a soil sampling process.
sampling date
soil sample date
soil sampling process date
soil sampling date
The depth at which a sample of soil is collected during a soil sampling process.
sample depth
sampling depth
soil sampling depth
Number of tillage processes over a given period.
tillage frequency
frequency of tillage process
Number of weeding processes over a given period.
weed management frequency
weeding frequency
frequency of weeding process
Number of harvesting processes over a given period.
harvesting frequency
frequency of harvesting process
An inter-cropping experiement dunring which two or more crops are grown on the same field. The planting of the second crop occurs after the first one has completed its development.
relay cropping experiment
A role that inheres in an organism that is harvested for food, clothing, livestock,fodder, biofuel, medicine, or other uses.
crop role
A crop role that inheres in a crop that is planted first on a land where more than one crop are planted.
first crop role
A crop role that inheres in a crop that is planted on the same field than another crop after the it has completed its development.
relay crop role
A role that inheres in an animal that is kept by humans and trained to perform tasks.
draft animal role
A role that inheres in a human to power an implement.
human power role
An agricultural implement used during a weeding process
weeding implement
An agricultural implement that is used to pull out plant from the soil. A weed puller is usually manual.
weed puller
An agricultural implement that is used to cut grass or any plant that grows on the ground.
mower
A crop residue which is the cut stalks of cereal plants left sticking out of the ground after the grain is harvested.
stubble
A crop residue which is the cut outter shell or coating of a seed.
husk
A localized irrigation process in which water is conveyed to the soil surface as a little stream, typically from a small diameter tube or a commercially available emitter. Because the application rates generally exceed the soil infiltration rates, small basins or furrows are needed to control the water distribution on the land.
bubbler irrigation process
A localized irrigation process in which water is conveyed under high pressure through small nozzles and sprayed in a fine mist of water over the plants.
mist irrigation process
A sprinkler irrigation process in which water is dispersed over the plant through a self-propelled irrigation systems with both ends of the system move at a constant speed up and down the area to irrigate.
sprinker by lateral move irrigation process
A sprinkler irrigation process in which water is dispersed over the plant through a system long lateral pipes mounted on 1 to 3 meter wheels in diameter, the pipe serving as an axle. When the desired amount of water has been applied to an area, a gasoline engine at the centre is used to move the side roll to the next area.
side roll sprinkler irrigation process
A process in which mulch is removed from the soil.
mulch removal process
An environmental zone prepared for growing plants.
land arrangement
seedbed
A seedbed that is flat. Flat beds are used where water availability is adequate and there are no drainage problem.
leveled land arrangement
leveled seedbed
flat seedbed
A seedbed that is raised-up. They are especially advantageous for clayey soils under high rainfall or wherever else drainage is likely to be poor.
raised seedbed
A seedbed that is below the surrounding soil level. Sunken beds conserve water much more effectively than raised bed
sunken seedbed
A raised seedbed which is long and narrow with steep sides.
ridge seedbed
A raised seedbed that is of rounded form and limited extent.
hill seedbed
A harvest implement for grain crops which cuts the stems and binds the stems into bundles or sheaves. The binder is now largely obsolete replaced by the combine harvester.
binder
An harvest implement that compresses a cut and raked crop into compact bales.
baler
A tillage implement that has multiple sets of vertical tines. Each set of tines is rotated on a vertical axis and tills the soil horizontally.
power harrow
An implement that is used in a mowing process.
mowing implement
The roller is an heavy agricultural tool used for flattening land or breaking up large clumps of soil, especially after ploughing or disc harrowing.
roller
An fallow land that is set aside for a period of time and kept free from vegetation by cultivation.
bare fallow land
weed role
A planned process in which a seedbed is prepared to grow plants.
seedbed preparation process
A seeding process that is the random scattering of seed.
broadcasting seed process
A seeding process during which seeds are sown in lines
line sowing process
A seeding process that consists in placing seeds in holes.
seed dibbling process
A seeding process which is dropping the seeds in furrow lines in a continuous flow and covering them with soil.
seed drilling process
A material entity that has a fertilizer role and that is derived from animal or vegetable matter.
organic fertilizer
A material entity that has a fertilizer role and that is mined from mineral deposits or manufactured from synthetic compounds.
inorganic fertilizer
A compost that is the product of the decomposition process using various species of worms, usually red wigglers, white worms, and other earthworms, to create a mixture of decomposing vegetable or food waste, bedding materials, and vermicast.
vermicompost
worm castings
A limestone that is derived from deposits of primarily calcium carbonate.
calcitic limestone
A limestone that is derived from deposits of calcium carbonate combined with magnesium carbonate and contains high levels of magnesium.
dolomitic limestone
A inorganic fertilizer that provides nitrogen, phosphorus, and potassium.
NPK fertilizer
An inorganic fertlizer that facilitates proper deep point placement of urea fertilizer, as urea is used as granules.
urea super granule
A crop that has been harvested after an harvesting process.
harvested crop
harvested row
A plant transplanting process that is done manual by a human being.
manual plant transplanting process
A plant transplanting process that is done mechanically.
mechanical plant transplanting process
A weeding process in which chemical is used to manage unwanted weeds.
chemical weeding process
A weeding process in which physical means such as barriers, traps and handpicking, or physical conditions like high temperature, are used to control unwanted weeds.
mechanical control weeding process
A weeding process in which extremely cold temperature are used to kill plant.
cold treatment weeding process
A weeding process in which plants are directly burned and flamed.
fire treatment weeding process
A mechanical weeding process in which unwanted organisms are removed by hands.
handweeding
hand picking weeding process
A mechanical control weeding process in wich extremely hot temperature are used to kill weeds.
heat treatment weeding process
A mechanical control weeding process in which a forceful stream of water is used to dislodge unwanted plants.
water pressure spraying weeding process
An enviromental material that has a role of fertilization
agronomic fertilizer
A organic fertilizer role that is derived from plants directly growned on the area to be fertilized.
green manure role
A fertilizer that is obtained by acid chemical attack of a phosphate rock with sulfuric acid. It contains 16 to 20% P2O5. It comes in the form of grey granules.
A product made by reaction of phosphate rock with sulfuric acid, usually containing 7 to 10% P (16 to 22% P2O5), composed of monocalcium phosphate, Ca(H2PO4)2, and gypsum, CaSO4.
normal superphosphate
ordinary superphoshate
single superphosphate
A fertilizer that is obtained by acid chemical attack of a phosphate rock with phosphoric acid. It contains around 46% P2O5
A product made from phosphate rock and phosphoric acid, usually containing 19 to 21% P (44 to 48% P2O5), and composed of monocalcium phosphate monohydrate, Ca(H2PO4)2 . 2H2O.
concentrated superphosphate
treble superphosphate
triple superphosphate
A fertilizer that is produced by the condensation between urea and formaldehyde consisting of short chains from methylene-diurea to tetramethylenepentaurea. It is a slow release nitrogenous fertilize, sparingly soluble, and contains at least 35 percent total nitrogen, with at least 60 percent of the total Nitrogen as cold-water-insoluble Nitrogen (CWIN). The unreacted urea Nitrogen content is usually less than 15 percent of the total Nitrogen.
ureaform
A fertilizer that is produced by the condensation between urea and formaldehyde consisting of short chains from methylene-diurea to tetramethylenepentaurea. It is a slow release nitrogenous fertilize, sparingly soluble. The total N content of these polymers is 39 to 40 percent, with between 25 and 60 percent of the N present as CWIN. The unreacted urea N content generally is in the range of 15 to 30 percent of the total N.
methylene urea
A fertilizer that is a single compound made by the condensation of 2 mols of acetaldehyde and 2 mols of urea.
crotonylidene diurea
A fertilizer that is made by coating urea with sulphur and wax to increases nitrogen efficiency.
sulfur coated urea
A planned process which occurs in an agricultural field.
agricultural process
A measurement datum that is the measure of the latitude coordinate of an agricultural plot.
plot latitude
plot latitude coordinate measurement datum
A measurement datum that is the measure of the longitude coordinate of an agricultural plot.
plot longitude coordinate measurement datum
Proportion of residue incorporated into the soil during a residue management process.
residue incorporation percentage
number of land levelling passes
number of tillage passes
Area of soil surface covered by crop residues.
Mass of organic fertilizer applied on a given surface area.
organic amendment rate
organic fertilizer amount
organic fertilizer application rate
organic fertilizer quantity
Mass of inorganic fertilizer applied on a given surface area.
inorganic fertilizer amount
inorganic fertilizer quantity
number of weeding process
harvested weight
number of puddling operations
number of puddling passes
The time of a conventional tillage process
The time of a conservation tillage process
The time of a laser land levelling process
The time of a traditional land levelling process
The time of a crop residue burning process
The time of a crop residue spreading process
The time of a localized irrigation process
The time of a sprinkler irrigation process
The time of a surface irrigation process
The time of a mechanical pest destruction process
The time of a mechanical pest exclusion process
The time of a mechanical pest removal process
The time of a mechanical pest control process
The time of a biological pest control process
The time of a chemical pest control process
The time of a pitcher irrigation process
The time of a subsurface drip irrigation process
The time of a subsurface textile irrigation process
The time of a bubbler irrigation process
The time of a center-pivot irrigation process
The time of a sprinker by lateral move irrigation process
sprinker by lateral move irrigation date
The time of a side roll sprinkler irrigation process
The time of a uncontrolled flooding process
The time of a diatomaceous earth spreading
The time of a water pressure spraying process
The time of a soil solarization treatment
The time of a manual plant transplanting process
The time of a mechanical plant transplanting process
date of crop establishement
The time of a intensive rotational grazing
The time of a cold treatment weeding process
The time of a fire treatment weeding process
The time of a hand picking weeding process
hand weeding date
handweeding date
timing of handweeding
The time of a heat treatment weeding process
The time of a water pressure spraying weeding process
The time of a crop residue management process
harvest date
pruning date
The time of a plant transplanting process
transplanting date
The time of a seedbed preparation process
The time of an agronomic fertilization process
amendment application date
amendment date
fertilizer application date
The time of a mechanical control weeding process
Fresh crop residue
wet crop residue
fresh crop residue
Crop residue that have been dried
dry crop residue
obsolete concentration of carbon dioxide in soil
obsolete A role that inheres in a material entity that is mined from mineral deposits or manufactured from synthetic compounds and that excludes carbon-containing materials except ureas.
obsolete inorganic fertilizer role
Fence established by planting large cuttings, that easily produce roots and on which several strings of wire are attached with the obvious purpose of keeping livestock in or out.
live fence
"Harvey, C.A., Villanueva, C., Villacís, J., Chacón, M., Muñoz, D., López, M., Ibrahim, M., Gómez, R., Taylor, R., Martinez, J. and Navas, A., 2005. Contribution of live fences to the ecological integrity of agricultural landscapes. Agriculture, ecosystems & environment, 111(1-4), pp.200-230. ecological integrity of agricultural landscapes"
Live fence made of trees. Boundary planting are used to delimitate property, agricultural fields, pastures, roads or any other place where fences might be located.
trees on boundary
boundary planting
Baker, K., Baumann, D., Michaud, J.S., van Mossel-Forrester, B., 2014. Technical Specification Boundary Planting. Registered Plan Vivo Project: The CommuniTree Carbon Project. 64p. URL: https://takingroot.org/wp-content/uploads/2015/04/takingroot-boundary-planting.pdf
Technical Specification Boundary Planting. https://takingroot.org/wp-content/uploads/2015/04/takingroot-boundary-planting.pdf
Windbreaks are linear plantings of trees and shrubs designed to enhance crop production, protect people and livestock, and benefit soil and water conservation.
windbreak
Multiple row windbreaks that are planted for both production of tree crops and environmental benefits like wind protection, soil conservation, wildlife habitat.
timberbelt
Fence where one or more rows of trees and/or shrubs are specifically planted to provide a visual screen or intercept light, odour, dust, and noise or a combination thereof.
buffer
buffer planting
Tree plantings which are grown in hedgerows but have been allowed to reach their full height and width.
hedgerow trees
Fodder collected to provide cattle farmers with high quality fodder for the dry season.
fodder bank
Woodlands which exist in farms.
farm woodland
BRENCHLEY, W. The Management of Farm Woodlands. Nature 146, 475 (1940). https://doi.org/10.1038/146475a0
Trees which have ecological functions in landscapes like offering shelter and food sources for animals, enhancing landscape connectivity by acting as stepping stones, and functioning as nuclei for plant regeneration in disturbed landscapes.
isolated trees
paddock trees
pasture trees
remnant trees
Scattered trees may enhance the provision of ecosystem services that might benefit farmers and owners of rural properties, such as pollination of crops, shading for cattle, regulation of nitrogen dynamics and carbon sequestration, herbaceous production, and wood provision.
scattered trees
An agroforestry process where peasant farmers are permitted to seed crops between trees during the establishment phase of plantation forestry.
taungya farming
An agroforestry practice based on trees, shrubs and perennial plants to create a carefully designed and maintained ecosystem of useful plants modelled on the structure of young natural woodland, utilising plants of direct and indirect benefit to people.
Woodland garden
forest garden practice
A cropping system in which relatively short periods of cultivation are followed by relatively long periods of fallow.
swidden agriculture
swidden farming
shifting cultivation
FAO, 1982. University of Ibadan Workshop on Shifting Cultivation and Extension, in Ibadan. https://www.fao.org/3/r1340E/r1340e04.htm
Agroforestry practice in which grazing occurs in a forest area.
plantation grazing
forest grazing
An agricultural experiment during which at least two different crops are grown at the same time.
inter-cropping experiment
A environmental material which contains living microorganisms, which, when applied to seeds, plant surfaces, or soil, colonize the rhizosphere or the interior of the plant and promotes growth by increasing the supply or availability of primary nutrients to the host plant.
biofertilizer
biochar
An animal manure composoed of the excrement of seabirds and bats.
bird guano
A tillage process during which the tillage occurs at 25-30 cm depth. It can be used for deep rooted crop like pigeonpea.
deep tillage
Fish fertilizer is any fish product that is used specifically to feed plants and soil.
fish fertilizer
Process to remove unwanted plants from an area of ground.
weed control method
weed management type
weeding management type
weeding process
Inorganic fertilizer that contains nitrogen
nitrogen fertilizer
Inorganic fertilizer that contains phosphorus
phosphorus fertilizer
Inorganic fertilizer that contains potassium
potassium fertilizer
An area density quality which inheres in ammonium dihydrogen phosphate by virtue of some influence exerted by the mass of ammonium dihydrogen phosphate applied in a given surface area.
amount of ammonium dihydrogen phosphate applied
Generated by pattern 'agro/patterns/chemical_area_density', using dosdp-tools and ROBOT tool
ammonium dihydrogen phosphate area density
An area density quality which inheres in ammonium magnesium phosphate by virtue of some influence exerted by the mass of ammonium magnesium phosphate applied in a given surface area.
amount of ammonium magnesium phosphate applied
ammonium magnesium phosphate area density
An area density quality which inheres in ammonium magnesium phosphate hexahydrate by virtue of some influence exerted by the mass of ammonium magnesium phosphate hexahydrate applied in a given surface area.
amount of ammonium magnesium phosphate hexahydrate applied
ammonium magnesium phosphate hexahydrate area density
An area density quality which inheres in ammonium nitrate by virtue of some influence exerted by the mass of ammonium nitrate applied in a given surface area.
An area density quality which inheres in ammonium nitrate phosphate by virtue of some influence exerted by the mass of ammonium nitrate phosphate applied in a given surface area.
amount of ammonium nitrate phosphate applied
An area density quality which inheres in ammonium phosphate sulfate by virtue of some influence exerted by the mass of ammonium phosphate sulfate applied in a given surface area.
amount of ammonium phosphate sulfate applied
An area density quality which inheres in ammonium polyphosphate by virtue of some influence exerted by the mass of ammonium polyphosphate applied in a given surface area.
amount of ammonium polyphosphate applied
An area density quality which inheres in ammonium sulfate by virtue of some influence exerted by the mass of ammonium sulfate applied in a given surface area.
An area density quality which inheres in ammonium sulfate nitrate by virtue of some influence exerted by the mass of ammonium sulfate nitrate applied in a given surface area.
amount of ammonium sulfate nitrate applied
An area density quality which inheres in ammonium sulfate urea by virtue of some influence exerted by the mass of ammonium sulfate urea applied in a given surface area.
An area density quality which inheres in ammonium thiosulfate by virtue of some influence exerted by the mass of ammonium thiosulfate applied in a given surface area.
An area density quality which inheres in calcium ammonium nitrate by virtue of some influence exerted by the mass of calcium ammonium nitrate applied in a given surface area.
amount of calcium ammonium nitrate applied
An area density quality which inheres in calcium bis(dihydrogenphosphate) by virtue of some influence exerted by the mass of calcium bis(dihydrogenphosphate) applied in a given surface area.
amount of calcium bis(dihydrogenphosphate) applied
calcium bis(dihydrogenphosphate) area density
An area density quality which inheres in calcium carbonate by virtue of some influence exerted by the mass of calcium carbonate applied in a given surface area.
An area density quality which inheres in calcium cyanamide by virtue of some influence exerted by the mass of calcium cyanamide applied in a given surface area.
An area density quality which inheres in calcium dichloride by virtue of some influence exerted by the mass of calcium dichloride applied in a given surface area.
An area density quality which inheres in calcium nitrate by virtue of some influence exerted by the mass of calcium nitrate applied in a given surface area.
An area density quality which inheres in calcium oxide by virtue of some influence exerted by the mass of calcium oxide applied in a given surface area.
An area density quality which inheres in copper(II) sulfate by virtue of some influence exerted by the mass of copper(II) sulfate applied in a given surface area.
An area density quality which inheres in cyanoguanidine by virtue of some influence exerted by the mass of cyanoguanidine applied in a given surface area.
An area density quality which inheres in diammonium hydrogen phosphate by virtue of some influence exerted by the mass of diammonium hydrogen phosphate applied in a given surface area.
amount of diammonium hydrogen phosphate applied
diammonium hydrogen phosphate area density
An area density quality which inheres in gypsum by virtue of some influence exerted by the mass of gypsum applied in a given surface area.
An area density quality which inheres in limestone by virtue of some influence exerted by the mass of limestone applied in a given surface area.
An area density quality which inheres in magnesium carbonate by virtue of some influence exerted by the mass of magnesium carbonate applied in a given surface area.
An area density quality which inheres in magnesium nitrate by virtue of some influence exerted by the mass of magnesium nitrate applied in a given surface area.
An area density quality which inheres in magnesium oxide by virtue of some influence exerted by the mass of magnesium oxide applied in a given surface area.
An area density quality which inheres in magnesium sulfate by virtue of some influence exerted by the mass of magnesium sulfate applied in a given surface area.
An area density quality which inheres in phosphoric acid by virtue of some influence exerted by the mass of phosphoric acid applied in a given surface area.
An area density quality which inheres in potassium carbonate by virtue of some influence exerted by the mass of potassium carbonate applied in a given surface area.
An area density quality which inheres in potassium chloride by virtue of some influence exerted by the mass of potassium chloride applied in a given surface area.
An area density quality which inheres in potassium dihydrogen phosphate by virtue of some influence exerted by the mass of potassium dihydrogen phosphate applied in a given surface area.
amount of potassium dihydrogen phosphate applied
potassium dihydrogen phosphate area density
An area density quality which inheres in potassium metaphosphate by virtue of some influence exerted by the mass of potassium metaphosphate applied in a given surface area.
amount of potassium metaphosphate applied
An area density quality which inheres in potassium nitrate by virtue of some influence exerted by the mass of potassium nitrate applied in a given surface area.
An area density quality which inheres in sodium nitrate by virtue of some influence exerted by the mass of sodium nitrate applied in a given surface area.
An area density quality which inheres in sodium selenate by virtue of some influence exerted by the mass of sodium selenate applied in a given surface area.
An area density quality which inheres in urea by virtue of some influence exerted by the mass of urea applied in a given surface area.
An area density quality which inheres in urea ammonium nitrate by virtue of some influence exerted by the mass of urea ammonium nitrate applied in a given surface area.
An area density quality which inheres in zinc sulfate by virtue of some influence exerted by the mass of zinc sulfate applied in a given surface area.
A planned process in which fertilizer is applied to an environmental material to promote the growth of a plant.
fertilization
fertilizer application
agronomic fertilization process
Group together tillage and no-till processes
An experiment in which a scientific method is implemented for testing crop yield.
crop yield experiment
A planned process during which the environment of a crop plant is maintained such that the plant grows
crop cultivation process
Multiple sites within which agricultural experimental process is conducted
agricultural experimental multiplot
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
A measurement datum that is the output of counting.
count
The planned process of finding the number of elements in a finite set of objects.
counting
software source code version control repository
A document that comprises at least one source code module and provenance data about who contributed the set of files making up the module(s), and optionally comprises also multiple versions of files with detailed change history about who committed files and when, a license for the software, readme files, documentation, executables, etc.
Refers to the stuff that lives on GitHub, not to GitHub or the git software on which it is based
source code repository
process of compiling software
A planned process that converts human-written or curated software into a machine-executable or interpretable set of instructions.
It's compiling "software" (scare quotes) and not "source code" because you can compile Java bytecode to machine code, and Java bytecode is not technically "source code". Compiling source code would be a subclass of this class (as would compiling Java bytecode, etc.).
Source code can be automatically generated to some extent, but we're assuming humans still curate it minimally. Also, in the case of Java and its JVM, it's machine interpretable instructions, not directly executable. Ditto for other languages with intermediate form like Java byte code.
compiling software
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
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]
continuant
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
A continuant that is either dependent on one or other independent continuant bearers or inheres in or is borne by other entities.
obsolete dependent continuant
BFO 2 Reference: Spatial regions do not participate in processes.
Spatial region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the union of a spatial point and a spatial line that doesn't overlap the point, or two spatial lines that intersect at a single point. In both cases the resultant spatial region is neither 0-dimensional, 1-dimensional, 2-dimensional, or 3-dimensional.
A spatial region is a continuant entity that is a continuant_part_of spaceR as defined relative to some frame R. (axiom label in BFO2 Reference: [035-001])
All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001])
(forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001]
(forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001]
spatial region
Temporal region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the mereological sum of a temporal instant and a temporal interval that doesn't overlap the instant. In this case the resultant temporal region is neither 0-dimensional nor 1-dimensional
A temporal region is an occurrent entity that is part of time as defined relative to some reference frame. (axiom label in BFO2 Reference: [100-001])
All parts of temporal regions are temporal regions. (axiom label in BFO2 Reference: [101-001])
Every temporal region t is such that t occupies_temporal_region t. (axiom label in BFO2 Reference: [119-002])
(forall (r) (if (TemporalRegion r) (occupiesTemporalRegion r r))) // axiom label in BFO2 CLIF: [119-002]
(forall (x y) (if (and (TemporalRegion x) (occurrentPartOf y x)) (TemporalRegion y))) // axiom label in BFO2 CLIF: [101-001]
(forall (x) (if (TemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [100-001]
temporal region
an infinitely thin plane in space.
the surface of a sphere-shaped part of space
A two-dimensional spatial region is a spatial region that is of two dimensions. (axiom label in BFO2 Reference: [039-001])
(forall (x) (if (TwoDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [039-001]
two-dimensional spatial region
the spatiotemporal region occupied by a human life
the spatiotemporal region occupied by a process of cellular meiosis.
the spatiotemporal region occupied by the development of a cancer tumor
A spatiotemporal region is an occurrent entity that is part of spacetime. (axiom label in BFO2 Reference: [095-001])
All parts of spatiotemporal regions are spatiotemporal regions. (axiom label in BFO2 Reference: [096-001])
Each spatiotemporal region at any time t projects_onto some spatial region at t. (axiom label in BFO2 Reference: [099-001])
Each spatiotemporal region projects_onto some temporal region. (axiom label in BFO2 Reference: [098-001])
Every spatiotemporal region occupies_spatiotemporal_region itself.
Every spatiotemporal region s is such that s occupies_spatiotemporal_region s. (axiom label in BFO2 Reference: [107-002])
(forall (r) (if (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion r r))) // axiom label in BFO2 CLIF: [107-002]
(forall (x t) (if (SpatioTemporalRegion x) (exists (y) (and (SpatialRegion y) (spatiallyProjectsOntoAt x y t))))) // axiom label in BFO2 CLIF: [099-001]
(forall (x y) (if (and (SpatioTemporalRegion x) (occurrentPartOf y x)) (SpatioTemporalRegion y))) // axiom label in BFO2 CLIF: [096-001]
(forall (x) (if (SpatioTemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [095-001]
(forall (x) (if (SpatioTemporalRegion x) (exists (y) (and (TemporalRegion y) (temporallyProjectsOnto x y))))) // axiom label in BFO2 CLIF: [098-001]
spatiotemporal 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 entity
A zero-dimensional spatial region is a point in space. (axiom label in BFO2 Reference: [037-001])
(forall (x) (if (ZeroDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [037-001]
zero-dimensional spatial region
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]
quality
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 (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]
specifically dependent continuant
John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married.
the priest role
the role of a boundary to demarcate two neighboring administrative territories
the role of a building in serving as a military target
the role of a stone in marking a property boundary
the role of subject in a clinical trial
the student role
A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts.
BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives.
b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001])
(forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001]
role
or with divisions drawn by cognitive subjects for practical reasons, such as the division of a cake (before slicing) into (what will become) slices (and thus member parts of an object aggregate). However, this does not mean that fiat object parts are dependent for their existence on divisions or delineations effected by cognitive subjects. If, for example, it is correct to conceive geological layers of the Earth as fiat object parts of the Earth, then even though these layers were first delineated in recent times, still existed long before such delineation and what holds of these layers (for example that the oldest layers are also the lowest layers) did not begin to hold because of our acts of delineation.Treatment of material entity in BFOExamples viewed by some as problematic cases for the trichotomy of fiat object part, object, and object aggregate include: a mussel on (and attached to) a rock, a slime mold, a pizza, a cloud, a galaxy, a railway train with engine and multiple carriages, a clonal stand of quaking aspen, a bacterial community (biofilm), a broken femur. Note that, as Aristotle already clearly recognized, such problematic cases – which lie at or near the penumbra of instances defined by the categories in question – need not invalidate these categories. The existence of grey objects does not prove that there are not objects which are black and objects which are white; the existence of mules does not prove that there are not objects which are donkeys and objects which are horses. It does, however, show that the examples in question need to be addressed carefully in order to show how they can be fitted into the proposed scheme, for example by recognizing additional subdivisions [29
the FMA:regional parts of an intact human body.
the Western hemisphere of the Earth
the division of the brain into regions
the division of the planet into hemispheres
the dorsal and ventral surfaces of the body
the upper and lower lobes of the left lung
BFO 2 Reference: Most examples of fiat object parts are associated with theoretically drawn divisions
b is a fiat object part = Def. b is a material entity which is such that for all times t, if b exists at t then there is some object c such that b proper continuant_part of c at t and c is demarcated from the remainder of c by a two-dimensional continuant fiat boundary. (axiom label in BFO2 Reference: [027-004])
(forall (x) (if (FiatObjectPart x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y) (and (Object y) (properContinuantPartOfAt x y t)))))))) // axiom label in BFO2 CLIF: [027-004]
fiat object
fiat object part
an edge of a cube-shaped portion of space.
A one-dimensional spatial region is a line or aggregate of lines stretching from one point in space to another. (axiom label in BFO2 Reference: [038-001])
(forall (x) (if (OneDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [038-001]
one-dimensional spatial region
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
a cube-shaped region of space
a sphere-shaped region of space,
A three-dimensional spatial region is a spatial region that is of three dimensions. (axiom label in BFO2 Reference: [040-001])
(forall (x) (if (ThreeDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [040-001]
three-dimensional spatial region
Manhattan Canyon)
a hole in the interior of a portion of cheese
a rabbit hole
an air traffic control region defined in the airspace above an airport
the Grand Canyon
the Piazza San Marco
the cockpit of an aircraft
the hold of a ship
the interior of a kangaroo pouch
the interior of the trunk of your car
the interior of your bedroom
the interior of your office
the interior of your refrigerator
the lumen of your gut
your left nostril (a fiat part – the opening – of your left nasal cavity)
b is a site means: b is a three-dimensional immaterial entity that is (partially or wholly) bounded by a material entity or it is a three-dimensional immaterial part thereof. (axiom label in BFO2 Reference: [034-002])
(forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002]
site
atom
cell
cells and organisms
engineered artifacts
grain of sand
molecule
organelle
organism
planet
solid portions of matter
star
BFO 2 Reference: BFO rests on the presupposition that at multiple micro-, meso- and macroscopic scales reality exhibits certain stable, spatially separated or separable material units, combined or combinable into aggregates of various sorts (for example organisms into what are called ‘populations’). Such units play a central role in almost all domains of natural science from particle physics to cosmology. Many scientific laws govern the units in question, employing general terms (such as ‘molecule’ or ‘planet’) referring to the types and subtypes of units, and also to the types and subtypes of the processes through which such units develop and interact. The division of reality into such natural units is at the heart of biological science, as also is the fact that these units may form higher-level units (as cells form multicellular organisms) and that they may also form aggregates of units, for example as cells form portions of tissue and organs form families, herds, breeds, species, and so on. At the same time, the division of certain portions of reality into engineered units (manufactured artifacts) is the basis of modern industrial technology, which rests on the distributed mass production of engineered parts through division of labor and on their assembly into larger, compound units such as cars and laptops. The division of portions of reality into units is one starting point for the phenomenon of counting.
BFO 2 Reference: Each object is such that there are entities of which we can assert unproblematically that they lie in its interior, and other entities of which we can assert unproblematically that they lie in its exterior. This may not be so for entities lying at or near the boundary between the interior and exterior. This means that two objects – for example the two cells depicted in Figure 3 – may be such that there are material entities crossing their boundaries which belong determinately to neither cell. Something similar obtains in certain cases of conjoined twins (see below).
BFO 2 Reference: To say that b is causally unified means: b is a material entity which is such that its material parts are tied together in such a way that, in environments typical for entities of the type in question,if c, a continuant part of b that is in the interior of b at t, is larger than a certain threshold size (which will be determined differently from case to case, depending on factors such as porosity of external cover) and is moved in space to be at t at a location on the exterior of the spatial region that had been occupied by b at t, then either b’s other parts will be moved in coordinated fashion or b will be damaged (be affected, for example, by breakage or tearing) in the interval between t and t.causal changes in one part of b can have consequences for other parts of b without the mediation of any entity that lies on the exterior of b. Material entities with no proper material parts would satisfy these conditions trivially. Candidate examples of types of causal unity for material entities of more complex sorts are as follows (this is not intended to be an exhaustive list):CU1: Causal unity via physical coveringHere the parts in the interior of the unified entity are combined together causally through a common membrane or other physical covering\. The latter points outwards toward and may serve a protective function in relation to what lies on the exterior of the entity [13, 47
BFO 2 Reference: an object is a maximal causally unified material entity
BFO 2 Reference: ‘objects’ are sometimes referred to as ‘grains’ [74
b is an object means: b is a material entity which manifests causal unity of one or other of the types CUn listed above & is of a type (a material universal) instances of which are maximal relative to this criterion of causal unity. (axiom label in BFO2 Reference: [024-001])
object
The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity.
the pdf file on your laptop, the pdf file that is a copy thereof on my laptop
the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule.
A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time.
b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001])
(iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001]
generically dependent continuant
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
the boundary between the 2nd and 3rd year of your life.
p is a process boundary =Def. p is a temporal part of a process & p has no proper temporal parts. (axiom label in BFO2 Reference: [084-001])
Every process boundary occupies_temporal_region a zero-dimensional temporal region. (axiom label in BFO2 Reference: [085-002])
(forall (x) (if (ProcessBoundary x) (exists (y) (and (ZeroDimensionalTemporalRegion y) (occupiesTemporalRegion x y))))) // axiom label in BFO2 CLIF: [085-002]
(iff (ProcessBoundary a) (exists (p) (and (Process p) (temporalPartOf a p) (not (exists (b) (properTemporalPartOf b a)))))) // axiom label in BFO2 CLIF: [084-001]
process boundary
the temporal region during which a process occurs.
BFO 2 Reference: A temporal interval is a special kind of one-dimensional temporal region, namely one that is self-connected (is without gaps or breaks).
A one-dimensional temporal region is a temporal region that is extended. (axiom label in BFO2 Reference: [103-001])
(forall (x) (if (OneDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [103-001]
one-dimensional temporal region
a flame
a forest fire
a human being
a hurricane
a photon
a puff of smoke
a sea wave
a tornado
an aggregate of human beings.
an energy wave
an epidemic
the undetached arm of a human being
An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time.
BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60
BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity.
BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here.
A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002])
Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002])
every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002])
(forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002]
(forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002]
(forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002]
material entity
b is a continuant fiat boundary = Def. b is an immaterial entity that is of zero, one or two dimensions and does not include a spatial region as part. (axiom label in BFO2 Reference: [029-001])
BFO 2 Reference: In BFO 1.1 the assumption was made that the external surface of a material entity such as a cell could be treated as if it were a boundary in the mathematical sense. The new document propounds the view that when we talk about external surfaces of material objects in this way then we are talking about something fiat. To be dealt with in a future version: fiat boundaries at different levels of granularity.More generally, the focus in discussion of boundaries in BFO 2.0 is now on fiat boundaries, which means: boundaries for which there is no assumption that they coincide with physical discontinuities. The ontology of boundaries becomes more closely allied with the ontology of regions.
BFO 2 Reference: a continuant fiat boundary is a boundary of some material entity (for example: the plane separating the Northern and Southern hemispheres; the North Pole), or it is a boundary of some immaterial entity (for example of some portion of airspace). Three basic kinds of continuant fiat boundary can be distinguished (together with various combination kinds [29
Continuant fiat boundary doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the mereological sum of two-dimensional continuant fiat boundary and a one dimensional continuant fiat boundary that doesn't overlap it. The situation is analogous to temporal and spatial regions.
Every continuant fiat boundary is located at some spatial region at every time at which it exists
(iff (ContinuantFiatBoundary a) (and (ImmaterialEntity a) (exists (b) (and (or (ZeroDimensionalSpatialRegion b) (OneDimensionalSpatialRegion b) (TwoDimensionalSpatialRegion b)) (forall (t) (locatedInAt a b t)))) (not (exists (c t) (and (SpatialRegion c) (continuantPartOfAt c a t)))))) // axiom label in BFO2 CLIF: [029-001]
continuant fiat boundary
BFO 2 Reference: Immaterial entities are divided into two subgroups:boundaries and sites, which bound, or are demarcated in relation, to material entities, and which can thus change location, shape and size and as their material hosts move or change shape or size (for example: your nasal passage; the hold of a ship; the boundary of Wales (which moves with the rotation of the Earth) [38, 7, 10
immaterial entity
The Equator
all geopolitical boundaries
all lines of latitude and longitude
the line separating the outer surface of the mucosa of the lower lip from the outer surface of the skin of the chin.
the median sulcus of your tongue
a one-dimensional continuant fiat boundary is a continuous fiat line whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [032-001])
(iff (OneDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (OneDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [032-001]
one-dimensional continuant fiat boundary
On a somewhat higher level of complexity are what we shall call rate process profiles, which are the targets of selective abstraction focused not on determinate quality magnitudes plotted over time, but rather on certain ratios between these magnitudes and elapsed times. A speed process profile, for example, is represented by a graph plotting against time the ratio of distance covered per unit of time. Since rates may change, and since such changes, too, may have rates of change, we have to deal here with a hierarchy of process profile universals at successive levels
One important sub-family of rate process profiles is illustrated by the beat or frequency profiles of cyclical processes, illustrated by the 60 beats per minute beating process of John’s heart, or the 120 beats per minute drumming process involved in one of John’s performances in a rock band, and so on. Each such process includes what we shall call a beat process profile instance as part, a subtype of rate process profile in which the salient ratio is not distance covered but rather number of beat cycles per unit of time. Each beat process profile instance instantiates the determinable universal beat process profile. But it also instantiates multiple more specialized universals at lower levels of generality, selected from rate process profilebeat process profileregular beat process profile3 bpm beat process profile4 bpm beat process profileirregular beat process profileincreasing beat process profileand so on.In the case of a regular beat process profile, a rate can be assigned in the simplest possible fashion by dividing the number of cycles by the length of the temporal region occupied by the beating process profile as a whole. Irregular process profiles of this sort, for example as identified in the clinic, or in the readings on an aircraft instrument panel, are often of diagnostic significance.
The simplest type of process profiles are what we shall call ‘quality process profiles’, which are the process profiles which serve as the foci of the sort of selective abstraction that is involved when measurements are made of changes in single qualities, as illustrated, for example, by process profiles of mass, temperature, aortic pressure, and so on.
b is a process_profile =Def. there is some process c such that b process_profile_of c (axiom label in BFO2 Reference: [093-002])
b process_profile_of c holds when b proper_occurrent_part_of c& there is some proper_occurrent_part d of c which has no parts in common with b & is mutually dependent on b& is such that b, c and d occupy the same temporal region (axiom label in BFO2 Reference: [094-005])
(forall (x y) (if (processProfileOf x y) (and (properContinuantPartOf x y) (exists (z t) (and (properOccurrentPartOf z y) (TemporalRegion t) (occupiesSpatioTemporalRegion x t) (occupiesSpatioTemporalRegion y t) (occupiesSpatioTemporalRegion z t) (not (exists (w) (and (occurrentPartOf w x) (occurrentPartOf w z))))))))) // axiom label in BFO2 CLIF: [094-005]
(iff (ProcessProfile a) (exists (b) (and (Process b) (processProfileOf a b)))) // axiom label in BFO2 CLIF: [093-002]
process profile
a marriage bond, an instance of requited love, an obligation between one person and another.
b is a relational quality = Def. for some independent continuants c, d and for some time t: b quality_of c at t & b quality_of d at t. (axiom label in BFO2 Reference: [057-001])
(iff (RelationalQuality a) (exists (b c t) (and (IndependentContinuant b) (IndependentContinuant c) (qualityOfAt a b t) (qualityOfAt a c t)))) // axiom label in BFO2 CLIF: [057-001]
relational quality
a two-dimensional continuant fiat boundary (surface) is a self-connected fiat surface whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [033-001])
(iff (TwoDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (TwoDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [033-001]
two-dimensional continuant fiat boundary
the geographic North Pole
the point of origin of some spatial coordinate system.
the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet
zero dimension continuant fiat boundaries are not spatial points. Considering the example 'the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet' : There are many frames in which that point is zooming through many points in space. Whereas, no matter what the frame, the quadripoint is always in the same relation to the boundaries of Colorado, Utah, New Mexico, and Arizona.
a zero-dimensional continuant fiat boundary is a fiat point whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [031-001])
(iff (ZeroDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (ZeroDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [031-001]
zero-dimensional continuant fiat boundary
a temporal region that is occupied by a process boundary
right now
the moment at which a child is born
the moment at which a finger is detached in an industrial accident
the moment of death.
temporal instant.
A zero-dimensional temporal region is a temporal region that is without extent. (axiom label in BFO2 Reference: [102-001])
(forall (x) (if (ZeroDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [102-001]
zero-dimensional temporal region
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
anatomical entity
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.
A potassium salt that is the dipotassium salt of carbonic acid.
A compound used with herbicides that reduces the effect of the herbicide on crop plants or otherwise improves the selectivity of the herbicide for weed species over the crop plant.
A reagent that lightens or whitens a substrate through chemical reaction. Bleaching reactions usually involve oxidative or reductive processes that degrade colour systems. Bleaching can occur by destroying one or more of the double bonds in the conjugated chain, by cleaving the conjugated chain, or by oxidation of one of the other moieties in the conjugated chain. Their reactivity results in many bleaches having strong bactericidal, disinfecting, and sterilising properties.
A prodrug that, on administration, undergoes chemical conversion by biochemical (enzymatic), chemical (possibly following an enzymatic step), or physical (e.g. photochemical) activation processes before becoming the pharmacologically active pesticide for which it is a propesticide.
A compound that, on administration, must undergo chemical conversion by biochemical (enzymatic), chemical (possibly following an enzymatic step), or physical (e.g. photochemical) activation processes before becoming the pharmacologically active herbicide for which it is a proherbicide.
A compound that, on administration, undergoes conversion by biochemical (enzymatic), chemical (possibly following an enzymatic step), or physical (e.g. photochemical) activation processes before becoming the active agent for which it is a pro-agent.
An atom of an element that exhibits properties that are between those of metals and nonmetals, or that has a mixture of them. The term generally includes boron, silicon, germanium, arsenic, antimony, and tellurium, while carbon, aluminium, selenium, polonium, and astatine are less commonly included.
A Bronsted acid derived from one or more inorganic compounds. Inorganic acids (also known as mineral acids) form hydrons and conjugate base ions when dissolved in water.
Any main group molecular entity that is gaseous at standard temperature and pressure (STP; 0degreeC and 100 kPa).
A cyclic tetrapyrrole anion that is the carbanion obtained by removal of the acidic proton from position 21 of any chlorophyll. Major species at pH 7.3
An isotopically modified compound in which the abundance of a (13)C isotope at one or more positions has been increased above that of the naturally occurring level.
Any molecular entity in which the isotopic ratio of nuclides for at least one element deviates measurably from that occurring in nature. The term includes both isotopically substituted compounds (in which essentially all the molecules of the compound have only the indicated nuclide(s) at each designated position) and isotopically labeled compounds (a formal mixture of an isotopically unmodified compound with one or more analogous isotopically substituted compound(s).
A chemical compound that causes a substantial proportion of exposed people or animals to develop an allergic reaction in normal tissue after repeated exposure to the compound.
A mixture of ammonium sulfate and ammonium nitrate used as a feriliser to provide both nitrogen and sulfur nutrients.
An inorganic ammonium salt composed of ammonium and thiosulfate ions in a 2:1 ratio. It is used in the leaching of gold and silver, as a fertilizer and as a photographic fixing salt.
An inorganic ammonium salt of polyphosphate. It is used as a flame retardant and as a fertilizer. The chain length (n) of this polymer is variable and can be linear or branched.
An inorganic sulfate salt obtained by reaction of sulfuric acid with one equivalent of ammonium phosphate.
ammonium dihydrogen phosphate hydrogen sulfate
A mixture that contains ammonium nitrate mixed with potash and/or phosphate. It is used in the fertilizer industry. Such high analysis mixtures i.e., rich in nitrogen and phosphorus, can be applied directly to the soil or can be mixed with other fertilizer ingredients to provide a complete fertilizer.
ammonium nitrate fertilizers, with phosphate or potash
A guanidine in which one of the amino hydrogens of guanidine itself is substituted by a cyano group. It is used in the manufacture of fertilizers, pharmaceuticals, explosives, oil well drilling muds, and dyestuffs.
A phosphate salt obtained by reacting 3,4-dimethyl-1H-pyrazole with one equivalent of phosphoric acid. It is a nitrification inhibitor and when used on crops, it prevents nitrogen loss from soil, increases nitrogen use efficiency, and boosts crop yields.
Any inhibitor added to nitrogen fertilizers which can reduce the rate at which ammonium is converted to nitrate. Under appropriate conditions, this can help reduce nitrogen losses through denitrification and leaching.
A member of the class of pyrazoles that is 1H-pyrazole which is substituted by methyl groups at positions 3 and 4.
A potassium salt of metaphosphoric acid.
An inorganic phosphate that is the ammonium magnesium salt of phosphoric acid.
phosphoric acid, ammonium magnesium salt
A hydrate that is the hexahydrate form of ammonium magnesium phosphate. It is a constituent of urinary calculi.
ammonium magnesium phosphate--water (1/6)
magnesium ammonium phosphate hexahydrate
ammonium magnesium phosphate hexahydrate
Any agent that induces nausea and vomiting.
A divalent inorganic anion obtained by removal of both protons from selenic acid.
A divalent inorganic anion obtained by removal of both protons from hydrogen sulfide.
A molecular entity that can accept an electron, a pair of electrons, an atom or a group from another molecular entity.
An oxygen hydride consisting of an oxygen atom that is covalently bonded to two hydrogen atoms
A monoatomic monoanion resulting from the addition of an electron to any halogen atom.
A divalent inorganic anion obtained by removal of both protons from thiosulfuric acid.
An azane that consists of a single nitrogen atom covelently bonded to three hydrogen atoms.
A sulfur hydride consisting of a single sulfur atom bonded to two hydrogen atoms. A highly poisonous, flammable gas with a characteristic odour of rotten eggs, it is often produced by bacterial decomposition of organic matter in the absence of oxygen.
A sulfur oxoanion obtained by deprotonation of both OH groups of sulfuric acid.
A carbonyl group with two C-bound amine groups. The commercially available fertilizer has an analysis of 46-0-0 (N-P2O5-K2O).
A nitrile that is hydrogen cyanide in which the hydrogen has been replaced by an amino group.
A mineral that is an inorganic nutrient which must be ingested and absorbed in adequate amounts to satisfy a wide range of essential metabolic and/or structural functions in the human body.
The phosphorus oxoanion formed from polyphosphoric acid by proton loss from each of the phosphate units. The major species at pH 7.3.
A pseudohalide anion that is the conjugate base of hydrogen cyanide.
The carbon oxoanion resulting from the removal of a proton from carbonic acid.
A nitrogen oxoanion formed by loss of a proton from nitric acid. Principal species present at pH 7.3.
A mononuclear parent hydride consisting of covalently bonded hydrogen and chlorine atoms.
A molecular entity that can transfer ("donate") an electron, a pair of electrons, an atom or a group to another molecular entity.
A halide anion formed when chlorine picks up an electron to form an an anion.
An elemental molecule consisting of two trivalently-bonded nitrogen atoms.
An iron group element atom that has atomic number 26.
A phosphate ion that is the conjugate base of hydrogenphosphate.
A compound having the structure RC#N; thus a C-substituted derivative of hydrocyanic acid, HC#N. In systematic nomenclature, the suffix nitrile denotes the triply bound #N atom, not the carbon atom attached to it.
A one-carbon compound consisting of a methine group triple bonded to a nitrogen atom
A substance used to destroy pests of the subclass Acari (mites and ticks).
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).
The univalent carboacyl group formed by loss of -OH from the carboxy group of carbamic acid.
Organooxygen compounds that are salts or esters of carbonic acid, H2CO3.
A substance intended to sterilize any organism.
A halogen molecular entity containing one or more atoms of chlorine.
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 metal sulfate compound having copper(2+) as the metal ion.
Salts and C-organyl derivatives of hydrogen cyanide, HC#N.
A herbicide which when sprayed or dusted on plants causes its leaves to fall off.
An azole that is either one of a pair of heterocyclic organic compounds comprising three carbon atoms and two nitrogen atoms arranged in a ring.
Any substance which when absorbed into a living organism may modify one or more of its functions. The term is generally accepted for a substance taken for a therapeutic purpose, but is also commonly used for abused substances.
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 substance used to destroy fungal pests.
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.
Any organonitrogen compound containing a carbamimidamido (guanidino) group. Guanidines have the general structure (R(1)R(2)N)(R(3)R(4)N)C=N-R(5) and are related structurally to amidines and ureas.
A substance used to destroy plant pests.
A cyclic compound having as ring members atoms of carbon and at least of one other element.
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.
Any phosphate that contains no carbon atom.
Strictly, a substance intended to kill members of the class Insecta. In common usage, any substance used for preventing, destroying, repelling or controlling insects.
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.
mitochondrial electron transport chain inhibitors
mitochondrial electron-transport chain inhibitor
mitochondrial respiratory chain inhibitors
mitochondrial respiratory-chain inhibitor
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.
A substance used to destroy pests of the phylum Nematoda (roundworms).
Any organic ion with a net negative charge.
An oxide is a chemical compound of oxygen with other chemical elements.
Strictly, a substance intended to kill pests. In common usage, any substance used for controlling, preventing, or destroying animal, microbiological or plant pests.
Any organic aromatic compound with a structure based on a phenylpropane skeleton. The class includes naturally occurring phenylpropanoid esters, flavonoids, anthocyanins, coumarins and many small phenolic molecules as well as their semi-synthetic and synthetic analogues. Phenylpropanoids are also precursors of lignin.
Salts and esters of phosphoric and oligophosphoric acids and their chalcogen analogues. In inorganic chemistry, the term is also used to describe anionic coordination entities with phosphorus as central atom.
A phosphorus oxoacid that consists of one oxo and three hydroxy groups joined covalently to a central phosphorus atom.
An endogenous molecular entity that results in a colour of an organism as the consequence of the selective absorption of light.
Natural pigments containing a fundamental skeleton of four pyrrole nuclei united through the alpha-positions by four methine groups to form a macrocyclic structure.
Any alkali metal salt having potassium(1+) as the cation.
Any alkali metal salt having sodium(1+) as the cation.
A sulfur oxoacid that consists of two oxo and two hydroxy groups joined covalently to a central sulfur atom.
A natural pigment containing four pyrrole rings joined by one-carbon units linking position 2 of one pyrrole ring to position 5 of the next.
Poisonous substance produced by a biological organism such as a microbe, animal or plant.
Any nutrient required in small quantities by organisms throughout their life in order to orchestrate a range of physiological functions.
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.
Chemical element (nickel group element atom) with atomic number 28.
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.
A family of magnesium porphyrins, defined by the presence of a fifth ring beyond the four pyrrole-like rings. The rings can have various side chains which usually include a long phytol chain.
An ion of copper carrying a double positive charge.
The conjugate base formed when the carboxy group of a carboxylic acid is deprotonated.
A monoatomic monocation obtained from sodium.
A monoatomic monocation obtained from potassium.
A divalent inorganic anion resulting from the removal of two protons from ammonia.
A carboxamide derived from a monocarboxylic acid.
A member of the class of calcium oxides of calcium and oxygen in a 1:1 ratio.
A magnesium salt with formula CMgO3. Its hydrated forms, particularly the di-, tri-, and tetrahydrates occur as minerals.
A (13)C-modified compound that is urea in which the carbon is present as its (13)C isotope.
sulfuric acid, calcium salt (1:1), dihydrate
sulfuric acid, calcium(2+) salt, dihydrate
A metal chloride salt with a K(+) counterion.
A magnesium salt having sulfate as the counterion.
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.
An assembly consisting of a central atom (usually metallic) to which is attached a surrounding array of other groups of atoms (ligands).
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 substance that kills or slows the growth of microorganisms, including bacteria, viruses, fungi and protozoans.
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.
An agrochemical is a substance that is used in agriculture or horticulture.
A fertilizer is any substance that is added to soil or water to assist the growth of plants.
A substance used to destroy rodent pests.
A physiological role played by any substance of either plant, animal or artificial origin which contains essential body nutrients that can be ingested by an organism to provide energy, promote growth, and maintain the processes of life.
A molecular entity containing one or more atoms of an alkali metal.
An alkaline earth molecular entity is a molecular entity containing one or more atoms of an alkaline earth 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 hydracid is a compound which contains hydrogen that is not bound to oxygen, and which produces a conjugate base by loss of positive hydrogen ion(s) (hydrons).
A pnictogen oxoacid which contains phosphorus and oxygen, at least one hydrogen atom bound to oxygen, and forms an ion by the loss of one or more protons.
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.
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.
Any molecule that consists of a series of atoms joined together to form a ring.
A cyclically conjugated molecular entity with a stability (due to delocalization) significantly greater than that of a hypothetical localized structure (e.g. Kekule structure) is said to possess aromatic character.
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 cation consisting of more than one atom.
A carboxylic acid containing one or more amino groups.
Any organic molecule that consists of atoms connected in the form of a ring.
A heterocyclic compound formally derived from an arene by replacement of one or more methine (-C=) and/or vinylene (-CH=CH-) groups by trivalent or divalent heteroatoms, respectively, in such a way as to maintain the continuous pi-electron system characteristic of aromatic systems and a number of out-of-plane pi-electrons corresponding to the Hueckel rule (4n+2).
A substance used in a chemical reaction to detect, measure, examine, or produce other substances.
A substance used to destroy pests of the phylum Mollusca.
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 metal sulfate compound having zinc(2+) as the counterion.
A substance that diminishes the rate of a chemical reaction.
A substance that increases the rate of a reaction without modifying the overall standard Gibbs energy change in the reaction.
Any substance or mixture of substances that, in solution (typically aqueous), resists change in pH upon addition of small amounts of acid or base.
A derivative of ammonium, NH4(+), in which one (or more) of the hydrogens bonded to the nitrogen have been replaced with univalent organyl groups. The substituting carbon of the organyl group must not itself be directly attached to a heteroatom (thereby excluding protonated amides, hemiaminals, etc).
Compounds (NH4(+))Y(-) and derivatives, in which one or more of the hydrogens bonded to nitrogen have been replaced with univalent groups.
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 class of drugs producing both physiological and psychological effects through a variety of mechanisms involving the central nervous system.
An agent capable of relieving pain without the loss of consciousness or without producing anaesthesia. In addition, analgesic is a role played by a compound which is exhibited by a capability to cause a reduction of pain symptoms.
An EC 1.2.1.* (oxidoreductase acting on donor aldehyde/oxo group with NAD(+) or NADP(+) as acceptor) inhibitor that interferes with the action of aldehyde dehydrogenase (NAD(+)), EC 1.2.1.3.
CoA-independent aldehyde dehydrogenase inhibitor
CoA-independent aldehyde dehydrogenase inhibitors
EC 1.2.1.3 (aldehyde dehydrogenase (NAD(+))) inhibitor
EC 1.2.1.3 (aldehyde dehydrogenase (NAD(+))) inhibitors
EC 1.2.1.3 [aldehyde dehydrogenase (NAD(+))] inhibitors
NAD-dependent 4-hydroxynonenal dehydrogenase inhibitor
NAD-dependent 4-hydroxynonenal dehydrogenase inhibitors
NAD-dependent aldehyde dehydrogenase inhibitor
NAD-dependent aldehyde dehydrogenase inhibitors
NAD-linked aldehyde dehydrogenase inhibitor
NAD-linked aldehyde dehydrogenase inhibitors
aldehyde dehydrogenase (NAD(+)) (EC 1.2.1.3) inhibitor
aldehyde dehydrogenase (NAD(+)) (EC 1.2.1.3) inhibitors
aldehyde dehydrogenase (NAD(+)) inhibitor
aldehyde dehydrogenase (NAD(+)) inhibitors
m-methylbenzaldehyde dehydrogenase inhibitor
m-methylbenzaldehyde dehydrogenase inhibitors
propionaldehyde dehydrogenase inhibitors
EC 1.2.1.3 [aldehyde dehydrogenase (NAD(+))] inhibitor
A loosely defined group of drugs that tend to reduce the activity of the central nervous system.
An addition compound contains two or more simpler compounds that can be packed in a definite ratio into a crystal. The term covers donor-acceptor complexes (adducts) and a variety of lattice compounds.
An addition compound that contains water in weak chemical combination with another compound.
A drug that affects the rate or intensity of cardiac contraction, blood vessel diameter or blood volume.
A negative ion consisting solely of carbon and oxygen atoms, and therefore having the general formula CxOy(n-) for some integers x, y and n.
An EC 3.1.3.* (phosphoric monoester hydrolase) inhibitor which interferes with the activity of the enzyme protein tyrosine phosphatases (PTPs), EC 3.1.3.48, involved in the removal of phosphate groups from phosphorylated tyrosine residues on proteins.
EC 3.1.3.48 (protein-tyrosine-phosphatase) inhibitors
[phosphotyrosine]protein phosphatase inhibitor
[phosphotyrosine]protein phosphatase inhibitors
phosphoprotein phosphatase (phosphotyrosine) inhibitor
phosphoprotein phosphatase (phosphotyrosine) inhibitors
phosphotyrosine histone phosphatase inhibitor
phosphotyrosine histone phosphatase inhibitors
phosphotyrosine protein phosphatase inhibitor
phosphotyrosine protein phosphatase inhibitors
phosphotyrosylprotein phosphatase inhibitor
phosphotyrosylprotein phosphatase inhibitors
protein phosphotyrosine phosphatase inhibitor
protein phosphotyrosine phosphatase inhibitors
protein-tyrosine-phosphatase (EC 3.1.3.48) inhibitor
protein-tyrosine-phosphatase (EC 3.1.3.48) inhibitors
protein-tyrosine-phosphate phosphohydrolase inhibitor
protein-tyrosine-phosphate phosphohydrolase inhibitors
tyrosine O-phosphate phosphatase inhibitor
tyrosine O-phosphate phosphatase inhibitors
EC 3.1.3.48 (protein-tyrosine-phosphatase) inhibitor
A drug used to cause dilation of the blood vessels.
A drug used to prevent seizures or reduce their severity.
An antimicrobial agent that destroys fungi by suppressing their ability to grow or reproduce.
A phosphorus oxoanion that is the conjugate base of phosphoric acid.
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.
A subatomic particle known to have substructure (i.e. consisting of smaller particles).
Hadron is a subatomic particle which experiences the strong force.
A nucleus or any of its constituents in any of their energy states.
Any molecular entity consisting of more than one atom.
An ion consisting of more than one atom.
A coordination entity in which the central atom to which the ligands are attached comes from groups 1, 2, 13, 14, 15, 16, 17, or 18 of the periodic table.
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.
Compounds consisting of two acyl groups bonded to the same oxygen atom acyl-O-acyl.
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.
Any heteroatomic molecular entity that is a chemical compound of halogen with other 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 drug used for the treatment or prevention of cardiac arrhythmias. Anti-arrhythmia drugs may affect the polarisation-repolarisation phase of the action potential, its excitability or refractoriness, or impulse conduction or membrane responsiveness within cardiac fibres.
A compound composed of two or more pyrrole units.
Any organonitrogen compound containing a cyclic component with nitrogen and at least one other element as ring member atoms.
A ligand with two or more separate binding sites that can bind to a single metallic central atom, forming a chelate.
One of a class of drugs that acts by selective inhibition of calcium influx through cell membranes or on the release and binding of calcium in intracellular pools.
An EC 1.9.3.* (oxidoreductase acting on donor heme group, oxygen as acceptor) inhibitor that interferes with the action of cytochrome c oxidase (EC 1.9.3.1).
EC 1.9.3.1 (cytochrome c oxidase) inhibitors
complex IV (mitochondrial electron transport) inhibitor
complex IV (mitochondrial electron transport) inhibitors
cytochrome c oxidase (EC 1.9.3.1) inhibitor
cytochrome c oxidase (EC 1.9.3.1) inhibitors
ferrocytochrome-c:oxygen oxidoreductase inhibitor
ferrocytochrome-c:oxygen oxidoreductase inhibitors
mitochondrial cytochrome-c oxidase inhibitors
EC 1.9.3.1 (cytochrome c oxidase) inhibitor
Any agent that affects the transport of molecular entities across a biological membrane.
A membrane transport modulator that is able to regulate intracellular calcium levels.
Substance which produces loss of feeling or sensation.
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.
A volatile or volatilizable chemical compound utilized for control of pests in buildings, soil, grain, as well as during processing of goods to be imported or exported to prevent transfer of exotic organisms.
Any chemical substance that inhibits the life-cycle of an organism.
A monovalent inorganic anion that consists of phosphoric acid in which one of the three OH groups has been deprotonated.
A phosphate ion that is the conjugate base of dihydrogenphosphate.
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 liquid that can dissolve other substances (solutes) without any change in their chemical composition.
A nitrogen oxoacid of formula HNO3 in which the nitrogen atom is bonded to a hydroxy group and by equivalent bonds to the remaining two oxygen atoms.
A solvent that is composed of polar molecules. Polar solvents can dissolve ionic compounds or ionisable covalent compounds.
A polar solvent that is capable of acting as a hydron (proton) donor.
Solvent that is capable of acting as a hydron (proton) acceptor.
Self-ionizing solvent possessing both characteristics of Bronsted acids and bases.
Compounds derived from oxoacids RkE(=O)l(OH)m (l =/= 0) by replacing =O by =NR; thus tautomers of amides. In organic chemistry an unspecified imidic acid is generally a carboximidic acid, RC(=NR)(OH).
A carboximidic acid that is the imidic acid tautomer of urea, H2NC(=NH)OH, and its hydrocarbyl derivatives.
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.
A substance used either in the prevention or facilitation of pregnancy.
Any molecular entity that contains carbon.
A role played by a chemical compound to induce direct or indirect DNA damage. Such damage can potentially lead to the formation of a malignant tumour, but DNA damage does not lead inevitably to the creation of cancerous cells.
A chemical compound, or part thereof, which causes the onset of an allergic reaction by interacting with any of the molecular pathways involved in an allergy.
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.
Sulfate salts where the cation is a metal ion.
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.
A biological role which describes how a drug interacts within a biological system and how the interactions affect its medicinal properties.
Any molecule or ion capable of binding to a central metal atom to form coordination complexes.
Any substance introduced into a living organism with therapeutic or diagnostic purpose.
A polymerized phosphorus oxoacid of general formula HO[PO2OH]nH formed by condensation of orthophosphoric acid molecules and containing a backbone chain consisting of alternating P and O atoms covalently bonded together.
The biological role played by a material entity when bound by a receptor of the adaptive immune system. Specific site on an antigen to which an antibody binds.
A cyclic compound having as ring members atoms of at least two different elements.
An organic anion arising from deprotonation of a cyclic tetrapyrrole compound.
Compounds containing one or more phosphoric acid units.
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.
A mixture is a chemical substance composed of multiple molecules, at least two of which are of a different kind.
An atom or small molecule with a positive charge that does not contain carbon in covalent linkage, with a valency of one.
A molecular messenger in which the molecule is specifically involved in transmitting information between cells. Such molecules are released from the cell sending the signal, cross over the gap between cells by diffusion, and interact with specific receptors in another cell, triggering a response in that cell by activating a series of enzyme controlled reactions which lead to changes inside the cell.
A family of nitrogen molecular entities which are highly reactive and derived from nitric oxide (.NO) and superoxide (O2.(-)) produced via the enzymatic activity of inducible nitric oxide synthase 2 (NOS2) and NADPH oxidase respectively.
An inorganic sulfate salt obtained by reaction of sulfuric acid with two equivalents of ammonia. A high-melting (decomposes above 280degreeC) white solid which is very soluble in water (70.6 g/100 g water at 0degreeC; 103.8 g/100 g water at 100degreeC), it is widely used as a fertilizer for alkaline soils.
The ammonium salt of phosphoric acid (molar ratio 1:1).
A potassium salt in which dihydrogen phosphate(1-) is the counterion.
Orthophosphoric acid, monopotassium salt
The inorganic nitrate salt of potassium.
The chemical role played by a substance that stabilizes an emulsion by increasing its kinetic stability.
A food additive used to form or maintain a uniform emulsion of two (or more) phases in a food.
An inorganic phosphate, being the diammonium salt of phosphoric acid. The commercially available fertilizer has an analysis of 18-46-0 (N-P2O5-K2O) and is marketed under the name diammonium phosphate or DAP.
Any zinc ion that is positively charged.
The element or compound in a reduction-oxidation (redox) reaction that donates an electron to another species.
A substance that removes electrons from another reactant in a redox reaction.
A substance capable of undergoing rapid and highly exothermic decomposition.
Any substance which is added to food to preserve or enhance its flavour and/or appearance.
A food additive that is used to change or otherwise control the acidity or alkalinity of foods. They may be acids, bases, neutralising agents or buffering agents.
The calcium salt of cyanamide, formed when calcium carbide reacts with nitrogen
An organic nitrogen anion formed from cyanamide by loss of its two protons.
A polyphenylpropanoid derived from three monolignol monomers: trans-p-coumaryl alcohol, coniferol and trans-sinapyl alcohol. There is extensive cross-linking and no defined primary structure.
A food additive which is added to flour or dough to improve baking quality and/or colour.
An inorganic cation with a valency of two.
An organic molecular entity containing a single carbon atom (C1).
Any organic molecular entity that is acidic and contains carbon in covalent linkage.
The inorganic nitrate salt of magnesium.
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.
Substances which are added to food in order to prevent decomposition caused by microbial growth or by undesirable chemical changes.
Any substance which is used to neutralise stomach acidity.
Any compound used to suppress premature labour and immature birth by suppressing uterine contractions.
A chemosterilant intended to sterilize insects.
Any monocyclic heteroarene consisting of a five-membered ring containing nitrogen. Azoles can also contain one or more other non-carbon atoms, such as nitrogen, sulfur or oxygen.
An insecticide that acts as a repellent to insects.
Any molecule that consists of at least one carbon atom as part of the electrically neutral entity.
A compound that causes the contraction of body tissues, typically used to reduce bleeding from minor abrasions.
A chemical additive used to toughen or harden a polymer material by cross-linking of polymer chains.
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.
A gas in an atmosphere that absorbs and emits radiation within the thermal infrared range, so contributing to the 'greenhouse effect'.
A compressed gas or liquid with a boiling point lower than room temperature which to used to propel and dispense liquids such as deodorants, insecticides, paints, etc. from aerosol cans.
An enzyme inhibitor which interferes with the action of an oxidoreductase (EC 1.*.*.*).
An oxidoreductase inhibitor which interferes with the action of an oxidoreductase acting on the aldehyde or oxo group of donors (EC 1.2.*.*).
EC 1.2.* (oxidoreductase acting on donor aldehyde or oxo group) inhibitor
EC 1.2.* (oxidoreductase acting on donor aldehyde or oxo group) inhibitors
EC 1.2.* (oxidoreductase acting on donor aldehyde/oxo group) inhibitors
inhibitor of oxidoreductase acting on aldehyde or oxo group of donor
inhibitor of oxidoreductase acting on aldehyde or oxo group of donors
inhibitor of oxidoreductase acting on aldehyde/oxo group of donor
inhibitor of oxidoreductase acting on aldehyde/oxo group of donors
inhibitors of oxidoreductase acting on aldehyde or oxo group of donor
inhibitors of oxidoreductase acting on aldehyde or oxo group of donors
inhibitors of oxidoreductase acting on aldehyde/oxo group of donor
inhibitors of oxidoreductase acting on aldehyde/oxo group of donors
oxidoreductase acting on donor aldehyde or oxo group (EC 1.2.*) inhibitor
oxidoreductase acting on donor aldehyde or oxo group (EC 1.2.*) inhibitors
oxidoreductase acting on donor aldehyde or oxo group inhibitor
oxidoreductase acting on donor aldehyde or oxo group inhibitors
oxidoreductase acting on donor aldehyde/oxo group (EC 1.2.*) inhibitor
oxidoreductase acting on donor aldehyde/oxo group (EC 1.2.*) inhibitors
oxidoreductase acting on donor aldehyde/oxo group inhibitor
oxidoreductase acting on donor aldehyde/oxo group inhibitors
EC 1.2.* (oxidoreductase acting on donor aldehyde/oxo group) inhibitor
An oxidoreductase inhibitor which interferes with the action of an oxidoreductase acting on a heme group of donors (EC 1.9.*.*).
EC 1.9.* (oxidoreductase acting on a heme group of donors) inhibitor
EC 1.9.* (oxidoreductase acting on a heme group of donors) inhibitors
EC 1.9.* (oxidoreductase acting on donor heme group) inhibitors
oxidoreductase acting on a heme group of donors (EC 1.9.*) inhibitor
oxidoreductase acting on a heme group of donors (EC 1.9.*) inhibitors
EC 1.9.* (oxidoreductase acting on donor heme group) inhibitor
Any enzyme inhibitor that interferes with the action of a hydrolase (EC 3.*.*.*).
A hydrolase inhibitor that interferes with the action of any ester hydrolase (EC 3.1.*.*).
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 3.1.* (ester hydrolase) inhibitor that interferes with the action of any phosphoric monoester hydrolase (EC 3.1.3.*).
EC 3.1.3.* (phosphoric monoester hydrolase) inhibitors
inhibitor of phosphoric monoester hydrolase
inhibitor of phosphoric monoester hydrolase (EC 3.1.3.*)
inhibitors of phosphoric monoester hydrolase
inhibitors of phosphoric monoester hydrolase (EC 3.1.3.*)
phosphoric monoester hydrolase (EC 3.1.3.*) inhibitor
phosphoric monoester hydrolase (EC 3.1.3.*) inhibitors
phosphoric monoester hydrolase inhibitor
phosphoric monoester hydrolase inhibitors
EC 3.1.3.* (phosphoric monoester hydrolase) 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
An EC 1.2.* (oxidoreductase acting on donor aldehyde/oxo group) inhibitor that interferes with the action of any such enzyme using NAD(+) or NADP(+) as acceptor (EC 1.2.1.*).
EC 1.2.1.* (oxidoreductase acting on donor aldehyde/oxo group with NAD(+) or NADP(+) as acceptor) inhibitors
oxidoreductase acting on donor aldehyde/oxo group with NAD(+) or NADP(+) as acceptor (EC 1.2.1.*) inhibitor
oxidoreductase acting on donor aldehyde/oxo group with NAD(+) or NADP(+) as acceptor (EC 1.2.1.*) inhibitors
EC 1.2.1.* (oxidoreductase acting on donor aldehyde/oxo group with NAD(+) or NADP(+) as acceptor) inhibitor
An EC 1.9.* (oxidoreductase acting on donor heme group) inhibitor that interferes with the action of any such enzyme using oxygen as acceptor (EC 1.9.3.*).
EC 1.9.3.* (oxidoreductase acting on donor heme group, oxygen as acceptor) inhibitors
oxidoreductase acting on donor heme group, oxygen as acceptor (EC 1.9.3.*) inhibitor
oxidoreductase acting on donor heme group, oxygen as acceptor (EC 1.9.3.*) inhibitors
EC 1.9.3.* (oxidoreductase acting on donor heme group, oxygen as acceptor) inhibitor
An enzyme inhibitor that interferes with one or more steps in a metabolic pathway.
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.
A food additive that imparts colour to food. In European countries, E-numbers for permitted food colours are from E 100 to E 199, divided into yellows (E 100-109), oranges (E 110-119), reds (E 120-129), blues and violets (E 130-139), greens (E 140-149), browns and blacks (E 150-159), and others (E 160-199).
A calcium salt composed of calcium and phosphate/diphosphate ions; present in milk and used for the mineralisation of calcified tissues.
Any mammalian metabolite produced during a metabolic reaction in humans (Homo sapiens).
An inorganic sodium salt having selenate as the counterion.
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 food additive that is used to make or keep fruit or vegetable tissues firm and crisp. or which interacts with gelling agents such as pectin to produce or strengthen a gel.
A food preservative that acts by chelating with metal cations (particularly those of copper, iron and nickel) that catalyse the oxidation of fats in food.
A food additive which liberates gas so as to increase the volume of a dough or batter, resulting in a lighter and softer finished product.
A food additive that is a (generally inert) gas which is used to envelop foodstuffs during packing and so protect them from unwanted chemical reactions such as food spoilage or oxidation during subsequent transport and storage. The term includes propellant gases, used to expel foods from a container.
A propellant that is used to expel foods from an aerosol container.
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.
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.
Any compound that is added to manufactured materials to inhibit, suppress, or delay the production of flames and so prevent the spread of fire.
Any inorganic anion with a valency of three.
Any inorganic anion with a valency of two.
Any inorganic anion with a valency of one.
An animal metabolite produced by arthropods such as crabs, lobsters, crayfish, shrimps and krill.
A Daphnia metabolite produced by the species Daphnia magna.
A crustacean metabolite produced by the genus of small planktonic arthropods, Daphnia
Any eukaryotic metabolite produced during a metabolic reaction in algae including unicellular organisms like chlorella and diatoms to multicellular organisms like giant kelps and brown algae.
Any metal which causes the onset of an allergic reaction.
A mixture consisting of urea (typically 40-45%), ammonium nitrate (30-35%) and water (30-20%). It is used as a nitrogen fertilizer in agriculture.
A mixture obtained by combining ammonium nitrate, calcium nitrate and water. It is widely used as a nitrogen fertilizer in agriculture.
A mixture obtained by combining ammonium sulfate and urea.
An anthropogenic geographic feature is a geographic feature resulting from the influence of human beings on nature.
A primary administrative division of a country, such as a state in the United States.
A subdivision of a first-order administrative division.
A subdivision of a second-order administrative division.
A political association with effective dominion over a geographic area.
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.
A stream which, through permanent or seasonal flow processes, moves from elevated land towards lower elevations through a definite channel and empties either into a sea, lake, or another river or ends on land as bed seepage and evapotranspiration exceed water supply.
A watercourse which is linear and flows across the solid portion of a planetary surface.
An artificial body of water, often contained by a dam, constructed for the purpose of water storage.
A cylindrical hole, pit, or tunnel drilled or dug down to a depth from which water, oil, or gas can be pumped or brought to the surface.
A point where groundwater or steam flows out of the ground, and is thus where the aquifer surface meets the ground surface or where there is a fissure.
A sheet of saline water separated from the open sea by sand or shingle banks. The sheet of water between an offshore reef, especially of coral and mainland. The sheet of water within a ring or horseshoe shaped atoll.
An vegetated area which overlaps a wetland ecosystem.
A dense growth of shrubbery planted as a fence or boundary.
A swamp which is located in tropical or subtropical environments and is determined by communities of trees and shrubs growing saline coastal environments.
An accumulation of water of varying size.
A construction that has been assembled by deliberate human effort.
A permanent walled and roofed construction.
A barrier constructed across a watercourse to control the flow or raise the level of water.
An area of land which is used for the cultivation of crops or grazing of livestock, including any agricultural constructions therein.
A landform that extends above the surrounding terrain in a limited area.
A rounded elevation of limited extent rising above the surrounding land with local relief of less than 300m.
A region of general uniform slope, comparatively level, and of considerable extent.
An area of flat, low-lying land adjacent to a coast and separated from the interior by other features.
A landform consisting of loose rock particles such as sand, gravel, shingle, pebbles, cobble, or even shell fragments along the shoreline of a body of water.
A landform consisting of loose rock particles such as sand, gravel, shingle, pebbles, cobble, or even shell fragments along the shoreline of a sea.
A landform consisting of loose rock particles such as sand, gravel, shingle, pebbles, cobble, or even shell fragments along the shoreline of a lake.
A part of an astronomical body associated with a volcano - an opening, or rupture, in that body's surface or crust - which allows hot, molten rock, ash and gases to escape from deep below the surface.
A region rendered barren or partially barren by environmental extremes, especially by low rainfall.
Area of dry or relatively dry land surrounded by water or low wetland.
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.
An area in which grasses (Graminae) are a significant component of the vegetation.
A grassland ecosystem which contains a variety of annual, biennial and perennial plants growing on rolling or flat terrain.
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.
A vegetated area which is part of a tundra ecosystem.
A field which is located on land and used for agricultural purposes, such as the grazing of livestock or the cultivation of crops.
A forest that has been intentionally established by human intervention.
A geographical region whose affairs and population are administered by an authority.
A valley that no longer has a surface flow of water. Typically found in either Karst (limestone) or chalk terrain.
A valley that contains, and has been formed by, a stream.
A ridge of rocks, lying near the surface of the sea, which may be visible at low tide, but is usually covered by water.
A hydrographic feature characterized by the dominance of snow or ice.
Soil or rock and included ice or organic material at or below the freezing point of water (0 degrees Celsius or 32 degrees Fahrenheit) for two or more years.
The sloping margin of a watercourse, serving to confine it to its natural channel.
The sloping margin of a stream, serving to confine it to its natural channel.
The sloping margin of a river, serving to confine it to its natural channel.
Aragonite structures produced by living organisms, found in shallow, marine waters with little nutrients in the water.
A small, isolated, fertile or green area in a desert region, usually having a spring or well.
An oceanic island, often having a characteristic ring-like shape surrounding a lagoon. Atolls are formed when coral reef grows around a volcanic island that later subsides into the ocean.
A hill of sand built by eolian processes.
A landform elevated above the surrounding area.
An artificial slope or wall, usually earthen, which parallels the course of a river, built for the purpose of containing the river.
An elevated and comparatively level expanse of land.
A tributary valley with the floor at a higher relief than the main channel into which it flows. They are most commonly associated with U-shaped valleys when a tributary glacier flows into a glacier of larger volume.
A part of an astronomical body which is primarily composed of a continuous volume of solid material, shaped by one or more environmental processes.
Broken rock that appears at the bottom of crags, mountain cliffs or valley shoulders.
An island that does not sit on a continental shelf, and is of volcanic origin.
A wetland ecosystem which overlaps both terrestrial and marine ecosystems.
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 wetland which is inundated with water that contains low concentrations of salts.
An opening, or rupture, in the Earth's surface or crust, which allows hot, molten rock, ash and gases to escape from deep below the surface.
A valley that contains, or contained, a glacier and was formed by glacial activity. Typically U-shaped in cross-section.
An area which is subject to periodic flooding.
An area of land of low topographic relief that historically supported grasses and herbs, with few trees, and having generally a mesic (moderate or temperate) climate. Dominated by tall grasses (contrast steppe).
A grassland of the tropics or subtropics with scattered trees.
A plain without trees (apart from those near rivers and lakes); it is similar to a prairie, although a prairie is generally considered as being dominated by tall grasses, while short grasses are said to be normal in the steppe. It may be semi-desert, or covered with grass or shrubs or both, depending on the season and latitude.
A grassland ecosystem which is used for grazing of ungulate livestock as part of a farm or ranch.
A slope which separates different physiogeographic provinces that are typically composed of rocks of different age and compositoin.
A long and narrow elevation with steep sides.
An isolated hill with steep sides and a small flat top, smaller than mesas and plateaus. Buttes are formed by erosion when a cap of hard rock, usually of volcanic origin, covers a layer of softer rock that is easily worn away. This hard rock avoids erosion while the rock around it wears down.
An extent or area of land where surface water from rain and melting snow or ice converges to a single point at lower elevation, usually the exit of the basin, where the waters join another waterbody.
A flooded parcel of arable land used for growing rice and other semiaquatic crops.
Area covered with low-growing or stunted perennial vegetation and usually not mixed with trees.
The general region of indefinite width that extends from the sea inland to the first major change in terrain features.
That part of the land in immediate contact with a body of water including the area between high and low water lines.
A landform sunken or depressed below the surrounding area.
A fluvioglacial landform occurring as the result of blocks of ice calving from the front of a receding glacier and becoming partially to wholly buried by glacial outwash. Glacial outwash is generated when sediment laden streams of meltwater flow away from the glacier and are deposited to form broad outwash plains called sandurs. When the ice blocks melt, holes are left in the sandur.
The plain formed by the large amounts of silt and sediment, picked up as a glacier erodes the underlying rocks as it moves slowly downhill, and at the snout of the glacier, meltwater can carry this sediment away from the glacier and deposit it on a broad plain. The material in the outwash plain is often size-sorted by the water runoff of the melting glacier with the finest materials, like silt, being the most distantly re-deposited, whereas larger boulders are the closest to the original terminus of the glacier.
A zone beneath the land surface and above the level of permanent groundwater or phreatic zone in which water has a hydraulic head less than atmospheric pressure and is retained by a combination of adhesion and capillary action.
A compound astronomical body part which is located beneath the land surface and in which all interstices are filled with water that has a hydraulic head greater than atmospheric pressure due to the weight of overlying groundwater.
An abiotic mesoscopic feature made of the mineral material of the crust of the Earth.
A piece of rock that is two millimeters (2mm) in its largest dimension (about 1/12 of an inch) and no more than 75 millimeters (about 3 inches).
A large sea or ocean inlet larger than a bay, deeper than a bight, wider than a fjord, or it may identify a narrow sea or ocean channel between two bodies of land.
The physical confine of a river, slough or ocean strait consisting of a bed and banks.
A biome is an ecosystem to which resident ecological communities have evolved adaptations.
A biome which is primarily or completely situated on a landmass.
An aquatic biome which is determined by a marine water body.
A reservoir constructed for the purpose of providing water for irrigation.
A dam constructed for the purpose of holding water in a reservoir for irrigation.
An opening of the sea into the land, or of a lake into its shore.
That part of the land in immediate contact with a sea, including the intertidal zone.
The portion of the ground surface which lies below water.
A step-like feature between higher and lower ground: a relatively flat or gently inclined shelf of earth, backed and fronted by steep slopes or manmade detaining walls.
A generally circular saucer or bowl-shaped depression caused by explosive action.
A relatively undissected upland between adjacent stream valleys.
A ridge of sand just inland and parallel to the beach, usually in series.
An irregularly shaped hill or mound composed of sorted or stratified sand and gravel that is deposited in contact with the glacial ice. It can have an irregular shape. Kames are often associated with kettles, and this is referred to as kame and kettle topography. When the ice retreats further, the delta kame often collapses. Kame terraces are frequently found along the side of a glacial valley and are the deposits of meltwater streams flowing between the ice and the adjacent valley side.
A beach which is armoured with pebbles or small to medium sized cobbles.
An aquatic biome which is determined by a body of freshwater.
A rock is a naturally occurring solid aggregate of one or more minerals or mineraloids.
Soil is an environmental material which is primarily composed of minerals, varying proportions of sand, silt, and clay, organic material such as humus, gases, liquids, and a broad range of resident micro- and macroorganisms.
A significant accumulation of water which is part of a marine biome.
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.
Water that has been adversely affected in quality by anthropogenic influence.
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.
Sediment is an environmental substance comprised of any particulate matter that can be transported by fluid flow and which eventually is deposited as a layer of solid particles on the bedor bottom of a body of water or other liquid.
Minute solid particles with diameters less than 500 micrometers. Occurs in and may be deposited from, the atmosphere.
Water which contains a significant concentration of dissolved salts.
Water which has a low concentration of dissolved solutes, particularly that of sodium chloride.
An igneous rock that results from magma reaching the surface either as lava or fragmental ejecta.
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.
Wastewater that is contaminated with feces or urine,
A biome which is determined by a water body and which has ecological climax communities adapted to life in or on water.
Water that is found on the surface of an astronomical object.
The residual semi-solid material left from domestic or industrial processes, or wastewater treatment processes.
Sediment characterised by the absence of oxygen.
A sedimentary rock composed largely of the mineral calcite.
A sedimentary rock composed mainly of sand-size mineral or rock grains.
Sediment which has increased levels of one or more chemical compounds.
Mud which has no or neglible concentrations of dissolved oxygen.
A clastic rock with a particle size of 4 to 64 millimeters based on the Krumbein phi scale of sedimentology.
A rock or rock fragment with a particle size between 64 and 256 mm.
Water which has physicochemical properties that have been determined by the processes occuring in a sea or ocean.
Coastal sea water is sea water that is adjacent to a coast.
The aerobically decomposed remnants of organic materials.
Chemically-enriched sediment which has increased levels of organic compounds.
Chemically-enriched sediment which has increased levels of inorganic compounds.
A channel which is constructed by removing materials from land or submerged beds.
Arenosols are sandy soils, including both soils developed in residual sands after in situ weathering of usually quartz-rich sediments or rock, and soils developed in recently deposited sands such as dunes in deserts and beach lands.
Andosols are soils that develop in volcanic ejecta or glasses under almost any climate (except under hyperarid climate conditions). However, Andosols may also develop in other silicate-rich materials under acid weathering in humid and perhumid climates.
Acrisols are soils that have a higher clay content in the subsoil than in the topsoil as a result of pedogenetic processes (especially clay migration) leading to an argic subsoil horizon. Acrisols have in certain depths a low base saturation and low-activity clays.
Cambisols combine soils with at least an incipient subsurface soil formation. Transformation of parent material is evident from structure formation and mostly brownish discoloration, increasing clay percentage, and/or carbonate removal.
Chernozems are soils with a thick black surface layer that is rich in organic matter.
Kastanozems are dry grassland soils, among them the zonal soils of the short-grass steppe belt, south of the Eurasian tall-grass steppe belt with Chernozems. Kastanozems have a similar profile to that of Chernozems but the humus-rich surface horizon is thinner and not as dark as that of the Chernozems and they show more prominent accumulation of secondary carbonates.
Histosols comprise soils formed in organic material. These vary from soils developed in predominantly moss peat in boreal, arctic and subarctic regions, via moss peat, reeds/ sedge peat (fen) and forest peat in temperate regions to mangrove peat and swamp forest peat in the humid tropics. Histosols are found at all altitudes, but the vast majority occurs in lowlands.
Gleysols are wetland soils that, unless drained, are saturated with groundwater for long enough periods to develop a characteristic gleyic colour pattern. This pattern is essentially made up of reddish, brownish or yellowish colours at ped surfaces and/or in the upper soil layer or layers, in combination with greyish/bluish colours inside the peds and/or deeper in the soil.
Gypsisols are soils with substantial secondary accumulation of gypsum (calcium sulfate). These soils are found in the driest parts of the arid climate zone.
Ferralsols represent the classical, deeply weathered, red or yellow soils of the humid tropics. These soils have diffuse horizon boundaries, a clay assemblage dominated by low-activity clays (mainly kaolinite) and a high content of sesquioxides.
Nitisols are deep, well-drained, red, tropical soils with diffuse horizon boundaries and a subsurface horizon with more than 30 percent clay and moderate to strong angular blocky structure elements that easily fall apart into characteristic shiny, polyhedric (nutty) elements. Weathering is relatively advanced but Nitisols are far more productive than most other red, tropical soils.
Luvisols are soils that have a higher clay content in the subsoil than in the topsoil as a result of pedogenetic processes (especially clay migration) leading to an argic subsoil horizon. Luvisols have high-activity clays throughout the argic horizon and a high base saturation at certain depths.
Phaeozems accommodate soils of relatively wet grassland and forest regions in moderately continental climates. Phaeozems are much like Chernozems and Kastanozems but are leached more intensively. Consequently, they have dark, humus rich surface horizons that, in comparison with Chernozems and Kastanozems, are less rich in bases. Phaeozems may or may not have secondary carbonates but have a high base saturation in the upper metre of the soil.
Solonchaks are soils that have a high concentration of soluble salts at some time in the year. Solonchaks are largely confined to the arid and semi-arid climate zones and to coastal regions in all climates.
A soil in which there is a high content of expansive clay known as montmorillonite that forms deep cracks in drier seasons or years. Alternate shrinking and swelling causes self-mulching, where the soil material consistently mixes itself, causing vertisols to have an extremely deep A horizon and no B horizon.
Solonetz are soils with a dense, strongly structured, clayey subsurface horizon that has a high proportion of adsorbed Na and/or Mg ions. Solonetz that contain free soda (Na2CO3) are strongly alkaline (field pH > 8.5).
Regosols form a taxonomic remnant group containing all soils that could not be accommodated in any of the other RSGs. In practice, Regosols are very weakly developed mineral soils in unconsolidated materials that do not have a mollic or umbric horizon, are not very shallow or very rich in gravels (Leptosols), sandy (Arenosols) or with fluvic materials (Fluvisols). Regosols are extensive in eroding lands, particularly in arid and semi-arid areas and in mountainous terrain.
Podzols are soils with a typically ash-grey upper subsurface horizon, bleached by loss of organic matter and iron oxides, on top of a dark accumulation horizon with brown, reddish or black illuviated humus and/or reddish Fe compounds. Podzols occur in humid areas in the boreal and temperate zones and locally also in the tropics.
A soil composed of sand, silt, and clay in relatively even concentration (about 40-40-20% concentration respectively).
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).
Industrial wastes are liquid, solid and gaseous wastes originating from the manufacture of specific products.
Fluvisols accommodate genetically young, azonal soils in alluvial deposits.
Hay is grass, legumes or other herbaceous plants that have been cut, dried, and stored for use as animal fodder, particularly for grazing livestock such as cattle, horses, goats, and sheep.
A group of hydrous aluminium phyllosilicate (phyllosilicates being a subgroup of silicate minerals) minerals (see clay minerals), that are typically less than 2 micrometres in diameter. Clay consists of a variety of phyllosilicate minerals rich in silicon and aluminium oxides and hydroxides which include variable amounts of structural water.
A fermented, high-moisture forage that can be fed to ruminants.
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.
An industrial building is a building within which goods are produced and, optionally, stored or within which services are rendered.
An agricultural byproduct, the dry stalk of a cereal plant, after the nutrient grain or seed has been removed.
A portion of soil which is found in a savanna.
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 has, as a part, a portion of either fresh or processed animal manure.
Soil which is composed of a large proportion of mud, thus having properties resembling mud.
Soil which is found in a pasture and in which vegetation, such as the grass used for the grazing of ungulates, grows.
A portion of soil which is found in a steppe.
Water which has physicochemical properties determined by processes which occur beneath the planetary crust.
Mud which is part of a marine ecosystem.
A portion of environmental material is a fiat object part which forms the medium or part of the medium of an environmental system.
environmental
A layer of some material entity which is adjacent to one or more of its external boundaries and directly interacts with its immediate surroundings.
Airborne solid particles (also called dust or particulate matter (PM)) or liquid droplets.
An underground layer of water-bearing permeable rock or unconsolidated materials (gravel, sand, silt, or clay) from which groundwater can be usefully extracted using a water well.
Anthropogenic material in or on which organisms may live.
A liquid or semi-liquid mixture of water and some combination of soil, silt, and clay.
Silt is granular material of a size somewhere between sand and clay whose mineral origin is quartz and feldspar.
A naturally occurring granular material composed of finely divided rock and mineral particles.
Gravel is an environmental material which is composed of pieces of rock that are at least two millimeters (2mm) in its largest dimension and no more than 75 millimeters.
The marine pelagic biome (pelagic meaning open sea) is that of the marine water column, from the surface to the greatest depths.
The neritic epipelagic zone biome comprises the marine water column above a continental shelf.
The oceanic epipelagic zone biome comprises the marine water column offshore, beyond a continental shelf.
The oceanic sea surface microlayer (SML) biome comprises the top 1000 micrometers of the marine surface waters occurring offshore, away from a continental shelf. It is the boundary layer where all exchange occurs between the atmosphere and the ocean. The chemical, physical, and biological properties of the SML differ greatly from the sub-surface water just a few centimeters beneath.
The neritic sea surface microlayer (SML) biome comprises the top 1000 micrometers of marine surface waters occurring above a continental shelf. It is the boundary layer where all exchange occurs between the atmosphere and the ocean. The chemical, physical, and biological properties of the SML differ greatly from the sub-surface water just a few centimeters beneath.
A prominent or distinctive aspect, quality, or characteristic of environments occurring within the marine water column.
A marine biome which is determined by an ocean.
Particulate material is an environmental material which is composed of microscopic portions of solid or liquid material suspended in another environmental material.
particulate matter
Environmental material derived from living organisms and composed primarily of one or more biomacromolecules.
A shrubland biome is a terrestrial biome which includes, across its entire spatial extent, dense groups of shrubs.
A desert biome is a terrestrial biome which loses more liquid water by evapotranspiration than is supplied by precipitation and includes communities adapted to these conditions.
A terrestrial biome which comprises a tundra ecosystem that has reached its climax community.
An environmental condition is a range of a determinate quality or combination of qualities that are present in an environmental system.
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.
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.
An environmental condition in which annual precipitation is less than half of annual potential evapotranspiration.
A coastal scrubland is a scrubland which is part of a coast.
A scrubland which is located in a desert.
A cropland ecosystem in which dominant ecological communities are maintained in a stable state - mimicking a climax community - by human intervention.
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.
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 system which has the disposition to environ one or more material entities.
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.
Water vapour is a vapour which is the gas phase of water.
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.
Clastic sedimentary rocks are sedimentary rocks that are composed of silicate minerals and rock fragments that were transported by moving fluids. Clastic rocks are composed largely of quartz, feldspar, rock (lithic) fragments, clay minerals, and mica; numerous other minerals may be present as accessories and may be important locally.
A large unit of land or water containing a geographically distinct assemblage of species, natural communities, and environmental conditions.
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.
A layer is a quantity of some material which is spatially continuous, has comparable thickness, and usually covers some surface.
A layer that is part of a marine water body.
An endolithic environment is an environment that exists within solid rock.
A high temperature environment is an environment in which material entities are exposed to increased levels of heat radiation or which have molecules or atoms moving randomly with increased levels of average kinietic energy.
An aquatic environment which is determined by freshwater.
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.
An anthropogenic environment is an environmental system which is the product of human activity.
A high osmolarity environment is an environment in which entities are exposed to high concentrations of solutes.
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 layer in a water mass, itself composed primarily of water.
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.
A gravelly slope is a slope which has a surface primarily composed of gravel.
A hillside is a slope that is part of a hill.
A talus slope is a slope which has a surface layer composed of scree.
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.
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.
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.
A layer which is determined by a form of vegetation.
An tundra climatic condition is a polar condition in which at least one month's average temperature exceeds 0 degrees Celsius.
Biological waste is waste containing mostly natural organic materials (remains of plants, animal excrement, biological sludge from waste-water treatment plants and so forth).
A tropical marine condition is a tropical condition in which the ocean strongly influences the climate and a wet and dry season occur.
A semi-evergreen forest is a forest which undergoes a long dry season and, as a consequence, has a two-storey layer structure, a dry canopy, a leaf litter layer that only decays during moist periods trees with very small leaves or which shed their leaves to conserve water and which flower during the dry season and grow during the wet season.
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.
A building part is a construction which is part of a building.
Atmospheric carbon dioxide is an environmental material composed of carbon dioxide in its gaseous form present in an atmosphere.
A boundary wall is a constructed barrier which is usually opaque, constructed from masonry, and of greater structural strength than a fence.
A constructed barrier is a freestanding wall, berm, or fence built to limit movement of entities across a boundary.
A fence is a constructed barrier which is generally of lighter construction than a wall and used to provide visual sectioning of spaces.
Glass is an amorphous (non-crystalline) solid which is often transparent.
Silica-based glass is a glass composed primarily of silicon dioxide, the primary constituent of sand.
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
mass of biological material
A gas that is primarily composed of hydrocarbon molecules.
hydrocarbon gas
Charcoal is a light, black residue, consisting of carbon and any remaining ash, obtained by removing water and other volatile constituents from animal and vegetation substances. Charcoal is usually produced by slow pyrolysis, the heating of wood or other substances in the absence of oxygen.
charcoal
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
A lotic water body is a water body in which the accumulated water, in its totality, is flowing.
lotic water body
Vaporisation of an element or compound is process whereby that element or compound undergoes a phase transition from the liquid to vapor.
vaporisation
Hydrological condensation is a process in which atmospheric water vapour undergoes a phase transition from the gas phase to the liquid phase.
hydrological condensation process
A volcanic eruption is a process during which lava, tephra (ash, lapilli, volcanic bombs and blocks), and assorted gases are expelled from a volcanic vent or fissure.
volcanic eruption
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.
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.
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.
planetary mantle
A lithosphere is the outermost shell of a terrestrial-type planet or natural satellite that is defined by its rigid mechanical properties.
lithosphere
Magma is a mixture of molten or semi-molten rock, volatiles, and solids that is found beneath the uppermost solid layer of a planetary body. Besides molten rock, magma may also contain suspended crystals, dissolved gas and sometimes gas bubbles.
magma
A trench is a type of excavation or depression in the ground that is generally deeper than it is wide (as opposed to a wider gully or ditch), and narrow compared to its length (as opposed to a simple hole).
trench
stream channel
river channel
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
Contaminated air is air which has sufficient concentrations of environmental pollutants such that it may adversely affect a given ecosystem.
contaminated air
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.
coast
Hydrological precipitation is a process during which any product of the condensation of atmospheric water vapour is pulled to the planetary surface by gravity.
hydrological precipitation process
Hydrological evaporation is the evaporation of water, generally as part of a planetary water cycle.
hydrological evaporation
Soil degradation is a process which results in a change in soil health status resulting in a diminished capacity of the ecosystem in which the soil occurs to provide goods and services for its beneficiaries.
soil degradation
Soil erosion is a process in which exogenic processes remove soil from one location on the Earth's crust and transport it to another location where it is deposited.
soil erosion
An unusual accumulation of water above the ground caused by high tide, heavy rain, melting snow or rapid runoff from paved areas.
flood
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.
habitat
A process in which natural ecosystems present over an expanse of land are removed and replaced with anthropogenic ecosystems.
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 lithified mass of rock that lies under the loose softer material (regolith) at the surface of the Earth or other terrestrial planet.
bedrock
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.
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.
aeroform
Forest which originally covered a region before changes in the environment brought about by people. (Source: PHC)
primary forest
An area which is outside of a town, city, or urban area. Rural areas are primarily used for agriculture or pastoralism and may contain rural settlements.
rural area
A fire is a process whereby rapid and exothermic oxidation of a material through a combustion process releases heat, light, and other products.
fire
A conflagration which is uncontrolled and combusts material in a vegetated area, be it rural or wild.
wildfire
A fire which occurs in a large spatial area poses a risk to human life, animal life, health, and/or property.
conflagration
A portion of gas which is emitted by a fire or other exothermic reaction, is of increased temperature, and typically emits light in the visible range.
flame
A flame which is produced by the combustion of hydrocarbon fuel.
hydrocarbon flame
A process whereby a large volume of gas moves due to a disequilibrium of physical forces.
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.
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.
plasma
An object which is naturally occuring, bound together by gravitational or electromagnetic forces, and surrounded by space.
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.
An astronomical object which is composed primarily of luminous plasma held in a spherical form by gravitational forces.
An object which is composed of one or more gravitationally bound structures that are associated with a position in space.
astronomical object
A material part of an astronomical body.
astronomical body part
An environmental material which is in a solid state.
solid environmental material
An environmental material which is in a liquid state.
liquid environmental material
A biosphere is a part of an astronomical body which includes, as parts, 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.
biosphere
A cryosphere is that part of a planet which is primarily composed of water is in solid form.
cryosphere
An astronomical body part which is composed of the combined mass of water found on, under, and over the surface of a planet.
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.
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.
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.
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
water droplet
smoke
Combustion or burning is a high-temperature exothermic redox chemical reaction between a fuel and an oxidant that produces oxidized, often gaseous products, in a mixture termed as smoke.
combustion process
A chemical decomposition (the separation of a single chemical compound into its two or more elemental parts or to simpler compounds) caused by heat.
thermolysis
A thermolysis process in which organic material is decomposed in the absence of oxygen.
pyrolysis
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.
crystal
A crystal which is primarily composed of water ice.
water ice crystal
A vegetated area which includes a community of flowering plants that provide food for local pollinators.
flower strip
Marl is a mass of calcium carbonate derived from mollusk shells and mixed with silt and clay.
marl
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.
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.
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.
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.
area of gramanoid or herbaceous vegetation
A hydrological process in which irregular aggregates of snow fall to a planetary surface.
snowfall
Rainfall which occurs when the temperature of a planetary surface and its surrounding atmosphere are below the freezing point of water, resulting in supercooled raindrops which freeze upon impact with solid surfaces.
freezing rainfall
Regions of a planet which are not exposed to the planet's atmosphere or space, often comprising parts of one or more planetary structural layers.
planetary subsurface zone
An envirommental system which bridges two or more biomes and which includes ecological communities which blend these biomes' phylogenetic and phenotypic compositions.
ecotone
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.
natural environment
A process during which a natural environmental system is altered by human action.
anthropisation
An ecotone which overlaps at least one biome which supports the growth and persistence of trees and at least one that does not. Before ceasing altogether, tree growth becomes sparse and trees appear stunted as conditions become less favourable along this ecotone.
tree line ecotone
A planet that is composed primarily of silicate rocks or metals.
terrestrial planet
A process whereby a volume of liquid moves due to a disequilibrium of physical forces.
mass liquid flow
A process during which a volume of 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
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.
manufacturing process
An process during which natural or manufactured materials and products are processed and arranged by humans or their technology into structures.
human-directed construction process
An environmental system which is determined by materials bearing roughly homogeneous qualities.
environmental system determined by a quality
An environmental system within which an environmental material strongly influences the system's composition and properties.
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
Underground water which is located in pore spaces found in rock or unconsolidated deposits such as soil, clay, or gravel.
groundwater
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.
natural lake
A process during which energy is emitted or transmitted in the form of waves or particles through space or a material medium.
radiation
A radiation process during which waves (or their quanta, photons) of the electromagnetic field propagate (radiate) through space carrying electromagnetic energy.
electromagnetic radiation
An environment which is determined by materials which bear significant concentrations of salts.
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 the subsurface zone of a planet.
planetary subsurface environment
An environmental system which has its properties and dynamics determined by those parts of a planetary subsurface zone which are not saline.
non-saline planetary subsurface 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
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 plant, or a whole small plant.
environment associated with a plant part or small plant
crater lake
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.
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.
ecosystem
A physical space, which may or may not be in a construction, which is used to store animal manure for agricultural purposes.
manure storage space
Manure which has been collected directly or indirectly from dairy cattle, as from flushing of manure from concrete feed lanes, free stalls, and milking facilities.
bovine dairy liquid manure
A product which is composed primarily of animal manure that has been heat treated and packaged as a product for commercial or consumer use.
animal manure product
A planet which is primarily composed of hydrogen and helium.
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.
ice
A terrestrial planet which has a surface dominated by hot deserts.
desert planet
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.
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.
ice planet
Ice which is primarily composed of carbon dioxide.
carbon dioxide ice
Ice which is primarily composed of carbon monoxide.
carbon monoxide ice
A gas planet which has an atmosphere composed primarily of helium.
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.
volatile astrogeological material
An astrogeological volatile which is composed primarily of chemical compounds with boiling points around those of hydrogen and helium.
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.
geodiversity
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
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
An environmental zone which is bounded by material parts of a marine environment.
marine 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
An area of land used for the herding and grazing of livestock.
ranch
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
An electromagnetic radiation process during which electromagnetic waves or their quanta are emitted from a star.
stellar radiation
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 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.
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
A process during which humans rear animals or plants on land for harvest and consumption.
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 fire which occurs in an industrial area or building.
industrial fire
A vegetated area which has not been cleared or is sparsely settled, usually scrub-covered or forested
bush area
An environmental zone which is part of an atmosphere.
atmospheric zone
An oasis is a vegetated area located in a desert, supplied with water from a water source which it surrounds, and surrounded by arid soil, sand, or rock.
A vegetated area is a geographic feature which has ground cover dominated by plant communities.
A geographic feature which is primarily composed of a continuous volume of liquid water held in shape or sustained by an environmental process.
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.
saline water body
A body of water which is primarily composed of freshwater, with low solute content.
fresh 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 transport 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.
desert
A direction which inheres in an atmospheric wind, typically expressed as the inverse of the direction the wind is moving in.
atmospheric wind direction
atmospheric wind speed
The volume of water which has fallen during a precipitation process.
Niederschlagsmenge
volume of hydrological precipitation
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 ecosystem which 1) typically has monthly average temperatures below 10 degrees Celsius 2) has a low evapotranspiration ratio 3) is dominated by treeless terrain, covered by communities of low-growing vegetation such as dwarf shrubs, sedges and grasses, mosses, and lichens, 4) contains areas of soil underlain by permafrost with a thin active layer and 5) occurs in both polar and alpine regions (i.e., both high latitudes and high altitudes), and 5) does not have permanent snow or ice cover.
tundra ecosystem
This definition is a synthesis of the following sources: NSIDC Glossary accessed 2016, IPCC WGII AR5 2014, Van Everdingen International Permafrost Association 2005, AMS - glossary of meteorology, PhysicalGeography.net
A soil which has high mineral content and which contain no calcareous material, have less than 10% weatherable minerals its surface layer, and have less than 35% base saturation throughout its volume.
ultisol
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.
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.
agricultural land conversion process
An anthropogenic environmental process which includes all human activities undertaken in a natural, semi-natural, or anthropised environment.
land use process
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 an environment supports manufacturing facilities producing commodities that are sold with the expectation of recovering the total cost of production.
usage of an environment for industry
body of liquid
A part of an astronomical body which is primarily composed of a continuous volume of liquid material, shaped by one or more environmental processes.
liquid astronomical body part
A part of an astronomical body which is primarily composed of a continuous volume of gaseous material, shaped by one or more environmental processes.
gaseous astronomical body part
A part of an astronomical body which is primarily composed of a continuous volume of liquid or gaseous material, shaped by one or more environmental processes.
fluid astronomical body part
A surface layer where the solid or liquid material of an astronomical body comes into contact with an atmosphere or outer space.
surface of an astronomical body
An elevation which is flattened across its highest surface.
flattened elevation
An electromagnetic radiation process during which electromagnetic waves or their quanta are emitted from a manufactured product.
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.
material congelation process
Land which is below the freezing point of water.
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 ecoregion which is located on a landmass.
terrestrial ecoregion
A surface layer which is part of an ocean or sea.
sea surface layer
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.
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.
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
mass of environmental material
An object 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.
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
mass fluid flow
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 primarily composed of a continuous medium bearing liquid, gaseous, and solid material in varying 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
freshwater ecosystem
terrestrial ecosystem
An environmental process either driven by or primarily impacting the parts or emergent properties of an ecosystem.
ecosystem process
A forest ecosystem which is subject to tropical climate conditions.
tropical forest
A forest ecosystem which is subject to subtropical climate conditions.
subtropical forest
A grassland ecosystem which is subject to tropical climatic conditions.
tropical grassland
A grassland which is subject to subtropical climatic conditions.
subtropical grassland
A material entity which has been assembled through the intentional, instinctual, or deliberately programmed efforts of an organism or machine.
construction
A biome which is subject to tropical climatic conditions.
tropical biome
A biome which is subject to subtropical climatic conditions.
subtropical 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
A temperature of air at which air become saturated with water vapour and below which airborne water vapour will condense to form liquid water (dew).
dew point
Electromagnetic radidation which involves radiant energy in a spectral range (wave band) between 400 to 700 nanometers, that photosynthetic organisms are able to use in the process of photosynthesis.
photosynthetically active radiation
The concentration of carbon dioxide when measured in air that is part of an atmosphere.
concentration of carbon dioxide in an atmosphere
A depression in the ground resembling a hole or cavity, either natural or anthropogenic.
pit
A pit which is used for the collection and storage of manure.
manure pit
Coastal water is a marine water body bordering a coast.
A mixture of crushed and coarsely ground bones that is used as an organic fertilizer for plants and formerly in animal feed.
Food material which can be used to meet nutritional requirements of plants.
Dust which is derived from mineral material.
Dust which is composed primarily of some metallic material.
Dust which is derived from clay material.
fluid environmental material
A process in which includes the components of an environmental system as participants.
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.
atmospheric process
A process which diminishes the functioning of an ecosystem located on land.
A process during which humans apply technology to alter the magnitude, duration, rate, or impact of an environmental 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.
Evapotranspiration is the sum of evaporation and plant transpiration from the Earth's land and ocean surface to the atmosphere.
Evaporation is a form of vaporisation which occurs when a portion of the surface layer of a liquid in contact with a gaseous material, which is not saturated with the evaporating substance, vaporises.
Transpiration is the process of water movement through a plant and its evaporation from aerial parts of that plant, such as from leaves but also from stems and flowers.
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.
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.
material transport process
A depression which is part of a planetary crust, is of geographic scale, and is partially or completely enclosed.
geographic basin
A material transport process during which one or more environmental materials are transported by the action of wind.
aeolian transport process
Sediment which has been transported through the marine water column, settling on the seafloor.
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.
material transformation process
A desublimation process during which water vapour is frozen into water ice.
desublimation of water vapour into ice
A one-dimensional temporal region which is delimited by the occurrence of processes which serve as its delimiters.
season
A geographic feature which is primarily composed of a continuous mass of snow and/or ice.
cryoform
snow mass
A structure which traverses a mass of one or more environmental materials, and encloses a roughly tubular site.
channel
The concentration of nitrate and nitrite when measured in liquid water.
liquid water nitrate and nitrite concentration
concentration of nitrate and nitrite in liquid water
A season during which changes in atmospheric circulation associated with the asymmetric heating of land and sea cause moisture to be brought inland by monsoon winds, leading to increased rainfall as moisture-laden air rises and cools over land.
monsoon season
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.
chemically contaminated sediment
A soil horizon which is composed primarily of organic matter.
soil organic layer
organic surface layer
organic horizon
A layer which is parallel to the soil surface and which has roughly homogenous physical, chemical and biological properties relative to the soil layers above or beneath it.
soil horizon
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 freshwater.
concentration of carbon dioxide in freshwater
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 material accumulation process during which atmospheric carbon dioxide is captured and stored.
carbon sequestration process
The temperature of some environmental material.
The concentration of a ammonium when measured in soil.
The concentration of a nitrate when measured in soil.
The concentration of a nitrate when measured in groundwater.
A hydrological precipitation process with a reduced rate relative to some historical average, typically resulting in ecosystemic perturbations.
drought
A process which results in the formation of an island.
island formation process
A wastewater treatment plant that treats agriculatural wastewater. Agricultural wastewater treatment relates to the treatment of wastewaters produced in the course of agricultural activities. Agriculture is a highly intensified industry in many parts of the world, producing a range of wastewaters requiring a variety of treatment technologies and management practices.
charcoal that is used as a soil amendment.
hydrocarbon-based environmental material
An environment which is determined by an anatomical entity.
The concentration of ammonium when measured in liquid water.
concentration of ammonium in liquid water
The concentration of dioxygen when measured in liquid water.
concentration of dioxygen in liquid water
The concentration of hydrogen sulfide when measured in liquid water.
liquid water hydrogen sulfide concentration
concentration of hydrogen sulfide in liquid water
The concentration of nitrate when measured in liquid water.
concentration of nitrate in liquid water
The concentration of nitrite when measured in liquid water.
concentration of nitrite in liquid water
A substance, usually composed primarily of carbohydrates, fats, water and/or proteins, that can be eaten or drunk by an animal or human being for nutrition or pleasure.
Food material for humans and animals which is processed with the intention that it be consumable as a whole or added to other food products.
food product
This class includes food products which are derived from or produced by a plant.
plant food product
A relish, sauce, or seasoning added to food to impart a particular flavour or to complement the dish.
condiment
condiment food product
nut food product
plant seed food product
A vegetable product such as leaves, flowers, seeds and roots that is rich in essential oils and aromatic principles. Used mainly a a condiment.
herb and spice
herb or spice
spice or herb
Any plant food product which, typically, is constituted by intact parts from one or more annual plants cultivated as field and garden crops in the open and under glass, and used almost exclusively for food.
vegetable food product
Mature ovary of a plant, with a fleshy part of the carpel that develops with the seed to attract animals for aid in dispersal. Botanically, nuts are considered fruits.
botanical fruit food product
A one-celled fruit (pod) usually dehiscing down both sutures, and having the seed attached along a ventral suture. (Roubik 1995)
legume
legume food product
A bean vegetable food product is a human or animal food product - such as a snap, shell or dry bean product - derived from the fruit pod, seed, or leaf of one of several genera of the flowering plant family Fabaceae.
bean food product
A food product which normally exists as an ingredient to another food product, rather than eaten on its own, and is more complex than a chemical food component.
food product component
ginger
ginger food product
plant seed vegetable food product
soybean seed (field) food product
A soybean food product is a product derived from the soybean plant.
soy product
soybean food product
A food product consisting of food material derived primarily from a single organism.
food product by organism
Any substance that can be consumed by an organism to satisfy nutritional or other health needs, or to provide a social or organoleptic food experience
food
foodstuff
nourishment
sustenance
food material
Invertebrates are animals that neither possess nor develop a vertebral column (commonly known as a backbone or spine), derived from the notochord. This includes all animals apart from the subphylum Vertebrata.
animal
invertebrate animal
ginger root
A seed of a bean plant from one of several genera of the flowering plant family (Fabaceae).
bean
bean (whole)
A multicellular eukaryotic heterotrophic organism within the kingdom Animalia.
A food product not including meat and animal tissue products (such as gelatin or animal-derived rennet).
vegetarian food
vegetarian food product
A root of a ginger plant (Zingiber officinale)
elephant ginger
elephant ginger root
ginger root (whole)
A whole ginger root or some substance made from a processed ginger root.
ginger root (whole or parts)
A whole soybean or some substance made from a processed soybean.
soybean
soybean (whole or parts)
A seed of a soyabean plant (Glycine max).
soy bean
soya bean
soybean (whole)
A bean substance is a substance made by processing seed from a bean plant.
bean substance
A meal that is the by-product of the extraction of soybean oil.
soya bean meal
soybean meal
edible seed food product
soybean substance
ginger root (whole, raw)
A seed of a legume plant in the family Fabaceae.
legume (whole)
Seasoned product that contains multiple ingredients and that is used in limited amounts to accompany other foods; excludes flavors, spices and herbs.
dressing, condiment, gravy or sauce (us cfr)
Aromatic or pungent plant product used whole or ground as a seasoning in food products.
spice or herb (us cfr)
Any form of whole or milled grain, prepared grain product or starch containing product derived from non-grain sources. [FDA CFSAN 1995]
grain or starch product (us cfr)
Product that imparts or helps to impart a taste or aroma in food (21 CFR.170.3(n)(26). [FDA CFSAN 1995]
flavoring or seasoning (us cfr)
Food product prepared by milling a grain or by producing flour, meal or grits from a non-grain source such as beans, starchy roots or tubers. Refined starch is indexed under *REFINED OR PARTIALLY REFINED FOOD PRODUCT*.
milled grain or starch product (us cfr)
Vegetables in all forms except where a use-related product type descriptior (such as *PREPARED FOOD PRODUCT* or *SNACK FOOD*) takes precedence.
vegetable or vegetable product (us cfr)
Food product that is usually pungent, tart, salty, or spicy and is used to enhance the flavors of other foods; includes catsup, relish, prepared mustard, prepared horseradish, and condiment sauces.
condiment or relish (us cfr)
Fruits and vegetables in all forms. [FDA CFSAN 1995]
fruit or vegetable product (us cfr)
Nuts in all forms, including nut butters and pastes.
nut or nut product (us cfr)
Food group having common consumption, functional or manufacturing characteristics, e.g. *FRUIT OR VEGETABLE PRODUCT*, *DAIRY PRODUCT*, *CONFECTIONARY*, *PREPARED FOOD PRODUCT*, etc. [FDA CFSAN 1995]
USA agency food product type
nut or seed product (us cfr)
A food product type is a class of food products that is differentiated by its food composition, processing and/or consumption characteristics. This does not include brand name products but it may include generic food dish categories.
An agency food product type is a class of food product defined by an agency or consortium.
agency food product type
Food and Drugs, title 21, Code of Federal Regulations. Original food classification in LanguaL.
U.S. code of federal regulations, title 21 food product type
plant used for producing extract or concentrate
oil-producing plant
grain or seed-producing plant
protein-producing plant
vegetable-producing plant, above-ground parts
A legume is a plant or its fruit or seed in the family *Fabaceae* (or *Leguminosae*). Legumes are grown agriculturally, primarily for their grain seed called pulse, for livestock forage and silage, and as soil-enhancing green manure. Well-known legumes include alfalfa, clover, peas, beans, chickpeas, lentils, lupin bean, mesquite, carob, soybeans, peanuts and tamarind. [https://en.wikipedia.org/wiki/Legume]
pod or seed vegetable plant
edible seed producing plant
nut producing plant
A vertebrate animal is any species of organism within the subphylum Vertebrata (chordates with backbones). Vertebrates represent the overwhelming majority of the phylum Chordata, with currently about 69,276 species described.
vertebrate animal
This is a hierarchy of organisms, grouped minimally in a combination of taxonomy and consumer-oriented food groups.
food product organismal source
A bean plant is one of several genera of the flowering plant family Fabaceae, which has seed pods, seeds, and/or leaf material used for human or animal food.
bean plant
vegetable-producing plant
nut or edible seed producing plant
plant used for dietary supplements
Anatomical part of the plant or animal from which a food product or its major ingredient is derived.
part of organism
seed part
plant seed or nut food product
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. These actions are described from two distinct but related perspectives: (1) biochemical activity, and (2) role as a component in a larger system/process.
Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
Binding to one or more specific sites on a receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function.
Interacting selectively and non-covalently with one or more specific sites on a receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function.
The selective, non-covalent, often stoichiometric, interaction of a molecule with one or more specific sites on another molecule.
Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
Any process that mediates interactions between a cell and its surroundings. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment.
The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
signal transduction by cis-phosphorylation
signal transduction by conformational transition
signal transduction by protein phosphorylation
signal transduction by trans-phosphorylation
Binds to and increases the activity of an enzyme.
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.
Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end.
Any process that modulates the frequency, rate or extent of signal transduction.
Any process that activates or increases the frequency, rate or extent of signal transduction.
positive regulation of signaling pathway
positive regulation of signalling pathway
positive regulation of signal transduction
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.
Any process that modulates the frequency, rate or extent of a signaling receptor activity. Receptor activity is when a molecule combines with an extracellular or intracellular messenger to initiate a change in cell activity.
regulation of signalling receptor activity
regulation of signaling receptor activity
Any process that modulates the frequency, rate or extent of cell communication. Cell communication is the process that mediates interactions between a cell and its surroundings. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment.
Any process that increases the frequency, rate or extent of cell communication. Cell communication is the process that mediates interactions between a cell and its surroundings. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment.
positive regulation of cell communication
Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to another (acceptor).
transferase activity, transferring phosphorus-containing groups
Any process that modulates the frequency, rate or extent of a signaling process.
The entirety of a process in which information is transmitted within a biological system. This process begins with an active signal and ends when a cellular response has been triggered.
Any process that activates, maintains or increases the frequency, rate or extent of a signaling process.
positive regulation of signalling process
positive regulation of signaling process
Binds to and modulates the activity of an enzyme.
Binds to and modulates the activity of a receptor.
The function of interacting (directly or indirectly) with receptors such that the proportion of receptors in the active form is changed.
The function of interacting (directly or indirectly) with receptors such that the proportion of receptors in the active form is increased.
Any process that activates or increases the frequency, rate or extent of protein binding.
Receiving a signal and transmitting it in the cell to initiate a change in cell activity. A signal is a physical entity or change in state that is used to transfer information in order to trigger a response.
receptor activity involved in signal transduction
Any process that activates or increases the activity of an enzyme.
positive regulation of metalloenzyme activity
positive regulation of catalytic activity
Any process that modulates the frequency, rate or extent of protein binding.
Any process that activates or increases the rate or extent of a molecular function, an elemental biological activity occurring at the molecular level, such as catalysis or binding.
positive regulation of molecular function
The activity of a gene product that interacts with a receptor to effect a change in the activity of the receptor. Ligands may be produced by the same, or different, cell that expresses the receptor. Ligands may diffuse extracellularly from their point of origin to the receiving cell, or remain attached to an adjacent cell surface (e.g. Notch ligands).
Any process that activates or increases the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule.
positive regulation of physiological process
positive regulation of biological process
Any process that activates or increases the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level.
positive regulation of cellular physiological process
Any process that modulates the frequency, rate or extent of a response to a stimulus. Response to stimulus is 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.
Any process that activates, maintains or increases the rate of a response to a stimulus. Response to stimulus is 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.
positive regulation of response to stimulus
Any process that modulates the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule.
Any process that modulates the activity of an enzyme.
Any process that modulates the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level.
regulation of cellular physiological process
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 modulates the frequency, rate or extent of binding, the selective interaction of a molecule with one or more specific sites on another molecule.
Any process that activates or increases the rate or extent of binding, the selective interaction of a molecule with one or more specific sites on another molecule.
Any process that modulates the frequency, rate or extent of transferase activity, the catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
Any process that activates or increases the frequency, rate or extent of transferase activity, the catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from a donor compound to an acceptor.
positive regulation of transferase activity
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.
A compound molecular function in which an effector function is controlled by one or more regulatory components.
Any process that modulates a measurable attribute of any biological process, quality or function.
Any process that modulates the frequency, rate or extent of a molecular function, an elemental biological activity occurring at the molecular level, such as catalysis or binding.
A molecular function regulator regulates the activity of its target via non-covalent binding that does not result in covalent modification to the target. Examples of molecular function regulators include regulatory subunits of multimeric enzymes and channels. Mechanisms of regulation include allosteric changes in the target and competitive inhibition.
A molecular function that modulates the activity of a gene product or complex. Examples include enzyme regulators and channel regulators.
Any process that modulates the frequency, rate or extent of a protein or other molecule binding to a receptor.
Any process that activates or increases the frequency, rate or extent of a protein or other molecule binding to a receptor.
Any process that activates or increases the frequency, rate or extent of signaling receptor activity.
positive regulation of signalling receptor activity
positive regulation of signaling receptor activity
conditional specification
A directive information entity that specifies what should happen if the trigger condition is fulfilled.
PlanAndPlannedProcess Branch
OBI branch derived
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
experiment objective
narrative object
Examples of narrative objects are reports, journal articles, and patents submission.
A narrative object is an information content entity that is a set of propositions.
2009-08-10 Alan Ruttenberg: Larry Hunter suggests that this be obsoleted and replaced by 'textual entity' and 'figure'. Alan restored as there are OBI dependencies and this merits further discussion
agree - DENRIE. Issue(alan) do we only mean text? What about a story told by mime. Does music count? (no) what about an oral report. Regarding definition, saying it is a set of propositions means we loose the idea that wording matters. Maybe adjust saying a narrative object has some relationshop to a set of propositions
person:Chris Stoeckert
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
obsolete_digital entity
A digital entity is an information entity which is a collection of bits that can be interpreted by a computer. Two digital entities are the same if they are bitwise identical.
3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4 Superclass was 'digitial quality'
obsolete2_digital entity
journal article
Examples are articles published in the journals, Nature and Science. The content can often be cited by reference to a paper based encoding, e.g. Authors, Title of article, Journal name, date or year of publication, volume and page number.
A report that is published in a journal.
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.
model number
A model number is an information content entity specifically borne by catalogs, design specifications, advertising materials, inventory systems and similar that is about manufactured objects of the same class. The model number is an alternative term for the class. The manufactered objects may or may not also bear the model number. Model numbers can be encoded in a variety of other information objects, such as bar codes, numerals, or patterns of dots.
manufactered items may have more than one model number, sometimes by rebranding, or because companies are sold and the products issued new model numbers
binary digital entity
MS Word document, ZIP file, DICOM file, JPEG file
A binary digital entity is a digital entity that is encoded in a way that is not easily human readable and that contains other than text characters.
3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4 Superclass was 'digital entity'
digital_entity
obsolete2_binary digital entity
a unit of measure is the quality of some material entity compared to which another quality is some multiple of.
programming language
R, Perl, Java
A language in which source code is written that is intended to be executed/run by a software interpreter. Programming languages are ways to write instructions that specify what to do, and sometimes, how to do it.
data item
Data items include counts of things, analyte concentrations, and statistical summaries.
An information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements.
a data item is an information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements.
2/2/2009 Alan and Bjoern discussing FACS run output data. This is a data item because it is about the cell population. Each element records an event and is typically further composed a set of measurment data items that record the fluorescent intensity stimulated by one of the lasers.
2009-03-16: data item deliberatly ambiguous: we merged data set and datum to be one entity, not knowing how to define singular versus plural. So data item is more general than datum.
2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym.
2014-03-31: See discussion at http://odontomachus.wordpress.com/2014/03/30/aboutness-objects-propositions/
JAR: datum -- well, this will be very tricky to define, but maybe some information-like stuff that might be put into a computer and that is meant, by someone, to denote and/or to be interpreted by some process... I would include lists, tables, sentences... I think I might defer to Barry, or to Brian Cantwell Smith JAR: A data item is an approximately justified approximately true approximate belief
data
symbol
a serial number such as "12324X"
a stop sign
a written proper name such as "OBI"
An information content entity that is a mark(s) or character(s) used as a conventional representation of another entity.
20091104, MC: this needs work and will most probably change
2014-03-31: We would like to have a deeper analysis of 'mark' and 'sign' in the future (see https://github.com/information-artifact-ontology/IAO/issues/154).
PERSON: James A. Overton
based on Oxford English Dictionary
numeral
A symbol that denotes a number.
information content entity
Examples of information content entites include journal articles, data, graphical layouts, and graphs.
A generically dependent continuant that is about some thing.
2014-03-10: The use of "thing" is intended to be general enough to include universals and configurations (see https://groups.google.com/d/msg/information-ontology/GBxvYZCk1oc/-L6B5fSBBTQJ).
information_content_entity 'is_encoded_in' some digital_entity in obi before split (040907). information_content_entity 'is_encoded_in' some physical_document in obi before split (040907). Previous. An information content entity is a non-realizable information entity that 'is encoded in' some digital or physical entity.
integer numeral
A numeral that denotes an integer
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
time trigger
obsolete_study interpretation
A study interpretation is a textual entity about the implications of a study result. Examples include discussion of whether a hypothesis is false, whether the study failed to address the hypothesis, and whether the study results have led to new hypotheses
2009-03-16: definition was "A conclusion is a narrative object which can be published in a paper summerizing and interpreting a protocol application."
2009-03-16: work has been done on this term 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.
The obsoleting of narrative object required a modest change in the definition of this term. Circularity with "interpretation... interprets" has been removed, using "about the implications" instead.
Lawrence Hunter
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
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
text based digital entity
XML file, C++ source code file
A text based digital entity is a digital entity that is encoded so that it only contains text characters.
3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4 superclass was 'digital document'
obsolete2_text based digital entity
rule
example to be added
A rule is an executable which guides, defines, restricts actions.
MSI
PRS
contour plot
Contour plot of SSC-H, FSC-H, and FL1-H.
generically_dependent_continuants
group:Flow Cytometry community
report figure
A report figure is a report display element that has some aspect of illustration, but may be a composite of figures, images, and other elements
I prepended the 'report ' to make it clear that we mean parts of reports here. We may want a more generic version of 'figure', in which case this would become a defined class - figure and part_of some report
Replaced by defined version of figure
obsolete2_report figure
algorithm
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
adapted from discussion on OBI list (Matthew Pocock, Christian Cocos, Alan Ruttenberg)
software interpreter
R program, Perl interpreter, Java virtual machine
A software interpreter is a software application that executes some specified input software.
Do we care? Jennifer: Yes, there was a particular version of R that had a bug and it was fixed later. That would imply that we mean specific version of an interpreter. So an instance of this would be a particular version of the interpreter
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)
density plot
Density plot of SSC-H and FSC-H.
A density plot is a report graph which is a graphical representation of data where the tint of a particular pixel corresponds to some kind of function corresponding the the amount of data points relativelly with their distance from the the pixel.
report
Examples of reports are gene lists and investigation reports. These are not published (journal) articles but may be included in a journal article.
A document assembled by an author for the purpose of providing information for the audience. A report is the output of a documenting process and has the objective to be consumed by a specific audience. Topic of the report is on something that has completed. A report is not a single figure. Examples of reports are journal article, patent application, grant progress report, case report (not patient record).
2009-03-16: comment from Darren Natale: I am slightly uneasy with the sentence "Topic of the report is on something that has completed." Should it be restricted to those things that are completed? For example, a progress report is (usually) about something that definitely has *not* been completed, or may include (only) projections. I think the definition would not suffer if the whole sentence is deleted.
2009-03-16: this was report of results with definition: A report is a narrative object that is a formal statement of the results of an investigation, or of any matter on which definite information is required, made by some person or body instructed or required to do so.
2009-08-10 Alan Ruttenberg: Larry Hunter suggests that this be obsoleted and replaced by 'document'. Alan restored as there are OBI dependencies and this merits further discussion
disagreement about where reports go. alan: only some gene lists are reports. Is a report all the content of some document? The example of usage suggests that a report may be part of some article. Term needs clarification
report element
A report element is a narrative object in which information is presented and consumed by a human being, and is part of a report. Examples of report elements are figure (dot plot), table, text portion (may include a movie or audio clip on a web page).
2009-03-16: needs some more work (clarify relations).
2009-03-16: was report display element with definition: A report display element is a narrative object that is part of a report. Report display elements are set off from the textual parts of a report and are typically given a label(e.g. Figure 2) which is used to refer to the element from the text. Typically the 2d layout is part of the identity of such elements.
There will be some issue here about whether these are defined classes. As intended these are meant to denote the parts of the report that are not textual but are typically boxed and set within the text, labelled with some identifier, and referred to in the text
PERSON: Allyson Lister
obsolete_report element
binary executable
Binary executable is a digital entity consisting of the binary representation of machine instructions of a specific processor or they may be binary pseudocode for a virtual machine. A non-source executable file is also called an object program. It is assumed that the binary executable file contains properly-formatted computer instructions. (derived from Wikipedia, Nov 1, 2007)
person:Jennifer Fostel
obsolete2_binary executable
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.
report table
A report table is a report display element consisting of a matrix of cells layed out in a grid, some set of which are filled with some information content
2009-08-10 Alan Ruttenberg: Larry Hunter suggests that this be obsoleted and replaced by 'textual entity table'. Alan restored as there are OBI dependencies and this merits further discussion
obsolete_report table
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"
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.
2009-03-16: provenance: a term a plan was proposed for OBI (OBI_0000344) , edited by the PlanAndPlannedProcess branch. Original definition was " a plan is a specification of a process that is realized by an actor to achieve the objective specified as part of the plan". It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term.
2014-03-31: A plan specification can have other parts, such as conditional specifications.
Alternative previous definition: a plan is a set of instructions that specify how an objective should be achieved
2/3/2009 Comment from OBI review. Action specification not well enough specified. Conditional specification not well enough specified. Question whether all plan specifications have objective specifications. Request that IAO either clarify these or change definitions not to use them
digital document
A digital document is a digital entity consisting of an electronic file which can be rendered into human-readable form by one or more computational applications. The digital document does not refer to the information content of the document but to an instance of the file.
3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4 superclass was 'digial entity'
obsolete2_digital document
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?
_identifier is a container under information content entity for collecting types of terms to indicate a specific instance or clas of what was used or participated in an investigation. Identifiers are borne by a product or its packaging, and can be encoded in a variety of other information objects, such as bar codes, numerals, or patterns of dots. Note: everybody agreed that identifier is probably a too general term. We however felt that it would be appropriate to group "identifiying" terms under some kind of umbrella. We therefore propose to use _identifier for that purpose. As per OBI conventions, the _ prefixing identifier indicates that this is a helper class and shouldn't be considered as final.
version number
A version number is an information content entity which is a sequence of characters borne by part of each of a class of manufactured products or its packaging and indicates its order within a set of other products having the same name.
Note: we feel that at the moment we are happy with a general version number, and that we will subclass as needed in the future. For example, see 7. genome sequence version
serial number
A serial number is an information content entity which is a unique sequence of characters borne by part of manufactured product or its packaging that is assigned to each individual in some class of products, and so can serve as a way to identify an individual product within the class. Serial numbers can be encoded in a variety of other information objects, such as bar codes, numerals, or patterns of dots.
Note: during the call there was some confusion between serial number and model number. We agreed that it would be very helpful for all those terms to have example of usages - please add if you have any :-)
lot number
A lot number is an information content entity which is an identical sequence of character borne by part of manufactured product or its packaging for each instances of a product class in a discrete batch of an item. Lot numbers are usually assigned to each separate production run of an item. Manufacturing as a lot might be due to a variety of reasons, for example, a single process during which many individuals are made from the same portion of source material. Lot numbers can be encoded in a pattern of other information objects, such as bar codes, numerals, or patterns of dots.
batch number
A settings datum is a datum that denotes some configuration of an instrument.
2/3/2009 Feedback from OBI This should be a "setting specification". There is a question of whether it is information about a realizable or not. Pro other specification are about realizables. Cons sometimes specifies a quality which is not a realizable.
Alan grouped these in placeholder for the moment. Name by analogy to measurement datum.
setting datum
3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4
Need to rework digital entity. Digital quality was suggested by Barry.
conclusion textual entity
that fucoidan has a small statistically significant effect on AT3 level but no useful clinical effect as in-vivo anticoagulant, a paraphrase of part of the last paragraph of the discussion section of the paper 'Pilot clinical study to evaluate the anticoagulant activity of fucoidan', by Lowenthal et. al.PMID:19696660
A textual entity that expresses the results of reasoning about a problem, for instance as typically found towards the end of scientific papers.
2009/09/28 Alan Ruttenberg. Fucoidan-use-case
2009/10/23 Alan Ruttenberg: We need to work on the definition still
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
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.
Venn diagram
A Venn diagram is a report graph showing all hypothetically possible logical relations between a finite collection of sets.
WEB: http://en.wikipedia.org/wiki/Venn_diagram
obsolete_survival curve
A survival curve is a report graph which is a graphical representation of data where the percentage of survival is plotted as a function of time.
WEB: http://www.graphpad.com/www/book/survive.htm
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
A photograph is created by projecting an image onto a photosensitive surface such as a chemically treated plate or film, CCD receptor, etc.
PERSON:Joanne Luciano
WEB: http://en.wiktionary.org/wiki/photograph
photograph
photographic print
A photographic print is a material entity upon which a photograph generically depends.
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.
textual entity
Words, sentences, paragraphs, and the written (non-figure) parts of publications are all textual entities
A textual entity is a part of a manifestation (FRBR sense), a generically dependent continuant whose concretizations are patterns of glyphs intended to be interpreted as words, formulas, etc.
AR, (IAO call 2009-09-01): a document as a whole is not typically a textual entity, because it has pictures in it - rather there are parts of it that are textual entities. Examples: The title, paragraph 2 sentence 7, etc.
MC, 2009-09-14 (following IAO call 2009-09-01): textual entities live at the FRBR (http://en.wikipedia.org/wiki/Functional_Requirements_for_Bibliographic_Records) manifestation level. Everything is significant: line break, pdf and html versions of same document are different textual entities.
text
citation
Verspoor, K., Cohen, KB., Hunter, L. Textual characteristics of traditional and Open Access scientific journals are similar, BMC Bioinformatics 2009, 10:183.
A textual entity intended to identify a particular publication.
author identification
L. Hunter
A textual entity intended to identify a particular author
institutional identification
University of Colorado Denver School of Medicine
A textual entity intended to identify a particular institution
caption
Figure 1: A system diagram describing the modules of the Hanalyzer. Reading methods (green) take external sources of knowledge (blue) and extract information from them, either by parsing structured data or biomedical language processing to extract information from unstructured data. Reading modules are responsible for tracking the provenance of all knowledge. Reasoning methods (yellow) enrich the knowledge that results from reading by, for example, noting two genes that are annotated to the same ontology term or database entry. All knowledge sources, read or reasoned, are assigned a reliability score, and all are combined using that score into a knowledge network (orange) that represents the integration of all sorts of relationship between a pair of genes and a combined reliability score. A data network (also orange) is created from experimental results to be analyzed. The reporting modules (pink) integrate the data and knowledge networks, producing visualizations that can be queried with the associated drill-down tool.
A textual entity that describes a figure
document title
Textual characteristics of traditional and Open Access scientific journals are similar
A textual entity that names a document
table
| T F --+----- T | T F F | F F
A textual entity that contains a two-dimensional arrangement of texts repeated at regular intervals across a spatial range, such that the spatial relationships among the constituent texts expresses propositions
table of abbreviations
IAO information artifact ontology OBI ontology of biomedical investiations GO gene ontology
A table where the constituent texts are abbreviations and their expansions
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
publication
journal article, newspaper story, book, etc.
A document that is the output of a publishing process.
PERSON: Jie Zheng
published document
Revisit the term in Octorber 2020. Improve the defintion.
publication about an investigation
Most scientific journal articles
A publication that is about an investigation
scientific publication
patent
US Patent 6,449,603
A document that has been accepted by a patent authority
document part
An abstract, introduction, method or results section.
An information content entity that is part of a document.
abstract
The profusion of high-throughput instruments and the explosion of new results in the scientific literature, particularly in molecular biomedicine, is both a blessing and a curse to the bench researcher. Even knowledgeable and experienced scientists can benefit from computational tools that help navigate this vast and rapidly evolving terrain. In this paper, we describe a novel computational approach to this challenge, a knowledge-based system that combines reading, reasoning and reporting methods to facilitate analysis of experimental data. Reading methods extract information from external resources, either by parsing structured data or biomedical language processing to extract information from unstructured data, and track knowledge provenance. Reasoning methods enrich the knowledge that results from reading by, for example, noting two genes that are annotated to the same ontology term or database entry. Reasoning is also used to combine all sources into a knowledge network that represents the integration of all sorts of relationships between a pair of genes, and to calculate a combined reliability score. Reporting methods combine the knowledge network with a congruent network constructed from experimental data and visualize the combined network in a tool that facilitates the knowledge-based analysis of that data.
A summary of the entire document that is substantially smaller than the document it summarizes. It is about the document it summarizes.
precis
introduction to a publication about an investigation
Section labelled 'introduction' of a typical scientific journal article
A part of a publication about an investigation that is about the objective specification (why the investigation is being done)
background
introduction
overview
methods section
The section labelled 'Methods' or 'Materials and Methods' in a typical scientific journal article.
A part of a publication about an investigation that is about the study design of the investigation
experimental
experimental methods
experimental procedures
experimental section
method
methodology
methods
results section
The section labelled 'results' in a typical scientific journal article
A part of a publication about an investigation that is about a study design execution
results
discussion section of a publication about an investigation
A part of a publication about an investigation that is about the study interpretation of the investigation
discussion
discussion section
discussions
references section
The list of citations found at the end of a scientific publication, grant proposal or patent application, sometimes called "literature cited" or "bibliography"
A part of a document that has citations as parts
literature cited
reference
reference list
references
author list
Lawrence Hunter and Kevin Brettonel Cohen
A part of a document that enumerates the authors of the document
institution list
The University of Colorado Denver School of Medicine and the University of Colorado Boulder.
A part of a document that has parts that are institution identifications associated with the authors of the document
author contributions section
LH conceived of the hypothesis, designed the study and contributed to the writing of the manuscript. KBC executed the experiments, analyzed the data, and contributed to the writing of the manuscript.
A part of a publication that is about the specific contributions of each author
author contributions
authors' contribution
authors' contributions
authors' roles
contributions by the authors
contributorship
acknowledgements section
The authors wish to thank Alan Ruttenberg for his constructive comments about an earlier draft of this manuscript
Part of a publication that is about the contributions of people or institutions other than the authors.
acknowledgement
acknowledgements
acknowledgment
acknowledgments
footnote
The referent in the text is usually indicated by a special typographic character such as * or a superscripted number, which is also used to indicate the footnote that refers to that text.
A part of a document that is about a specific other part of the document. Usually footnotes are spatially segregated from the rest of the document.
endnote
footnotes
supplementary material to a document
A part of a document that is segregated from the rest of the document due to its size
additional file
additional files
additional information
appendix
electronic supplementary material
electronic supplementary materials
supplemental data
supplemental information
supplemental material
supplementary data
supplementary files
supplementary information
supplementary material
supplementary materials
supporting information
table of contents
A table that relates document parts to specific locations in a document (usually page numbers). This is also a document part (subsumption there should be inferred).
table of figures
A table that relates figures in a document to specific locations in that document (usually page numbers). This is also a document part (subsumption there should be inferred).
running title
A shorter version of a document title
copyright section
This work is licensed under a Creative Commons Attribution-Share Alike 3.0 United States License.
A document part that describes legal restrictions on making or distributing copies of the document
A cartesian spatial coordinate datum is a representation of a point in a spatial region, in which equal changes in the magnitude of a coordinate value denote length qualities with the same magnitude
2009-08-18 Alan Ruttenberg - question to BFO list about whether the BFO sense of the lower dimensional regions is that they are always part of actual space (the three dimensional sort) http://groups.google.com/group/bfo-discuss/browse_thread/thread/9d04e717e39fb617
AR notes: We need to discuss whether it should include site.
cartesian spatial coordinate datum
A cartesion spatial coordinate datum that uses one value to specify a position along a one dimensional spatial region
one dimensional cartesian spatial coordinate datum
A cartesion spatial coordinate datum that uses two values to specify a position within a two dimensional spatial region
two dimensional cartesian spatial coordinate datum
A cartesion spatial coordinate datum that uses three values to specify a position within a three dimensional spatial region
three dimensional cartesian spatial coordinate datum
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
A scalar measurement datum that is the result of measurement of mass quality
mass measurement datum
hypothesis textual entity
A textual entity that expresses an assertion that is intended to be tested.
A scalar measurement datum that is the result of measuring a temporal interval
time measurement datum
A textual entity that is used as directive to deliver something to a person, or organization
2010-05-24 Alan Ruttenberg. Use label for the string representation. See issue https://github.com/information-artifact-ontology/IAO/issues/59
postal address
email address
Alan Ruttenberg 1/3/2012 - Provisional id, see issue at https://github.com/information-artifact-ontology/IAO/issues/130&thanks=130&ts=1325636583
Person:Chris Stoeckart
author role
A role inhering in a person or organization that is realized when the bearer participates in the work which is the basis of the document, in the writing of the document, and signs it with their name.
A planned process in which journal articles are read or processed and data items are extracted, typically for further analysis or indexing
data item extraction from journal article
A planned process of making information, such as literature, music, and software etc., available to the public for sale or for free.
Person: Jie Zheng
VEuPathDB
publishing process
A document that is in preparation for submission to be published.
EFO_0001795 in preparation
document in preparation for publication
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
line graph
A line graph is a type of graph created by connecting a series of data points together with a line.
line chart
WEB: http://en.wikipedia.org/wiki/Line_chart
A new pubmed ID being created for a journal article, and the associated pubmed record containing information to the journal article. A license plate number registered at the DMV to be belonging to a specific vehicle and owner. Placing a barcode on a product and entering information in a database that this barcode is assigned.
A planned process in which a new CRID is created, associated with an entity, and stored in the CRID registry thereby registering it as being associated with some entity
2014-05-05: It is the CRID registry that assigns CRIDs, not the users of the registry.
Person:Melanie Courtot
assigning a centrally registered identifier
Articles in Pubmed are reviewed by curators who add MESH terms to the Pubmed records in order to categorize them better and improve the ability to search for them.
A planned process in which a CRID registry associates an information content entity with a CRID symbol
associating information with a CRID in the CRID registry
associating information with a centrally registered identifier in its registry
a planned process with the objective to establish a system that allows to refer to specific entities of a certain kind and store information about them, by establishing a CRID registry and plan specifications for the process of 1) assigning a CRID and 2) looking up a CRID.
MC, 20101124: deprecated following discussion at IAO call 20101124. Term was deemed not necessary - no use case for now.
The sentence "The article has Pubmed ID 12345." contains a CRID that has two parts: one part is the CRID symbol, which is '12345'; the other part denotes the CRID registry, which is Pubmed.
A symbol that is part of a CRID and that is sufficient to look up a record from the CRID's registry.
PERSON: Bill Hogan
Original proposal from Bjoern, discussions at IAO calls
centrally registered identifier symbol
An information content entity that consists of a CRID symbol and additional information about the CRID registry to which it belongs.
2014-05-05: In defining this term we take no position on what the CRID denotes. In particular do not assume it denotes a *record* in the CRID registry (since the registry might not have 'records').
Alan, IAO call 20101124: potentially the CRID denotes the instance it was associated with during creation.
Note, IAO call 20101124: URIs are not always CRID, as not centrally registered. We acknowledge that CRID is a subset of a larger identifier class, but this subset fulfills our current needs. OBI PURLs are CRID as they are registered with OCLC. UPCs (Universal Product Codes from AC Nielsen)are not CRID as they are not centrally registered.
centrally registered identifier
PubMed is a CRID registry. It has a dataset of PubMed identifiers associated with journal articles.
A CRID registry is a dataset of CRID records, each consisting of a CRID symbol and additional information which was recorded in the dataset through a assigning a centrally registered identifier process.
centrally registered identifier registry
Going to the PubMed website and entering a PubMed ID in order to retrieve the Pubmed information associated with that ID.
A planned process in which a request to a CRID registry is made to return the information associated with a CRID symbol
looking up a centrally registered identifier
time stamped measurement datum
pmid:20604925 - time-lapse live cell microscopy
A data set that is an aggregate of data recording some measurement at a number of time points. The time series data set is an ordered list of pairs of time measurement data and the corresponding measurement data acquired at that time.
experimental time series
time sampled measurement data set
written name
"Bill Clinton"
"The Eiffel Tower"
"United States of America"
A textual entity that denotes a particular in reality.
The qualifier "written" is to set it apart from spoken names. Also, note the restrictions to particulars. We are not naming universals. We could however, be naming, attributive collections which are particulars, so "All people located in the boundaries of the city of Little Rock, AR on June 18, 2011 at 9:50a CDT" would be a name.
A software method (also called subroutine, subprogram, procedure, method, function, or routine) is software designed to execute a specific task.
PERSON: Michel Dumontier
software method
A software module is software composed of a collection of software methods.
PERSON: Melanei Courtot
software module
A software library is software composed of a collection of software modules and/or software methods in a form that can be statically or dynamically linked to some software application.
software library
A software application is software that can be directly executed by some processing unit.
software application
A software script is software whose instructions can be executed using a software interpreter.
software script
abbreviation textual entity
From Shiba et al. Acta Neuropathol Commun. 2013; 1: 45. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3893467/): BAC: Bacterial artificial chromosome; CR: Calretinin; GFAP: Glial fibrillary acidic protein; MAP: Microtubule-associated protein; MRI: Magnetic resonance imaging; NSC: Neural stem cell; PDA: Patent ductus arteriosus; PMG: Polymicrogyria; PNH: Periventricular nodular heterotopia; VSD: Ventricular septal defect.
A textual entity listing abbreviations and their expansions that are used in a document.
PERSON: Bill Baumgartner
abbreviations section
The section labelled 'abbreviations' in a typical scientific journal article.
A part of a document where abbreviations and their long-forms used within the document are listed.
abbreviation and acronyms
abbreviation list
abbreviations
abbreviations and acronyms
abbreviations list
abbreviations used
definitions for abbreviations
list of abbreviations
list of abbreviations used
non-standard abbreviations
nonstandard abbreviations
nonstandard abbreviations and acronyms
author information section
The section labelled 'author information' in a typical scientific journal article, e.g. in Takon. Ann Gen Psychiatry. 2011; 10: 25. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3204268/)
A part of a document about the authors that provides biographical information and may discuss how the authors' professional experiences are relevant to the work described in the document.
author information
authors’ information
biographies
contributor information
author information textual entity
From Takon. Ann Gen Psychiatry. 2011; 10: 25. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3204268/): IT [the author] is the lead paediatrician for ADHD services in East Hertfordshire, UK, where she runs a weekly joint ADHD clinic with the Child and Adolescent psychiatrist and works within an ADHD specialist team. IT also sees children with other neurodisability issues who may have comorbid ADHD, where the presentation may be more complex and challenging to manage. IT has vast experience in managing children with complex ADHD. She has 18 years of experience in paediatrics and also has extensive experience in the use of psychopharmacologic agents in managing children with ADHD.
A textual entity expression information about an author of a document. This information may include biographical information and may discuss how the authors' professional experiences are relevant to the work described in the document.
author summary section
The section labelled 'synopsis' in a typical scientific journal article, e.g. in Pendse et al. BMC Genomics. 2013; 14: 136. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3608171/)
A part of a document, distinct from the abstract, that describes the significance and broader context of the document content. The author summary is often written in a non-technical manner and is aimed at both scientists and non-scientist readers.
author summary
summary
synopsis
Article submission guidelines for PLoS Genetics (http://journals.plos.org/plosgenetics/s/submission-guidelines)
author summary textual entity
From Pendse et al. BMC Genomics. 2013; 14: 136. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3608171/): The search for genetic risk factors for common human diseases often relies on the use of linkage and association studies to establish correlation between genomic markers and disease risk. These studies require additional functional evaluation of candidate genes, including their possible interaction with diet and environment. The number of candidate genes is typically large and the development of appropriate genetic tools in mammalian systems is slow. By contrast, large-scale genetic screens, using widely available genetic tools, are routinely conducted in the fruit fly Drosophila melanogaster. In this study, we used Drosophila to screen candidate genes identified in human genome-wide scans as associated with risk of metabolic abnormalities such as type 2 diabetes. We show that a number of human candidate genes have fly orthologs that play an important role in Drosophila tolerance to high dietary sucrose. We further explored some of the specific metabolic abnormalities that can result when these genes’ activities are reduced in flies, focusing on a gene we call dHHEX (CG7056), the fly ortholog of human HHEX.
A textual entity, distinct from the abstract, that describes the significance and broader context of the document content. The author summary is often written in a non-technical manner and is aimed at both scientists and non-scientist readers, e.g as described in the article submission guidelines for PLoS Genetics (http://journals.plos.org/plosgenetics/s/submission-guidelines).
availability section
The section labelled 'availability and requirements' in a typical scientific journal article, e.g. Qi et al. BMC Bioinformatics. 2014; 15: 11. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3897912/).
A part of a document about a resource described in the document, e.g. software, that describes where and/or how that resource can be obtained.
availability
availability of data
data archiving
data availability
data availability statement
data sharing statement
availability textual entity
From Qi et al. BMC Bioinformatics. 2014; 15: 11. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3897912/): Project home page:http://krux.googlecode.com
A textual entity expressing the location of a resource, e.g. software, or the manner in which a resource can be obtained.
case report section
The section labelled 'case report' in a typical scientific journal article, e.g. in Taglia et al. Acta Myol. 2012 Dec; 31(3): 201–203. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3631801/)
A part of a document about the medical history of a specific patient as it relates to the topic of the document.
case presentation
case report
case report textual entity
Excerpt from Taglia et al. Acta Myol. 2012 Dec; 31(3): 201–203. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3631801/): The patient is a 50-year-old man. His medical history was not contributory. At the age of 37 years, he complained of persistent fatigue and dyspnoea even for modest efforts and oedema of lower limbs. The patient was examined at the department of internal medicine of the local hospital, and hospitalised with a diagnosis of dilated cardiomyopathy probably consequence of a myocarditis process. Soon after he was transferred to the cardiologic department of the regional hospital, and pharmacologically treated for heart failure and pulmonary hypertension.
A textual entity that expresses a detailed account of a portion of the medical history for a specific patient.
conclusion section
The section labelled 'conclusion' in a typical scientific journal article.
A part of a document used to summarize the findings discussed in the document. The conclusion section is typically found near the end of a document.
concluding remarks
conclusion
conclusions
findings
conflict of interest section
The section labelled 'conflict of interest statement' in a typical scientific journal article.
A part of a document used to declare any competing interests regarding the authors and/or funding organization for the work described in the document.
authors' disclosures of potential conflicts of interest
competing financial interests
competing interests
conflict of interest
conflict of interest statement
conflict of interests
conflicts of interest
declaration of competing interest
declaration of competing interests
declaration of interest
declaration of interests
disclosure of conflict of interest
disclosure of potential conflicts of interest
duality of interest
statement of interest
SD [an author] is a Merck employee and Merck is the sponsor of this study. [Taken from 'Effects of obstructive sleep apnoea risk on postoperative respiratory complications: protocol for a hospital-based registry study' Shin et al. 2016 (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4735131/)]
A textual entity that expresses a situation involving one or more of the authors, or the funding source of a document whereby the authors or funding source stand to potentially gain (typically financially) from the results reported in the document.
conflict of interest textual entity
consent section
The section labelled 'consent' in a typical scientific journal article, e.g. Shiba et al. Acta Neuropathol Commun. 2013; 1: 45. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3893467/)
A part of a document about the consent process that was used to enroll patients in a study.
consent
consent textual entity
From Shiba et al. Acta Neuropathol Commun. 2013; 1: 45. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3893467/): Written informed consent was obtained from the patient’s parents for publication of this Case report and any accompanying images. A copy of the written consent is available for review by the Editor-in chief of this journal.
A textual entity that documents the consenting process used to enroll patients in a study.
ethical approval section
The section labelled 'ethical approval' in a typical scientific journal article.
A part of a document about the governance body responsible for approving the work discussed in a document on an ethical basis.
ethical approval
ethical requirements
ethics
ethics statement
ethical approval textual entity
From McLean et al. Br J Gen Pract. 2014 Jul; 64(624): e440–e447 (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4073730/): The NHS National Research Ethics Service had previously approved the use of these anonymised data for research purposes and this analysis did not require independent review.
A textual entity that documents the ethical approval of some study design.
figures section
The section labelled 'figures' in a typical scientific journal article.
A part of a document that contains one or more figures.
figures
funding source declaration section
The section labelled 'funding' in a typical scientific journal article.
A part of a document used to detail information regarding the source of funding used in support of the generation of the document content.
financial support
funding
funding information
funding sources
funding statement
funding/support
grants
role of the funding source
source of funding
sources of funding
study funding
funding souce declaration textual entity
From Stephan et al. Accid Anal Prev. 2011 May; 43(3): 1062–1067. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3062852/): This study was supported by the International Collaborative Research Grants Scheme with joint grants from the Wellcome Trust UK (GR071587MA) and the Australian NHMRC (268055). The funding sources played no role in study design, data collection, analysis or interpretation, writing the report, or the decision to submit the paper for publication.
A textual entity documenting the source of funding that supported some study.
funding source declaration textual entity
future directions section
The section labelled 'future directions' in a typical scientific journal article.
A part of a document detailing extensions of the described work that may be implemented at some future point in time.
future challenges
future considerations
future developments
future directions
future outlook
future perspectives
future plans
future prospects
future research
future research directions
future studies
future work
outlook
future directions textual entity
Excerpt from Wang and Li. Acta Pharmacol Sin. 2016 Jan; 37(1): 25–33. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4722976/): In the future, several questions will need to be resolved regarding the physiological assembly of KCNQ channels and their functional implications in complex neural circuits. First, we still lack sufficiently selective inhibitors and activators among the KCNQ family members.
A textual entity expressing ideas regarding future work relevant to work described in a document that could be done.
genome announcement section
The section labelled 'genome announcement' in a typical scientific journal article, e.g. in Kim et al. J Bacteriol. 2011 Oct; 193(19): 5537. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3187466/)
A document part announcing the publication of a novel draft genome sequence.
genome announcement
genome announcement textual entity
Excerpt from Kim et al. J Bacteriol. 2011 Oct; 193(19): 5537. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3187466/): Here we report the genome sequence of Lactobacillus malefermentans KCTC 3548, which we obtained using a whole-genome shotgun strategy (4) with Roche 454 GS (FLX Titanium) pyrosequencing (257,559 reads totaling ∼89.8 Mb; ∼45-fold coverage of the genome) at the Genome Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB).
A textual entity that describes the generation and public release of a novel, draft genome sequence.
keyword textual entity
From: Fu and Lin. Identification of gene-oriented exon orthology between human and mouse. BMC Genomics. 2012; 13(Suppl 1): S10. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3303729/): Exon orthology; alternative splicing; exon duplication; intron-exon structure.
A textual entity listing keywords indicating the major theme(s) of a document.
keywords section
The section labelled 'keywords' in a typical scientific journal article.
A part of a document where keywords selected by the author to categorize the major theme(s) of a document are listed.
keywords
study limitations section
The section labelled 'limitations' in a typical scientific journal article.
A part of a document about biases or short comings related to the study design and execution.
limitations
study limitations
Author guidelines published by The Society for Academic Emergency Medicine. (http://onlinelibrary.wiley.com/journal/10.1111/(ISSN)1553-2712/homepage/ForAuthors.html)
study limitations textual entity
Excerpt from the Limitations section of Fermann et al 2015, Acad Emerg Med. 2015 Mar; 22(3): 299–307 (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4405051/). Owing to the nature of a post hoc study, any significant values must be interpreted with caution. In the current analysis, no multiple testing was conducted and p-values remain unadjusted. Moreover, a selection bias arising from the randomized open-label design of the original EINSTEIN PE study cannot be ruled out.
A textual entity addressing a shortcoming or bias of a study design or execution.
materials section
The section labelled 'materials' in a typical scientific journal article, e.g. Nguyen et al. BMC Bioinformatics. 2010; 11: 279. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2889936/)
A part of a document about the materials required to reproduce the content of the document.
materials
notes section
The section labelled 'notes' in a typical scientific journal article, e.g. McLean et al. Br J Gen Pract. 2014 Jul; 64(624): e440–e447 (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4073730/):
A part of a document containing typically short notes about the document itself and/or the authors. Often the notes section contains subsections related to funding, competing interests, ethical approval, etc.
notes
patients section
The section labelled 'patients' in a typical scientific journal article, e.g. in Citak et al. Acta Orthop. 2013 Jun; 84(3): 326–327. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3715825/)
A part of a document about the patients that participated in a study.
patients textual entity
Excerpt from Citak et al. Acta Orthop. 2013 Jun; 84(3): 326–327. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3715825/): Between January 1996 and February 2012, we treated 4 patients with interprosthetic femoral fractures (3 of them women) (Figure 2) using a custom-made interposition device (Waldemar Link GmbH, Hamburg, Germany) (Figure 1). Mean age was 74 (59–86) years. The fractures occurred mean 18 (13–28) years after primary THA and mean 14 (10–17) years after primary TKA. At the latest follow-up, after mean 8 (0.5–16) years, revision surgery with a total femur replacement was required in 1 case due to aseptic loosening. No other complications requiring revision surgery occurred.
A textual entity expressing information regarding the patients used in a study.
pre-publication history section
The section labelled 'pre-publication history' in a typical scientific journal article, e.g. in Xiao et al. BMC Anesthesiol. 2013; 13: 33. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4016475/)
A part of the document about the publication history of a document. This section typically details dates of document submission to a journal and dates of any re-submissions as well as reviewer comments and responses to reviewers by the authors.
notice of republication
pre-publication history
pre-publication history textual entity
From Xiao et al. BMC Anesthesiol. 2013; 13: 33. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4016475/): The pre-publication history for this paper can be accessed here: http://www.biomedcentral.com/1471-2253/13/33/prepub
A textual entity that expresses the pre-publication history (submission dates, reviewer comments, etc) for a document, often including a hyperlink to a web page detailing the information.
related work section
The section labelled 'related work' in a typical scientific journal article, e.g. Žitnik and Zupan. Bioinformatics. 2015 Jun 15; 31(12): i230–i239. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4542780/)
A part of a document about work in other publications that is relevant to the content of the document.
related literature
related work
related work textual entity
Excerpt from Žitnik and Zupan. Bioinformatics. 2015 Jun 15; 31(12): i230–i239. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4542780/): Our work presented here is similar in spirit to our recently developed methodology for data fusion via collective matrix factorization (Žitnik and Zupan, 2015).
A textual entity that discusses work from other publications and expresses their relevancy to the content of a document.
requirements section
A part of a document about a resource described in the document, e.g. software, that describes the requirements necessary to use the resource, e.g. operating systems, hardware, etc. in the case of a software resource.
requirements
requirements textual entity
From Qi et al. BMC Bioinformatics. 2014; 15: 11. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3897912/): • Operating systems: Platform independent • Programming language: Matlab, R, Python • Other requirements: None • License: GNU GPL v3 • Any restrictions to use by non-academics: None
A textual entity that expresses the requirements necessary to use a resource, e.g. software.
statistical analysis textual entity
From Mondo et al. Cardiovasc J Afr. 2013 Mar; 24(2): 28–33. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3734881/): Data were captured into EPI-DATA (version 3.1), cleaned and then exported to Stata version 10 for analysis. Continuous variables were summarised as mean (± standard deviation) and median (inter-quartile range), and presented in the tables. Categorical data were analysed using frequency and percentages, and results are presented in frequency tables and bar charts. Test of significance (p-value) was determined using the chi-square test. A p-value of less than 0.05 was considered significant.
A textual entity documenting statistical analysis tools and techniques employed.
statistical analysis section
The section labelled 'statistical analysis' in a typical scientific journal article, e.g. Mondo et al. Cardiovasc J Afr. 2013 Mar; 24(2): 28–33. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3734881/)
A part of the document used to describe the statistical methodologies employed in the work presented in the document.
statistical analysis
tables section
The section labelled 'tables' in a typical scientific journal article.
A part of a document that contains one or more tables.
tables
An identifier that denotes some postal delivery route, some aggregate of postal delivery routes or a geographical region and was created for the purpose of sorting and delivering mail.
postal code
A plan specification that if realized, is realized by the delivery of mail to some facility or mailbox within some geographical region.
Postal delivery route
A postal code that is used in the United States for the purpose of sorting and delivering mail, and that denotes some postal delivery route or some aggregate of postal delivery routes.
ZIP code
zone improvement plan code
database extract, transform, and load process
A planned process which takes as input a database and fills another database by extracting concretizations of information entities from the first, transforming them, and loading the transformed concretizations into the second.
Alan Ruttenberg 12/21/16: Maybe this definition instead: A planned process which takes as input a database and copies concretizations from the first, optionally transforms then copies the result to the second
Alan Ruttenberg 12/21/16: We don't define database in IAO, currently, as the bare word is ambiguous. Reasonable interpretations of the word might be the material entity, an information structure, an information content entity. However this definition commits, at least, to there being some material thing which bear concretizations of information entities and that there are new concretizations created during the process. We consider the ETL process in terms of information entities rather than the concretizations. No committment is made as to whether the specified output.
ETL
descriptive data section
A document part that lists and defines data variables, describes data characteristics (e.g. missing data information) and any assumptions and simplifications made.
additional results section
A results section that reports analyses other than main results of the study (e.g. subgroups analyses, adjusted analyses, sensitivity analyses, etc.)
research participants section
A document part that describes human subject(s) that participated in a study (e.g. inclusion & exclusion criteria, recruitment methods, reasons for non-participation, grouping and randomisation, methods of follow-up, etc.).
measurement methods section
A methods section that describes details of data assessment methods (data measurement).
research settings section
A document part that describes the physical/social/cultural conditions around a research trial.
study bias section
A study limitations section that describes systematic error introduced into sampling or testing by selecting or encouraging one outcome or answer over others.
graphical abstract
An abstract that is pictorial summary of the main findings described in the document.
visual abstract
identifier
An identifier is an information content entity that is the outcome of a dubbing process and is used to refer to one instance of entity shared by a group of people to refer to that individual entity.
ontology module
I have placed this under 'data about an ontology part', but this can be discussed. I think this is OK if 'part' is interpreted reflexively, as an ontology module is the whole ontology rather than part of it.
ontology file
This class and it's subclasses are applied to OWL ontologies. Using an rdf:type triple will result in problems with OWL-DL. I propose that dcterms:type is instead used to connect an ontology URI with a class from this hierarchy. The class hierarchy is not disjoint, so multiple assertions can be made about a single ontology.
base ontology module
An ontology module that comprises only of asserted axioms local to the ontology, excludes import directives, and excludes axioms or declarations from external ontologies.
editors ontology module
An ontology module that is intended to be directly edited, typically managed in source control, and typically not intended for direct consumption by end-users.
source ontology module
main release ontology module
An ontology module that is intended to be the primary release product and the one consumed by the majority of tools.
TODO: Add logical axioms that state that a main release ontology module is derived from (directly or indirectly) an editors module
bridge ontology module
An ontology module that consists entirely of axioms that connect or bridge two distinct ontology modules. For example, the Uberon-to-ZFA bridge module.
import ontology module
A subset ontology module that is intended to be imported from another ontology.
TODO: add axioms that indicate this is the output of a module extraction process.
import file
subset ontology module
An ontology module that is extracted from a main ontology module and includes only a subset of entities or axioms.
ontology slim
subset ontology
curation subset ontology module
A subset ontology that is intended as a whitelist for curators using the ontology. Such a subset will exclude classes that curators should not use for curation.
analysis ontology module
An ontology module that is intended for usage in analysis or discovery applications.
analysis subset ontology module
single layer ontology module
A subset ontology that is largely comprised of a single layer or strata in an ontology class hierarchy. The purpose is typically for rolling up for visualization. The classes in the layer need not be disjoint.
ribbon subset
single layer subset ontology module
exclusion subset ontology module
A subset of an ontology that is intended to be excluded for some purpose. For example, a blacklist of classes.
antislim
external import ontology module
An imported ontology module that is derived from an external ontology. Derivation methods include the OWLAPI SLME approach.
external import
species subset ontology module
A subset ontology that is crafted to either include or exclude a taxonomic grouping of species.
taxon subset
reasoned ontology module
An ontology module that contains axioms generated by a reasoner. The generated axioms are typically direct SubClassOf axioms, but other possibilities are available.
generated ontology module
An ontology module that is automatically generated, for example via a SPARQL query or via template and a CSV.
TODO: Add axioms (using PROV-O?) that indicate this is the output-of some reasoning process
template generated ontology module
An ontology module that is automatically generated from a template specification and fillers for slots in that template.
taxonomic bridge ontology module
ontology module subsetted by expressivity
obo basic subset ontology module
A subset ontology that is designed for basic applications to continue to make certain simplifying assumptions; many of these simplifying assumptions were based on the initial version of the Gene Ontology, and have become enshrined in many popular and useful tools such as term enrichment tools. Examples of such assumptions include: traversing the ontology graph ignoring relationship types using a naive algorithm will not lead to cycles (i.e. the ontology is a DAG); every referenced term is declared in the ontology (i.e. there are no dangling clauses). An ontology is OBO Basic if and only if it has the following characteristics: DAG Unidirectional No Dangling Clauses Fully Asserted Fully Labeled No equivalence axioms Singly labeled edges No qualifier lists No disjointness axioms No owl-axioms header No imports
ontology module subsetted by OWL profile
EL++ ontology module
purple photosynthetic bacteria and relatives
non-protein amino acid accumulating clade
Colletotrichum gloeosporioides species complex
The soybean or soya bean (Glycine max) is a species of legume native to East Asia, widely grown for its edible bean, which has numerous uses. Traditional unfermented food uses of soybeans include soy milk, from which tofu and tofu skin are made. Fermented soy foods include soy sauce, fermented bean paste, nattō, and tempeh.
glycine max
Rhizobium leguminosarum symbiovar trifolii
Colletotrichum gloeosporioides (Penz.) Penz. & Sacc., 1884
whales, hippos, ruminants, pigs, camels etc.
planned process
A process that realizes a plan which is the concretization of a plan specification.
a regulatory role involved with making and/or enforcing relevant legislation and governmental orders
regulator role
Biological_feature_identification_objective is an objective role carried out by the proposition defining the aim of a study designed to examine or characterize a particular biological feature.
biological feature identification objective
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.
regulatory role
a role realized through the process of supplying materials such as animal subjects, reagents or other materials used in an investigation.
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
Is a material entity that is created or changed during material processing.
processed material
investigation
a planned process that consists of parts: planning, study design execution, documentation and which produce conclusion(s).
a role that inheres in a material entity that is realized in an assay in which data is generated about the bearer of the evaluant role
evaluant role
A planned process with the objective to produce information about the material entity that is the evaluant, by physically examining it or its proxies.
assay
A planned process which results in physical changes in a specified input material
material processing
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
specimen role
An intervention design is a study design in which a controlled process applied to the subjects (the intervention) serves as the independent variable manipulated by the experimentalist. The treatment (perturbation or intervention) defined can be defined as a combination of values taken by independent variable manipulated by the experimentalists are applied to the recruited subjects assigned (possibly by applying specific methods) to treatment groups. The specificity of intervention design is the fact that independent variables are being manipulated and a response of the biological system is evaluated via response variables as monitored by possibly a series of assays.
a population is a collection of individuals from the same taxonomic class living, counted or sampled at a particular site or in a particular area
population
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.
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.
organization
Organism_feature_identification_objective is a biological_feature_identification_objective role describing a study designed to examine or characterize a biological feature monitored at the level of the organism, e.g. height, weight, stage of development, stage of life cycle.
organism feature identification objective
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.
protocol
is a process with the objective to place a material entity bearing the 'material to be added role' into a material bearing the 'target of material addition role'.
adding a material entity into a target
material to be added role is a protocol participant role realized by a material which is added into a material bearing the target of material addition role in a material addition process
material to be added role
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
a process of creating or modifying a plan specification
planning
An averaging objective is a data transformation objective where the aim is to perform mean calculations on the input of the data transformation.
averaging objective
is the specification of an objective to add a material into a target material. The adding is asymmetric in the sense that the target material largely retains its identity
adding material objective
an objective specification to determine a specified type of information about an evaluated entity (the material entity bearing evaluant role)
assay objective
target of material addition role is a role realized by an entity into which a material is added in a material addition process
target of material addition role
A regulatory agency is a organization that has responsibility over or for the legislation (acts and regulations) for a given sector of the government.
regulatory agency
an objective specifiction that creates an specific output object from input materials.
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
is the objective to manufacture a material of a certain function (device)
manufacturing objective
a planned process that carries out a study design
Manufacturer role is a role which inheres in a person or organization and which is realized by a manufacturing process.
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.
clustered data set
is a material processing with the objective to combine two or more material entities as input into a single material entity as output.
A planned process with the objective of collecting a specimen.
A class prediction data transformation (sometimes called supervised classification) is a data transformation that has objective class prediction.
class prediction data transformation
A data item that is produced as the output of a center calculation data transformation and represents the center value of the input data.
center value
A data item that is produced as the output of an averaging data transformation and represents the average value of the input data.
average value
A objective specification to obtain a material entity for potential use as an input during an investigation.
is an objective to obtain an output material that contains several input materials.
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.
A decision tree building data transformation is a data transformation that has objective decision tree induction.
decision tree building data transformation
a software that provides access to more than 100 tools for gene expression analysis, proteomics, SNP analysis and common data processing tasks.
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
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.
k-nearest neighbors
A material sample role is a specimen role borne by a material entity that is the output of a material sampling process.
A specimen gathering process with the objective to obtain a specimen that is representative of the input material entity
A material entity that has the material sample role
A CART (classification and regression trees) is a data transformation method for producing a classification or regression model with a tree-based structure.
CART
a directive information entity that is part of a study design. Independent variables are entities whose values are selected to determine its relationship to an observed phenomenon (the dependent variable). In such an experiment, an attempt is made to find evidence that the values of the independent variable determine the values of the dependent variable (that which is being measured). The independent variable can be changed as required, and its values do not represent a problem requiring explanation in an analysis, but are taken simply as given. The dependent variable on the other hand, usually cannot be directly controlled
study design independent variable
A data transformation which assesses how the results of a statistical analysis will generalize to an independent data set.
An organization formed with a goal to have its members conduct investigations
A person or organization that has a manufacturer role
the part of the execution of an intervention design study which is varied between two or more subjects in the study
a process that achieves a training objective
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 specimen that has been intentionally physically modified.
An objective specification which is fulfilled by the provision of some training.
A label that is part of a categorical datum and that indicates the value of the data item on the categorical scale.
a directive information entity that describes the dose that will be administered to a target
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.
a material transformation objective aims to create genetically modified organism or cell
genetic transformation objective
An age measurement datum that is the result of the measurement of the age of an organism since planting, the process of placing a plant in media (e.g. soil) to allow it to grow, which excludes sowing.
age since planting measurement datum
An age measurement datum that is the result of the measurement of the age of an organism since germination, the process consisting of physiological and developmental changes by a seed, spore, pollen grain (microspore), or zygote that occur after release from dormancy, and encompassing events prior to and including the first visible indications of growth.
age since germination measurement datum
An age measurement datum that is the result of the measurement of the age of an organism since sowing, the process of placing a seed or spore in some media with the intention to invoke germination.
age since sowing measurement datum
A time measurement datum that is the result of measurement of age of an organism
age measurement datum
an objective specification to generate a population or type of organism within species that have some uniform behavioral, morphological, physiological, or genetic characteristics with similarly bred organisms.
selective organism creation objective
An organism that is bred to have some uniform behavioral, morphological, physiological, or genetic characteristics with similarly bred organisms
selectively maintained organism
A study design in which the pathological condition of a part, organ, or system of an organism is studied. The etiology may be from infection, genetic defect, or environmental stress.
A study design that assays differences between multiple strains, cultivars, serovars, isolates, lines from organisms of a single species.
A scalar measurement datum that represents the number of events occuring over a time interval
A measurement datum that is the measure of the latitude coordinate of a site.
latitude coordinate measurement datum
A measurement datum that is the measure of the longitude coordinate of a site.
longitude coordinate measurement datum
An information content entity that is inferred from data.
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
An information content entity that specifies a value within a classification scheme or on a quantitative scale.
An organization that provides funding support for projects such as investigations.
grant agency
A material entity that has two or more specimens as its parts.
collection of specimens
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 AJCC 7th edition
A categorical value specification that is a histologic grade assigned to a tumor slide specimen according to the Fuhrman Nuclear Grading System.
histologic grade according to the Fuhrman Nuclear Grading System
A categorical value specification that is a histologic grade assigned to a ovarian tumor.
A histologic grade for ovarian tumor that is from a two-tier histological classification of tumors.
histologic grade for ovarian tumor according to a two-tier grading system
A histologic grade for ovarian tumor that is from a histological classification by the World Health Organization (WHO).
histologic grade for ovarian tumor according to the World Health Organization
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.
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 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.
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 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.
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 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.
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 colorectal 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 colon and rectum 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 lung 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.
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 ovarian 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 ovary 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.
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 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.
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 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.
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 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.
pathologic distant metastases stage for ovary 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 according to AJCC 7th edition
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 cervical 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.
International Federation of Gynecology and Obstetrics ovarian cancer stage value specification
A categorical value specification that is an assessment of a participant's performance status (general well-being and activities of daily life).
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.
Eastern Cooperative Oncology Group score value specification
A performance status value specification designed for classifying patients 16 years of age or older by their functional impairment.
A person or organization that provides material supplies to other people or organizations.
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.
A material entity that has the specimen role.
specimen
data transformation
A planned process that produces output data from input data.
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
leave one out cross validation method
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).
k-means 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).
hierarchical clustering
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.
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.
principal components analysis dimensionality reduction
An planned process that creates images, diagrams or animations from the input data.
data visualization
An objective specification to transformation input data into output data
data transformation objective
An averaging data transformation is a data transformation that has objective averaging.
averaging data transformation
A partitioning data transformation is a data transformation that has objective partitioning.
partitioning data transformation
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.
partitioning objective
A class discovery data transformation (sometimes called unsupervised classification) is a data transformation that has objective class discovery.
class discovery data transformation
A center calculation objective is a data transformation objective where the aim is to calculate the center of an input data set.
center calculation 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.
class discovery 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.
class prediction objective
A center calculation data transformation is a data transformation that has objective of center calculation.
center calculation data transformation
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.
cross validation objective
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.
A pool of specimens is a mixture of a population of samples which have been gathered from one or more sample populations, obtained by the physical process of mixing individual specimens, e.g. mixing the DNA collected from the individual fish.
pool of specimens
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.
A randomized complete block design is_a study design which assigns randomly treatments to block. The number of units per block equals the number of treatment so each block receives each treatment exactly once (hence the qualifier 'complete'). The design was originally devised from field trials used in agronomy and agriculture. The analysis assumes that there is no interaction between block and treatment. The method was then used in other settings So The randomised complete block design is a design in which the subjects are matched according to a variable which the experimenter wishes to control. The subjects are put into groups (blocks) of the same size as the number of treatments. The members of each block are then randomly assigned to different treatment groups.
Latin square design is_a study design which allows in its simpler form controlling 2 levels of nuisance variables (also known as blocking variables).he 2 nuisance factors are divided into a tabular grid with the property that each row and each column receive each treatment exactly once.
A process by which a substance is intentionally given to an organism resulting in exposure of the organism to that substance.
administering substance in vivo
a material that is added to another one in a material combination process
A material entity into which another is being added in a material combinatino process
A disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism.
The totality of all processes through which a given disease instance is realized.
A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities
A physical quality inhering in a bearer by virtue of the bearer's scalar absolute value of the rate of change of the bearer's position.
A time quality inhering in a bearer by virtue of how long the bearer has existed.
A composite chromatic quality composed of hue, saturation and intensity parts.
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 orientation in space.
A quality that is the extent of space between two entities.
A physical quality which inheres in a bearer by virtue of the number of the bearer's repetitive actions in a particular time.
A physical quality inhering in a bearer by virtue of the bearer's resistance to pressure, being broken, or pierced
A quality inhering in a bearer by virtue of the bearer's possessing or displaying a distinctive feature in type or degree or effect or force.
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 spatial quality inhering in a bearer by virtue of the bearer's exhibiting repetition of placement of its parts.
A quality inhering in a bearer by virtue of the whether the bearer differs from normal or average.
The number of entities of this type that are part of the whole organism.
A quality that exists by virtue of being a particular point in the time of a cycle.
A quality inhering in a bearer by virtue of the bearer's disposition to detect or perceive external stimulation.
A morphology quality inhering in a bearer by virtue of the bearer's physical magnitude.
A 1-D extent quality inhering in a bearer by virtue of the bearer's vertical dimension of extension.
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 physical quality inhering in a bearer that has mass near a gravitational body. Important usage note: Note that this ontology has a class for a similar concept, mass (PATO:0000125). Mass and weight are not equivalent. For most use cases, the class mass is strongly preferred over weight.
A spatial quality inhering in a bearer by virtue of the bearer's placement which is defined by the angle between the bearer and an axis, or the angle between the bearer and another object.
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 inhering in a bearer by virtue of the bearer's sensitivity towards a fixed location or value where a change is observed; upper limit.
A quality of a single process inhering in a bearer by virtue of the bearer's occurrence per unit time.
A quality in which events occur in sequence.
A quality of a single physical entity which is held by a bearer when the latter exhibits a state of growth, differentiation, or development.
A reproductive quality inhering in a bearer by virtue of the bearer's initiating, sustaining, or supporting reproduction.
An achromatic color of maximum brightness; the color of objects that reflect nearly all light of all visible wavelengths.
A color hue with medium wavelength of that portion of the visible spectrum lying between orange and green, evoked in the human observer by radiant energy with wavelengths of approximately 570 to 590 nanometers.
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 texture quality inhering in a bearer by virtue of the bearer's irregular surface.
A 1-D extent quality which is equal to the dimension through an object as opposed to its length or width.
A 3-D extent quality inhering in a bearer by virtue of the bearer's amount of 3-dimensional space it occupies.
A 1-D extent quality which is equal to the distance from one side of an object to another side which is opposite.
A color consisting of dark orange, red, of very low intensity.
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 optical quality inhering in a bearer by virtue of the bearer's lacking opacity.
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 liquid 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 physical quality which inheres in a bearer by virtue of some influence is exerted by the bearer's mass per unit size.
A physical quality inhering in a bearer by virtue of the bearer's capacity to do work.
A physical quality that inheres in a bearer by virtue of the bearer's amount of force per unit area it exerts.
A physical quality which is equal to the energy transferred by a force to a moving object.
A physical quality inhering in a bearer by virtue of ratio of the bearer's output to the bearer's input.
A physical quality inhering in a bearer by virtue of the bearer's rate of change of momentum.
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 color consisting of yellow hue and high brightness.
A physical quality that inheres in an bearer by virtue of how that bearer interacts with electromagnetic radiation.
An EM radiation quality that is independent of the EM wavelength range.
A scalar EM radiation quality which obtains by the capacity of the bearer to scatter or reflect radiation.
A reflective quality restricted to a particular wavelength.
An EM radiation quality in which the EM radiation is within the fiat range of the spectrum visible deemed to be light.
A process quality inhering in a bearer by virtue of the bearer's magnitude of the temporal extent between the starting and ending point.
A 2-D extent quality inhering in a bearer by virtue of the bearer's two dimensional extent.
A morphology quality inhering in a bearer by virtue of the bearer's lack of distinct morphology.
A length quality which is equal to the length of any straight line segment that passes through the center of a circle and whose endpoints are on the circular boundary.
A density quality which inheres in a bearer by virtue of some influence exerted by the bearer's mass on a given area.
A density quality which is equal to the mass exerting an influence on a one-dimensional object.
A density quality which inheres in a bearer by virtue of some influence exerted by the bearer's mass on a given volume.
A shape quality that obtains by virtue of the bearer having inward facing edges; having a surface or boundary that curves or bulges outward, as the exterior of a sphere.
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 concentration quality inhering in a medium by virtue of the bearer's tendency to hydronate a specific reference base.
An organismal quality inhering in a bearer by virtue of the bearer's ability to produce new life or offspring.
A sensitivity quality inhering in a bearer by virtue of the bearer's dependence on oxygen.
A quality inhering in a bearer by virtue of the bearer's independence on oxygen.
A quality that is equal to the potential energy per unit charge associated with a static (time-invariant) electric field, also called the electrostatic potential.
A quality inhering in a bearer by virtue of the bearer's magnitude in respect to a related entity.
A shape quality inhering in a bearer by virtue of the bearer's having an oblique or slanted direction.
A monadic quality of continuant inhering in a bearer by virtue of the bearer's being intricate and compounded.
A complexity quality inhering in a bearer by virtue of the bearer's being intricate and compounded.
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.
The number of parts of a particular type that the bearer entity has. This is a relational quality, and thus holds between two entities: the bearer of the quality, and the type of parts.
extra or missing physical or functional parts
A mass which is higher than normal or average.
A physical quality inhering in a bearer by virtue of the bearer's motion characteristic.
A physical quality inhering in a bearer by virtue of the bearer's disposition to transmit of an entity through a medium.
A surface shape quality inhering in a bearer by virtue of the bearer's exhibiting a degree of bending.
A 1-D extent quality inhering in a bearer by virtue of the bearer's downward or backward or inward dimension.
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.
A quality inhering in a bearer by virtue of the bearer's exhibiting complete growth, differentiation, or development.
A size quality inhering in an bearer by virtue of the bearer's extension in one dimension.
A size quality inhering in an bearer by virtue of the bearer's extension in two dimensions.
A size quality inhering in an bearer by virtue of the bearer's extension in three dimensions.
An organismal quality inhering in a bearer by virtue of the bearer's disposition to lose an entitity by natural process.
A quality inhering in a plant by virtue of the bearer's disposition to being between evergeen and deciduous.
A quality that inheres in an bearer by virtue of how that bearer interacts with radiation.
A conductivity quality inhering in a bearer by virtue of the bearer's ability to convey electricity.
A composition quality inhering in a bearer by virtue of the bearer's containing granules.
A spatial pattern inhering in a bearer by virtue of the bearer's being confined or restricted to multiple locations.
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 shape quality in a bearer by virtue of the bearer's curving inward.
A convex 3-D shape quality inhering in a bearer by virtue of the bearer's exhibiting a consistently-sized round cross section.
A physical quality inhering in a bearer by virtue of the bearer's participation in movement.
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.
Surface shape that refers to the inward or outward curvature of the surface.
A complete three dimensional shape in which for every line connecting pair of points on the object is within the object. Or: a shape lacking cavities. Contrast: concave.
A structural quality that inheres in a bearer by virtue of the bearer's containing hollow areas.
A spatial pattern inhering in a bearer by virtue of the bearer's layered configuration.
A spatial pattern inhering in a bearer by virtue of the bearer's exhibiting a layered configuration.
A quality inhering in a bearer by virtue of the bearer's having an empty space or cavity within.
A quality inhering in a bearer by virtue of the bearer's processing the form of a thin plate sheet or layer.
A shape quality inhering in a bearer by virtue of the bearer's being free of curves, bends, or angles.
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 shape that inheres in a 3 dimensional entity.
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.
An orientation inhering in a bearer by virtue of the bearer's placement at an angle.
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.
The number of repeated events per unit time, occurring in a repeating series. (e.g. the number of heart beats occurring over 1 minute)
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
A material entity that consists of two or more organisms, viruses, or viroids.
collection of organisms
A collection of organisms, all of the same species, that live in the same place.
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.
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.
single-species collection of organisms
A collection of organisms that consists of two or more organisms from at least two species.
multi-species collection of organisms
A material entity that is one or more organisms, viruses or viroids.
organismal entity
A plant experimental condition (PECO:0007359) or set of conditions describing the application of an abiotic (PECO:0007191) or biotic plant exposure (PECO:0007357) or the combinatorial application thereof.
A fungal plant exposure (PECO:0007233) involving the exposure of plant to the pathogen belonging to Glomeromyetes class.
A Glomeromycota exposure (PECO:0001058) involving the exposure of compatible plants to mutualistic arbuscular mycorrhizal fungi.
arbuscular mycorrhizal fungal treatment (narrow)
An exposure involving growing plants in soil growth media with varying contents.
An exposure involving growing plants in varying textures of soil growth media.
An exposure involving growing plants in a sandy soil growth media.
An exposure involving growing plants in a growth media containing organic matter.
organic matter content treatment (narrow)
An exposure involving growing plants in a silty soil growth media.
An exposure involving growing plants in a clay soil growth media.
An abiotic plant exposure (PECO:0007191) involving the use of a solid or liquid substrate for growing plants or tissue-cultured plant samples.
A plant exposure (PECO:0001001) involving the application of chemical or non-biological factors.
A biotic plant exposure (PECO:0007357) involving exposure of a plant to a fungus or a combination of fungi.
A plant exposure (PECO:0001001) involving the application of a biotic or biological factor such as a microbe, insect, animal, or plant or a combination thereof.
A plant exposure (PECO:0001001) and/or study type (PECO:0007231) applied to a whole plant (PO:0000003), a plant structure (PO:00090119), and/or a plant population as part of an experiment to evaluate the plant response.
A plant structure (PO:0005679) which is a whole organism.
Examples include plant embryo (PO:0009009), megagametophyte (PO:0025279) and microgametophyte (PO:0025280).
A floral structure primordium (PO:0025477) that is committed to the development of an ovule (PO:0020003).
portion of ovule primordium tissue (exact)
The transition from ovule primordium to ovule occurs when an integument (PO:0020021) begins to develop from the protoderm (PO:0006210).
A floral structure primordium (PO:0025477) that is committed to the development of a gynoecium (PO:0009062).
portion of gynoecium primordium tissue (exact)
Use carpel primordium (PO:0004703) for the primordium (PO:0025127) of an individual carpel (PO:0009030).
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)
An undeveloped shoot system (PO:0009006).
A portion of meristem tissue (PO:0009013) which is the organogenic region of the meristem, characterized by higher rates of cell division.
A portion of reproductive shoot apical meristem tissue (PO:0008028) that gives rise to the floral organs (PO:0025395).
In Zea mays and other grasses, the floret meristem is part of a spikelet and develops into a specific type of floret. If you are annotating to this structure for Zea mays or other grasses, please also add an annotation to the spikelet type that the meristem is part of. Choose the most specific term possible from: spikelet (PO:0009051), ear spikelet (PO:0006320), ear pedicellate spikelet (PO:0006348), ear sessile spikelet (PO:0006349), tassel spikelet (PO:0006309), tassel pedicellate spikelet (PO:0006312), tassel sessile spikelet (PO:0006311).
A reproductive shoot system development stage (PO:0025530) that has as primary participant a inflorescence (PO:0009049).
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 swollen shoot axis (PO:0025029) that grows horizontally at or below the substrate surface and produces shoots above and roots or rhizoids below.
In ferns and many monocots, a rhizome is a primary axis (stem), while in other species, it is a branch. Usually produces scale-like leaves.
A shoot axis (PO:0025029) that develops from a branch (PO:0025073) and is radially enlarged for storage.
Functions in storage of photosynthate metabolites. This term should be used for tubers derived from branches, as found in Solanum spp. (e.g. potato) or Dioscorea spp. (e.g. yam) and other species. Use the term tuberous root tuber (PO:0025476) for tubers derived from roots, such as those found in Cassava, Ipomoea, or Hemerocallis.
A shoot system that is initiated from a shoot.
sistema de epiblasto (epiblastema) que nace en el epiblasto (epiblastema) (Spanish, exact)
A shoot-borne shoot system (PO:0004546) developing from a stem (PO:0009047).
A shoot axis tuber (PO:0004543) that develops below ground.
tub&#233rculo subterr&#225neo (Spanish, exact)
A phyllome primordium (PO:0025128) that develops from a carpel anlagen (PO:0006005) and is committed to the development of a carpel (PO:0009030).
portion of carpel primordium tissue (exact)
A bud (PO:0000055) that develops from an axillary bud meristem (PO:0000232).
An axillary shoot system (PO:0006343) that is part of a stem base (PO:0008039).
epiblasto (epiblastema) axilar basal (Spanish, exact)
A cardinal organ part (PO:0025001) of a shoot axis (PO:0025029) that is between two shoot axis nodes (PO:0005004).
internodo del epiblasto (epiblastema) (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 phyllome anlagen (PO:0025430) that will give rise to a carpel primordium (PO:0004703) and is part of a peripheral zone (PO:000225) of a flower meristem (PO:0000229).
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 reproductive shoot system (PO:0025082) that develops from an inflorescence (PO:0009049) and has as parts each infructescence axis (PO:0025242) and all of the fruits (PO:0009001) borne by those axes.
A shoot-borne shoot system (PO:0004545) that develops from an axillary bud (PO:0004709).
sistema axilar del epiblasto (epiblastema) (Spanish, exact)
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 shoot apical meristem (PO:0020148) that gives rise to the apical growth of reproductive tissues and organs.
meristema apical reproductivo del epiblasto (epiblastema) (Spanish, exact)
OBSOLETE. A young plant derived from a newly germinated seed.
A multi-tissue plant structure (PO:0025496) that develops from a gynoecium (PO:0009062), or a single carpel (PO:0009030), and at maturity may have as parts one or more seeds (PO:0009010).
A fruit (PO:0009001) may contain additional plant structures (PO:0009011) that were part of a flower (PO:0009046) and mature along with the gynoecium, such as a receptacle (PO:0009064). A fruit may develop without fertilization in cases of parthenocarpy, apomixis, or other hormone-induced conditions and may not always contain seeds (PO:0009010). When annotating to fruit (PO:0009001) that are referred to as ‘aggregate’, ‘multiple’, or ‘compound’, please annotate directly to the appropriate plant structure, such as receptacle, hypanthium (PO:0009065) or infructescence (PO:0006342). Fruits only occur in angiosperms.
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 whole plant (PO:0000003) that participates in the plant embryo stage (PO:0007631).
A plant embryo is generally formed after the first division of a plant zygote (PO:0000423), but in the case of a nucellar (adventitious) plant embryo (PO:0004537), somatic plant embryo (PO:0025302), microspore-derived cultured plant embryo (PO:0025305), and other embryos that arise through apogamy, it begins after the division of a single cell that is not a zygote. The end of the embryo stage varies among taxa; the beginning of a seed germination stage (PO:0007057) in seed plants, formation of the first vascular leaf (PO:0009025) in pteridophytes, the beginning of development of a sporangium (PO:0025094) in bryophytes, or the beginning of the formation of a plant organ (PO:0009008) such as a root (PO:0009005), shoot axis (PO:0025029), or vascular leaf (PO:0009025) in a cultured plant embryo (PO:0000010).
A multi-tissue plant structure (PO:0025496) that develops from a plant ovule (PO:0020003) and has as parts a plant embryo (PO:0009009) enclosed in a seed coat (PO:0009088).
A seed generally develops from an ovule (PO:0020003) after fertilization, but may develop without fertilization in the case of apogamy (e.g., adventitious embryos or somatic embryos). A seed is a reproductive unit of seed plants (gymnosperms, angiosperms, and fossil pteridosperms).
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 leaf-like organ on which one or more sporangia are borne.
A structure upon which (or in the axil of which) one or more megasporangia are borne; in flowering plants, a carpel.
A megasporophyll, almost always at the center of a flower, its margins more or less fused together or with other carpels to enclose the ovule(s).
In some cases, a gynoecium (PO:0009062) may consist of only one carpel, in which case annotations should go on carpel (PO:0009030). The word pistil is used synonymously with gynoecium, but if a gynoecium consists of a single carpel, then pistil may be used synonymously with carpel. If carpels are fused, the gynoecium is a syncarpous gynoecium, as in Poaceae, Brassicaceae and Solanaceae. If carpels are free, the gynoecium is an apocarpous gynoecium, as in Fabaceae. If you are annotating to this structure for Zea mays or other grasses, please also add an annotation to the corresponding floret type. Choose the most specific term possible from: spikelet floret (PO:0009082), ear floret (PO:0006354), upper floret of pedicellate spikelet of ear (PO:0006350), upper floret of sessile spikelet of ear (PO:0006352), tassel floret (PO:0006310), upper floret of pedicellate spikelet of tassel (PO:0006314), upper floret of sessile spikelet of tassel (PO:0006316).
A determinate reproductive shoot system (PO:0025082) that has as part at least one carpel (PO:0009030) or at least one stamen (PO:0009029) and does not contain any other determinate shoot system (PO:0009006) as a part.
The characteristic reproductive structure of angiosperms. May have as part one or more petals, sepals or tepals. May contain one or more pistillode (PO:0009078), staminode (PO:0009077) or other aborted organs that don't show up in mature form.
A shoot axis (PO:0025029) that is the primary axis of a plant.
A stem often bears leaves and buds. It is usually above ground, and is more or less negatively geotropic.
A reproductive shoot system (PO:0025082) that has as parts all of the shoot axes (PO:0025029) and flowers (PO:0009046; must have two or more) distal to the most distal leaf (PO:0009025).
An inflorescence is a reproductive shoot system from which at least two flowers develop. The growth pattern of an inflorescence may be monopodial (single main shoot axis), sympodial (growth only occurs from axillary meristems), or both. An inflorescence axis (PO:0020122) can be determinate or indeterminate. An inflorescence flower pedicel (PO:0009052) is the ultimate axis in an inflorescence. The flower (PO:0009046) of many plants, for example Magnolia spp., is solitary.
A bract (PO:0009055) subtending a branch of the inflorescence (PO:0009049) or borne on the inflorescence axis (PO:0020122) below any branch (PO:0025073) or flower (PO:0009046).
br&#225ctea de la inflorescencia (Spanish, exact)
A phyllome that subtends a reproductive structure.
A collective phyllome structure (PO:0025023) composed all of the carpels (PO:0009030) in a flower (PO:0009046).
gynoecium of lower floret of pedicellate spikelet of ear (narrow)
gynoecium of lower floret of pedicellate spikelet of tassel (narrow)
gynoecium of lower floret of sessile spikelet of ear (narrow)
gynoecium of lower floret of sessile spikelet of tassel (narrow)
gynoecium of upper floret of pedicellate spikelet of ear (narrow)
gynoecium of upper floret of pedicellate spikelet of tassel (narrow)
gynoecium of upper floret of sessile spikelet of ear (narrow)
gynoecium of upper floret of sessile spikelet of tassel (narrow)
If annotating gene expression to a gynoecium with a single carpel (PO:0009030), the annotation should go on carpel. A gynoecium with two or more carpels may be either syncarpous (carpels fused) or apopcarpous (carpels free) or the carpels may be partially fused. The word pistil is used synonymously with gynoecium for a synocarpous gynoecium, and synonymously with carpel for an apocarpous gynoecium, whether it has one or more carpels. In Zea mays, gynoecia of tassel florets and of the lower florets of ear spikelets usually do not develop fully, and they are present in a rudimentary state. If you are annotating to this structure for Zea mays or other grasses, please also add an annotation to the corresponding floret type. Choose the most specific term possible from: spikelet floret (PO:0009082), ear floret (PO:0006354), lower floret of pedicellate spikelet of ear (PO:0006353), lower floret of sessile spikelet of ear (PO:0006351), upper floret of pedicellate spikelet of ear (PO:0006350), upper floret of sessile spikelet of ear (PO:0006352), tassel floret (PO:0006310), lower floret of pedicellate spikelet of tassel (PO:0006313), lower floret of sessile spikelet of tassel (PO:0006315), upper floret of pedicellate spikelet of tassel (PO:0006314), upper floret of sessile spikelet of tassel (PO:0006316).
A plant organ (PO:0009008) that has as parts a nucellus (PO:0020020) in which a female gametophyte (PO:0025279) is located, one or two integuments (PO:0020021), and a funicle (PO:0020006).
A seed (PO:0009010) develops from a plant ovule. In angiosperms, a plant ovule is part of a plant ovary (PO:0009072). In conifers, a plant ovule is part of an ovuliferous scale (add term). If you are annotating to this structure for Zea mays or other grasses, please also add an annotation to the corresponding floret type. Choose the most specific term possible from: spikelet floret (PO:0009082), ear floret (PO:0006354), upper floret of pedicellate spikelet of ear (PO:0006350), upper floret of sessile spikelet of ear (PO:0006352).
A shoot axis (PO:0025029) that is part of an inflorescence (PO:0009049).
eje de la inflorescencia (Spanish, exact)
first order inflorescence branch (related)
An inflorescence axis (PO:0020122) has either a determinate apex, which terminates in a flower meristem (PO:0000229), or has an indeterminate apex, which terminates in an inflorescence apical meristem (PO:0009108). An inflorescence pedicel (PO:0009052) is the simplest example of a determinate inflorescence axis.
A pistillate inflorescence (PO:0025598) in Zea species that is highly compacted and bears the ear spikelets (PO:0006320) on a lateral inflorescence axis (PO:0020122).
oreja de la inflorescencia (Spanish, exact)
A shoot axis internode (PO:0005005) that is part of a stem (PO:0009047).
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 cardinal part of multi-tissue plant structure (PO:0025498) that is a proper part of a plant organ (PO:0009008) and includes portions of plant tissue (PO:0009007) of at least two different types.
parte de un &#243rgano cardinal (Spanish, exact)
Cardinal refers to the fact that these are biologically meaningful and not arbitrary parts. Examples include petiole (PO:0020038), lamina (PO:0025060), and leaflet (PO:0020049). See also collective organ part structure (PO:0025269), for plant structures composed of parts of multiple organs.
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 consists of two or more phyllomes (PO:0006001) originating from the same node or from one or more adjacent nodes with compressed shoot internodes (PO:0005005).
estructura colectiva del filoma (Spanish, exact)
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 native plant cell (PO:0025606) that is part of a plant embryo (PO:0009009).
c&#233lula embri&#243nica vegetal (Spanish, exact)
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 cardinal organ part (PO:0025001) that is elongated and sub-cylindrical to cylindrical and supports another cardinal organ part.
tallo de alto orden (secundario, terciario, etc) (Spanish, exact)
A shoot axis (PO:00025029) that develops from an axillary bud meristem (PO:0000232) or from equal divisions of a meristematic apical cell (PO:0030007).
In vascular plants, branches arise from an axillary bud meristem (PO:0000232) and from divisions of the meristematic apical cell (PO:0030007) in non-vascular plants.
A shoot system (PO:0009006) in the sporophytic phase that has as part at least one sporangium (PO:0025094).
sistema de brote reproductivo (Spanish, exact)
A plant structure (PO:0009011) that is part of an plant embryo (PO:0009009).
estructura vegetal embri&#243nica (Spanish, exact)
Includes plant structures that only occur in embryos (such as suspensor) as well as plant structures that are part of an embryo when a plant is in the embryonic phase (such as embryonic radicle).
A higher order infructescence axis (PO:0025243) which arises from a first order infructescence axis (PO:0025244) and develops from a second order inflorescence axis (PO:0006321).
eje de segundo de la infructescencia (Spanish, exact)
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 shoot apex that has as part a reproductive shoot apical meristem.
&#225pice reproductivo del epiblasto (epiblastema) (Spanish, exact)
A portion of plant tissue (PO:0009007) that is part of a plant embryo (PO:0009009).
portion of embryonic plant tissue (exact)
tejido embri&#243nico vegetal (Spanish, exact)
This class is for tissues that only occur as part of an embryo.
A reproductive shoot system that is part of an infructescence and has as parts a second order infructescence axis and any infructescence axes and fruits that arise from it.
infructescencia de segundo orden (Spanish, exact)
A shoot axis (PO:0025029) that is part of an infructescence (PO:0006342).
eje de la infructescencia (Spanish, exact)
An infructescence axis (PO:0025242), which is a branch (PO:0025073) in an infructescence (PO:0006342), that develops from a higher order inflorescence axis (PO:0009081).
ejen de la infructescencia (Spanish, exact)
A higher order infructescence axis is named according to its position in an infructescence (PO:0006342). Tenth order infructescence axis (PO:0025112) is the greatest specific infructescence axis (PO:0025242) order in the PO; when mapping annotations to an infructescence axis which is of an order higher than ten, or when order is ambiguous or unknown, annotate directly to higher order infructescence axis (PO:0025243).
An infructescence axis (PO:0025242), which is the primary or main axis of an infructescence (PO:0006342), that develops from a first order inflorescence axis (PO:0025104).
eje de la infructescencia de primer orden (Spanish, exact)
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 plant structure development stage (PO:0009012) that has as primary participant a collective plant structure (PO:0025497).
etapa de desarrollo de una estructura colectiva de la planta (Spanish, exact)
Includes flower development stage (PO:0007615), corolla development stage (PO:0007604), and inflorescence development stage (PO:0001083).
collective plant organ structure development stage
A plant organ (PO:0009008) that is part of a flower (PO:0009046).
Includes phyllomes such as anthers and petals, as well as shoot axes such as androphores and gynophores.
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 root (PO:0009005) that develops from a tuberous root (PO:0025523) and is further radially enlarged for storage.
Functions in storage. This term should be used for tubers derived from roots (PO:0009005), as found in Cassava or sweet potato (Ipomoea batatas), not for tubers derived from branches (PO:0025073), as found in potatoes and yams. Use the term shoot axis tuber (PO:0004543), aerial tuber (PO:0004548), or subterranean tuber (PO:0004547) for tubers derived from branches. A tuberous root tuber may be distinguished from a tuber that is derived from a branch by the presence of a root cap (PO:0020123) early in development, or the presence of lateral roots (PO:0020121) or their remnants. Sometimes tuber roots bear vegetative buds (PO:0000058) like a tuber derived from a branch. A tuberous root tuber usually develops from a shoot-borne root (PO:0000042) or a lateral root (PO:0020121).
A primordium (PO:0025127) that is committed to the development of a floral organ (PO:0025395) and is part of a reproductive shoot apex (PO:0025222).
floral structure primordia (exact, plural)
portion of floral structure primordium tissue (exact)
primordio de organo floral (Spanish, exact)
If annotating to a primordium of a floral structure, it is better to use the more specific term, such as petal primordium (PO:0000021) or anther primordium (PO:0006089).
A phyllome anlagen (PO:0025430) that will give rise to a bract primordium (PO:0025487) and is part of a peripheral zone (PO:000225) of a reproductive shoot apical meristem (PO:0008028).
A phyllome primordium (PO:0025487) that is committed to the development of a flower bract (PO:0009055).
portion of bract primordium tissue (exact)
primordio de la br&#225ctea (Spanish, exact)
A bract primordium (PO:0025128) is committed to the development of an inflorescence bract (PO:0009054).
inflorescence bract primordia (exact, plural)
primordio de la br&#225ctea de la inflorescencia (Spanish, exact)
portion of inflorescence bract primordium tissue (related)
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 structure (PO:0009011) that is a proper part of a multi-tissue plant structure (PO:0025496) and includes portions of plant tissues (PO:0009007) of at least two different types.
parte cardinal de estructura vegetal con m&#250ltiples tejidos (Spanish, exact)
複数の組織からなる植物構造の基本（主要）部分 (Japanese, exact)
Includes cardinal parts of plant organs (PO:0025001) as well as parts of other multi-tissue plant structures. Cardinal refers to the fact that these are biologically meaningful and not arbitrary parts. Most cardinal parts of multi-tissue plant structures have both fiat and bona-fide boundaries, including parts with large fiat boundaries, such as leaf base (PO:0020040) or fruit distal end (PO:0008001), and parts with primarily bona-fide boundaries, such as leaflet (PO:0020049).
cardinal part of multi-tissue plant structure
A plant axis (PO:0025004) that is radially enlarged.
Functions in storage of photosynthate metabolites. May develop from a branch (PO:0025073) or a root (PO:0009005). If you are annotating to tuber, you should pick the more specific child term: shoot axis tuber (PO:0004543) or tuberous root tuber (PO:0025476).
A root (PO:0009005) that is radially enlarged relative to other lateral roots (PO:0020121) or shoot-borne roots (PO:0000042) on the same plant, but not as enlarged as a tuberous root tuber (PO:0025476).
A collective plant organ structure development stage (PO:0025338) that begins with the onset of the plant organ development stage (PO:0025339) and ends with either gametophyte senescent stage (PO:0025343) or sporophyte senescent stage (PO:0007017) or death.
The shoot system (PO:0009006) develops fron the shoot apical meristem (PO:0020148) in the plant embryo (PO:0009009) in vascular plants. In lower plants the gametophore (PO:0030018) arises from a gametophore meristematic apical cell (PO:0030019) in the protonema (PO:0030003).
A shoot system development stage (PO:0025527) that has as primary participant a bud (PO:0009006).
A shoot system development stage (PO:0025527) that has as primary participant a reproductive shoot system (PO:0025082).
reproductive shoot system development stage
An infructescence (PO:0006342) in Zea species that bears kernels (i.e. caryopsis fruit; PO:0030104) on a compact ear infructescence axis (PO:0025623) and develops from the ear inflorescence (PO:0020136).
An inflorescence (PO:0009049) that includes as part only pistillate flowers (PO:0025599).
A flower (PO:0009046) that includes as part a single carpel (PO:0009030) or a gynoecium (PO:0009062), but the androecium (PO:0009061) is absent or has aborted during development.
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 first order infructescence axis (PO:0025244) in an ear infructescence (PO:0025597) that bears kernels (i.e. caryopsis fruit; PO:0030104).
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.
A fruit (PO:0009001) which develops from a carpel (PO:0009030) and at maturity comprises a dry exocarp (PO:0009085), dry mesocarp (PO:0009087), and dry endocarp (PO:0009086) that dehisce along two fruit valves (PO:0000033).
Legume fruit (PO:0030100) is characteristic of the plant family Fabaceae. Examples: pigeon pea (Cajanus cajan), chickpea (Cicer arietinum), peanut (Arachis hypogaea), soybean (Glycine max), and lentil (Lens culinaris subsp. culinaris).
A fruit (PO:0009001) which develops from a gynoecium (PO:0009062) and at maturity comprises a dry exocarp (PO:0009085), dry mesocarp (PO:0009087), and dry endocarp (PO:0009086) that are fused to a seed coat (PO:0009088).
Caryopsis fruit (PO:0030104) is characteristic of the Poaceae (the grass family). Caryopsis fruits develop from a pseudomonomerous gyneocium (PO:0009062), and contain only a single seed due to the abortion of two of the three carpels (PO:0009030). The pericarp of caryopsis fruits of some bamboo species is somewhat fleshy at maturity and is fused to the seed coat; these fruits are referred to in the literature as bacoid caryopses. Examples: barley (Hordeum vulgare), rice (Oryza spp.), wheat (Triticum spp.), corn (Zea mays), sorghum (Sorghum bicolor), oat (Avena spp.), zebra grass (Miscanthus spp.), Tausch’s goatgrass (Aegilops tauschii), stiff brome (Brachypodium distachyon), cutgrass (Leersia perrieri), and foxtail millet (Setaria italica).
A fruit (PO:0009001) which at maturity comprises a fleshy endocarp (PO:0009086), fleshy mesocarp (PO:0009087), and fleshy exocarp (PO:0009085).
Examples: pepper (Capsicum annuum), papaya (Carica papaya), avocado (Persea americana), may apple (Podophyllum peltatum), date palm (Phoenix dactylifera), tomato (Solanum lycopersicum), potato (Solanum tuberosum), chocolate (Theobroma cacao), blueberry (Vaccinium spp.), and grape (Vitis vinifera).
A berry fruit (PO:0030108) which develops from an inferior carpel (PO:0009030) and at maturity comprises a fleshy exocarp (PO:0009085), fleshy mesocarp (PO:0009087), and fleshy endocarp (PO:0009086), and has as a part a hard receptacle (PO:0009064) which surrounds, and is indistinct from, the exocarp (PO:0009085).
A pepo fruit (PO:0030111) is specialized type of berry fruit (PO:0030108) which is encapsuled by persistent, accrescent receptacle (PO:0009064) tissue. The rind, or tough outer covering, of pepo fruits comprises receptical tissue and at least the exocarp (PO:0009085) layer of the pericarp (PO:0009084). Examples: pumpkin (Cucurbita pepo), cucumber (Cucumis sativus), and watermelon (Citrullus lanatus) and banana (Musa acuminata).
An inflorescence (PO:0009049) with a monopodial growth habit, which at flowering stage (PO:0007616), is composed of sessile flowers (PO:0009046) on an indeterminate, first order inflorescence axis (PO:0025104).
The basal-most flowers of some spike inflorescences have short inflorescence flower pedicels (PO:0009052), such as in ladies'-tresses orchids (Spiranthes; Orchidaceae). Examples include black pepper (Piper nigrum; Piperaceae).
An inflorescence (PO:0009049) with a monopodial growth habit, which at flowering stage (PO:0007616) is composed of pedicellate flowers (PO:0009046) or spikelets (PO:0009051) on determinate inflorescence axes (PO:0020122).,
Examples include the majority of species in the grass family Poaceae including oats (Avena spp.), brome (Brachypodium spp.), barley (Hordeum vulgare), cutgrass (Leersia perrieri), rice (Oryza spp.), foxgrass (Setaria spp.), wheat (Triticum aestivum), wild rice (Zizania palustris), and the staminate inflorescence of cultivated corn (Zea mays), as well as grapes (Vitis spp.; Vitaceae), and Polemonium caeruleum (Polemoniaceae). Panicle inflorescences are most often conical in shape.
A material entity consisting of multiple components that are causally integrated.
Average weight of the panicle from the plants or tillers in a given study.
A plant trait (TO:0000387) which is a morphological quality of a plant anatomical entity (PO:0025131) or a constituent cellular component (GO:0005575) contained therein.
A panicle morphology trait (TO:0000847) which is the measurement in centimeters from panicle base to tip.
A plant axis morphology trait (TO:0000738) which is a quality of a root (PO:0025025).
A moisture content trait (TO:0000228) which is the amount of moisture of the caryopsis fruit (PO:0030104).
A whole plant morphology trait (TO:0000398) which is a quality of a plant embryo (PO:0009009).
A collective plant organ structure morphology trait (TO:0000842) which is a quality of a shoot system (PO:0009006).
The average dry weight of the root determined in a study.
A root system morphology trait (TO:0000985) which is the number of roots (PO:0009005) in a root system (PO:0025025).
Proportion of usable (economically significant) biomass over total (biological) biomass, expressed as a percentage.
A leaf morphology trait (TO:0000748) which is the length of a leaf (PO:0025034).
Relative yield was calculated as the ratio of biomass in stress to that of control.
A grain yield trait (TO:0000396) which is the proportion of kernels remaining after milling to remove the bran.
A shoot axis internode morphology trait (TO:0000755) which is the length of a shoot axis internode (PO:0005005).
A seed morphology trait (TO:0000184) which is the length of a seed (PO:0009010).
A seed morphology trait (TO:0000184) which is the width of a seed (PO:0009010).
A panicle morphology trait (TO:0000847) which is the average number of panicles per plant in a study.
number of effective tiller per plant (related)
seed setting tillers per plant (related)
Relative yield is calculated as a ratio of yield in stress to that of control.
A fruit quality trait (TO:0002728) that is the commercial and /or economical value of the grain (i.e. fruit (PO:0009001)), or its overall improvement.
A seed morphology trait (TO:0000184) which is the weight of a seed (PO:0009010).
A multi-tissue plant structure morphology trait (TO:0000836) which is a quality of a seed (PO:0009010).
A whole plant morphology trait (TO:0000398) which is the height of a whole plant (PO:0000003).
A grain yield trait (TO:0000396) which is the amount of whole (3/4 of original length or longer) milled kernels separated from the total amount of milled rice.
A carpel morphology trait (TO:0006012) which is a quality of a pistil.
A root morphology trait (TO:0000043) which is the length of a root (PO:0009005).
A plant quality trait (TO:0000597) which is the amount of moisture in a plant structure (PO:0009011).
A shoot system morphology trait (TO:0000077) which is the number of leaves (PO:0025034) in a shoot system (PO:0009006) of a plant.
A grain weight (TO:0000919) which is the weight of a sample of 100 grains (caryopsis fruit; PO:0030104), with the caryopsis hull (PO:0006000).
An inflorescence morphology trait (TO:0000373) trait which is the length of an inflorescence (PO:0009049).
A plant trait (TO:0000387) which is a quality of a chemical entity (CHEBI:24431), a plant metabolite (CHEBI:76924), or a molecular function (GO:0003674), which occurs in a cellular component (GO:0005575), plant anatomical entity (PO:0025131) or during a plant structure development stage (PO:0009012).
The ratio determined from the parameters evaluated for root length and the shoot length in a study.
root length to shoot length ratio (exact)
A root morphology trait (TO:0000043) which is the weight of a root (PO:0009005).
The trait associated with an assay to determine the affected metabolite's profile.
A yield trait (TO: 0000371) that is the amount of a plant structure (PO:0009011) or portion of plant substance (PO:0025161) produced by the shoot system (PO:0009006) which is harvested.
A shoot axis morphology trait (TO:0000739) which is the quality of a stem (PO:0009047).
A leaf morphology trait (TO:0000748) which is the width of a leaf (PO:0025034).
A plant trait (TO:0000387) which is a harvestable product that is a plant anatomical entity (PO:0025131) or one or more constituent cellular components (GO:0005575) contained therein.
A reproductive shoot system morphology trait (TO:0000786) that is a quality of an inflorescence (PO:0009049).
A grain weight (TO:0000919) which is the weight of a sample of 1000 grains (caryopsis fruit; PO:0030104), with the caryopsis hull (PO:0006000).
A measurable or observable characteristic of a cellular component (GO:0005575), biological process (GO:0008150) or molecular function (GO:0003674) that is part of, or has participant a plant anatomical entity (PO:0025131) and/or a plant structure development stage (PO:0009012).
A seed morphology trait (TO:0000184) which is the size of a seed (PO:0009010).
A fruit yield trait (TO:0000871) that is the amount of grain.
A caryopsis fruit morphology trait (TO:0001079) which is the size of the grain (caryopsis fruit; PO:0030104).
A plant structure morphology trait (TO:0000839) which is a quality of a whole plant (PO:0000003).
An ear infructescence morphology trait (TO:0000976) that is the length of an ear infructescence (PO:0025597) from base to tip.
An infructescence yield trait (TO:0000936) that is the number of ears (ear infructescence; PO:0025597) on a plant or the average number present in population.
A fruit morphology trait (TO:0002629) which is the number of seeds (PO:0009010) in a fruit (PO:0009001).
Average weight of dehulled grains per plant.
Average weight of dehulled grains per panicle.
A ratio of number of tiller bearing the panicles to the total number of tillers in rice.
A biochemical trait (TO:0000277) that is the amount of a particular mineral or ion constituent occurring in a plant anatomical entity (PO:0025131).
Amount of carbon present in the dry mass.
A leaf morphology trait (TO:0000748) which is the composition of a leaf (PO:0025034).
A pigment content trait (TO:0000494) which is a measure of the chlorophyll a and/or chlorophyll b content in a plant structure (PO:0009011).
A reproductive shoot system morphology trait (TO:0000786) which is a quality of a flower (PO:0009046).
A leaf morphology trait (TO:0000505) which is the weight of a leaf (PO:0025034).
A leaf morphology trait (TO:0000748) which is the total area of a leaf (PO:0025034).
A leaf morphology trait (TO:0000748) which is the ratio of leaf length (TO:0000135) to leaf width (TO:0000370).
A leaf composition trait (TO:0000493) which is the amount of nitrogen (CHEBI:51143) in the leaf (PO:0025034).
A shoot system morphology trait (TO:0000077) which is the number of rhizomes present in a shoot system (PO:0009006).
A shoot axis morphology trait (TO:0000739) which is a quality of a rhizome (PO:0004542).
The dry weight of the shoot without inflorescence.
A rhizome morphology trait (TO:0000549) which is the length of a rhizome (PO:0004542).
A rhizome morphology trait (TO:0000549) which is the dry weight of a rhizome (PO:0004542).
Weight of the shoot without inflorescence.
Fresh weight of the shoot without inflorescence.
A stem morphology trait (TO:0000361) which is the length of the stem (PO:0009047).
The average fresh weight of the root determined in a study.
A reproductive shoot system morphology trait (TO:0000786) which is the number of inflorescences (PO:0009049).
An infructescence morphology trait (TO:0000920) that is the average weight (mass) of an infructescence bearing mature fruit (PO:0009001).
A grain weight (TO:0000919) which is the average weight of a grain (caryopsis fruit; PO:0030104), including the caryopsis hull (PO:0006000).
A plant trait (TO:0000387) that contributes to the overall utility, nutritional, or economic value of a plant, plant structure (PO:0009011) or plant product
A biochemical trait which is a quality of an enzymatic reaction.
A mineral and ion content trait (TO:0000465) which is the potassium cation (CHEBI:29103) composition in a plant structure (PO:0009011).
An inflorescence width (TO:0000804) trait which is the width of a spike inflorescence (PO:0030117).
They are non-nutritive plant chemicals that have protective or disease preventive properties.
An inflorescence morphology trait (TO:0000373) which is the height of an inflorescence (PO:0009049) measured from ground to the attachment point.
An infructescence morphology trait (TO:0000920) which is the number of rows of kernels per ear infructescence (PO:0025597).
A infructescence yield trait (TO:0000936) which is the length of a kernel row from base to where kernels end on the ear infructescence (PO:0025597).
A yield trait (TO:0000371) which is the yield of starch from a plant structure (PO:0009011).
A caryopsis fruit morphology trait (TO:0001079) which is the length of a grain (caryopsis fruit; PO:0030104).
A multi-tissue plant structure morphology trait (TO:0000836) which is a quality of a plant organ (PO:0009008).
A plant organ morphology trait (TO:0000736) which is a quality of a plant axis (PO:0025004).
A plant axis morphology trait (TO:0000738) which is a quality of a shoot axis (PO:0025029).
A shoot axis morphology trait (TO:0000739) which is a quality of a branch (PO:0025073).
A plant axis morphology trait (TO:0000738) which is quality of a tuber (PO:0004543).
A tuber morphology trait (TO:0000741) which is a quality of a subterranean shoot axis tuber (PO:0004547).
subterranean shoot axis tuber morphology trait
A subterranean shoot axis tuber morphology trait (TO:0000742) which is the size of a subterranean shoot axis tuber (PO:0004547).
A subterranean shoot axis tuber morphology trait (TO:0000742) which is the mass of a subterranean shoot axis tuber (PO:0004547).
A plant organ morphology trait (TO:0000736) which is quality of a phyllome (PO:0006001).
A phyllome morphology trait (TO:0000747) which is quality of a leaf (PO:0025034).
A cardinal organ part of a multi-tissue plant structure morphology trait (TO:0000837) which is a quality of a cardinal organ part (PO:0025001).
A cardinal organ part morphology trait (TO:0000754) which is a quality of a shoot axis internode (PO:0005005).
A shoot axis internode morphology trait (TO:0000755) which is a quality of a stem internode (PO:0020142).
A shoot axis morphology trait (TO:0000739) which is a quality of an inflorescence axis (PO:0020122).
An inflorescence axis morphology trait (TO:0000782) which is the size of an inflorescence axis (PO:0020122).
A shoot system morphology trait (TO:0000077) that is a quality of a reproductive shoot system (PO:0025082).
reproductive shoot system morphology trait
An inflorescence morphology trait (TO:0000373) which is the weight of an inflorescence (PO:0009049).
An inflorescence morphology trait (TO:0000373) which is the width of an inflorescence (PO:0009049).
A plant structure morphology trait (TO:0000839) which is a quality of a multi-tissue plant structure (PO:0025496).
multi-tissue plant structure morphology trait
A plant structure morphology trait (TO:0000839) which is a quality of a cardinal organ part of a multi-tissue plant structure (PO:0025498).
cardinal part of a multi-tissue plant structure morphology trait
A plant morphology trait (TO:0000017) which is a quality of a plant structure (PO:0009011).
A plant structure morphology trait (TO:0000839) which is a quality of a collective plant structure (PO:0025497).
collective plant structure morphology trait
A collective plant structure morphology trait (TO:0000840) which is a quality of a collective plant organ structure (PO:0025007).
collective plant organ structure morphology trait
A plant structure morphology trait (TO:0000839) which is a quality of a portion of plant tissue (PO:0009007).
portion of plant tissue morphology trait
A collective plant organ structure morphology trait (TO:0000842) which is a quality of a collective phyllome structure (PO:0025023).
collective phyllome structure morphology trait
An inflorescence morphology trait (TO:0000373) which is a quality of a panicle inflorescence (PO:0030123).
A flower morphology trait (TO:0000499) which is the length of a flower (PO:0009046).
A plant organ morphology trait (TO:0000736) which is a quality of a floral organ (PO:0025395).
A phyllome morphology trait (TO:0000747) which is a quality of a sporophyll (PO:0009026).
A sporophyll morphology trait (TO:0000866) which is a quality of a megasporophyll (PO:0009027).
A shoot system yield trait (TO:0000327) which is comprised of leaves (PO:0025034) or parts of leaves.
A shoot system yield trait (TO:0000327) which is the yield of fruits (PO:0009001).
A leaf weight trait (TO:0000505) which is the the measure of the wet weight of a leaf (PO:0025034).
A stem morphology trait (TO:0000361) which is the size of a stem (PO:0009047).
An infructescence morphology trait (TO:0000920) which is the number of fruits (PO:0009001).
A harvest index (TO:0000128) which is the percent of usable fruit (PO:0009001).
A harvest index (TO:0000128) which is the percent of usable leaves (PO:0025034).
A harvest index (TO:0000128) which is the percent of usable seeds (PO:0009010).
A shoot system yield trait (TO:0000327) which is the yield of seeds (PO:0009010).
A caryopsis fruit morphology trait (TO:0001079) which is the weight of a caryopsis fruit (grain or kernel; PO:0030104).
A reproductive shoot system morphology trait (TO:0000786) which is a quality of the infructescence (PO:0006342).
A shoot axis morphology trait (TO:0000739) which is a quality of an infructescence axis (PO:0025242).
An infructescence axis morphology trait (TO:0000921) which is the weight of a cob.
An ear infructescence morphology trait (TO:0000976) that is the weight of an ear infructescence (PO:0025597).
A plant quality trait (TO:0000597) which is the commercial and /or economical value of a seed (PO:0009010) , or its overall improvement.
A shoot system yield trait (TO:0000327) which is a quality of an infructescence (PO:0006342), or the number born on a plant.
An infructescence yield trait (TO:0000936) that is the number of kernels (fruit; PO:0009001) per ear infructescence (PO:0025597).
An infructescence yield trait (TO:0000936) that is the number of kernels (fruit; PO:0009001) per row on an ear infructescence (PO:0025597).
An infructescence yield trait (TO:0000936) which is the number of ranks of cupules per ear infructescence (PO:0025597).
A stem morphology trait (TO:0000361) which is the weight of a stem (PO:0009047).
A shoot system morphology trait (TO:0000077) which is the number of stems (PO:0009047).
An infructescence axis morphology trait (TO:0000921) which is the length of a cob.
An infructescence axis morphology trait (TO:0000921) which is the width of a cob.
An infructescence axis morphology trait (TO:0000921) which is the area of a cob.
An inflorescence morphology trait (TO:0000373) which is a quality of an ear inflorescence (PO:0020136).
A caryopsis fruit morphology trait (TO:0001079) which is the width of a grain (PO:0009001).
An infructescence morphology trait (TO:0000920) which is a quality of the ear infructescence (PO:0025597).
A collective plant organ structure morphology trait (TO:0000842) which is a quality of a root system (PO:0025025).
A leaf weight trait (TO:0000505) which is the dry weight of a leaf (PO:0025034).
A ratio of root dry weight to total plant dry weight.
root dry weight to total plant dry weight ratio (related)
Volume of the sap exudate collected from the cut parts of a plant.
A mineral and ion content trait (TO:0000465) which is the phosphorus cation (CHEBI:33467) composition in a plant structure (PO:0009011).
It is a ratio of harvest index in stress to that of control environment.
A stem morphology trait (TO:0000361) which is the width of a stem (PO:0009047).
A yield trait (TO:0000371) which is the yield of roots (PO:0009005).
A root system morphology trait (TO:0000985) which is the width of the root system (PO:0025025).
A shoot system yield trait (TO:0000327) which is the yield of shoot axis tubers (PO:0004543).
A fruit morphology trait (TO:0002629) which is a quality of a berry fruit (PO:0030108).
A fruit morphology trait (TO:0002629) which is a quality of a caryopsis fruit (PO:0030104).
A fruit morphology trait (TO:0002629) which is a quality of a legume fruit (PO:0030100).
A berry fruit morphology trait (TO:0001077) which is the weight of a berry fruit (PO:0030108).
A legume fruit morphology trait (TO:0001082) which is the weight of a legume fruit (PO:0030100).
A berry fruit morphology trait (TO:0001077) which is a quality of a pepo fruit (PO:0030111).
A floral organ morphology trait (TO:0000862) which is the size of a floral organ (PO:0025395).
A pistil morphology trait (TO:0000223) which is the size of a pistil.
A pistil morphology trait (TO:0000223) which is the length of a pistil.
A floral organ morphology trait (TO:0000862) which is the length of a floral organ (PO:0025395).
A floral organ morphology trait (TO:0000862) which is the width of a floral organ (PO:0025395).
A fruit morphology trait (TO:0002629) which is the size of a fruit (PO:0009001).
A fruit morphology trait (TO:0002629) which is the length of a fruit (PO:0009001).
A fruit morphology trait (TO:0002629) which is the width of a fruit (PO:0009001).
A multi-tissue plant structure morphology trait (TO:0000836) which is a quality of a fruit (PO:0009001).
A leaf morphology trait (TO:0000748) which is the size of a leaf (PO:0025034).
A pistil morphology trait (TO:0000223) which is the number of pistils in the gynoecium (PO:0009062).
A plant structure morphology trait (TO:0000839) which is a quality of a plant cell (PO:0009002).
A plant cell morphology trait (TO:0002683) which is the size of a plant cell (PO:0009002) type.
A plant quality trait (TO:0000597) which is the commercial and /or economical value of a fruit (PO:0009001) , or its overall improvement.
An inflorescence morphology trait (TO:0000582 ) which is the number of flowers (PO:0009046).
A fruit morphology trait (TO:0002629) that is the weight of a fruit (PO:0009001).
A fruit number trait (TO:0000894) which is the number of grains (caryopsis fruit; PO:0030104) in an infructescence (PO:0006342).
A stem weight trait (TO:0000952) which is the fresh weight of a stem (PO:0009047).
A stem weight trait (TO:0000952) which is the dry weight of a stem (PO:0009047).
An infructescence weight trait (TO:0000583) which is the fresh weight of an infructescence (PO:0006342).
An infructescence weight trait (TO:0000583) which is the dry weight of an infructescence (PO:0006342).
A fruit weight trait (TO:0002746) that is the fresh weight of a fruit (PO:0009001).
A fruit weight trait (TO:0002746) that is the dry weight of a fruit (PO:0009001).
A reproductive shoot system morphology trait (TO:0000786) which is a quality of a second order infructescence (PO:0025241).
second order infructescence morphology trait
A second order infructescence morphology trait (TO:0003006) which is the fresh weight of a second order infructescence (PO:0025241).
A second order infructescence morphology trait (TO:0003006) which is the dry weight of a second order infructescence (PO:0025241).
A tuberous root tuber morphology trait (TO:1000007) which is the weight of a tuberous root tuber (PO:0025476).
A tuberous root tuber weight trait (TO:0003009) which is the fresh weight of a tuberous root tuber (PO:0025476).
A tuberous root tuber weight trait (TO:0003009) which is the dry weight of a tuberous root tuber (PO:0025476).
A subterranean shoot axis tuber weight trait (TO:0000746) which is the fresh weight of a subterranean shoot axis tuber (PO:0004547).
subterranean shoot axis tuber fresh weight
A subterranean shoot axis tuber weight trait (TO:0000746) which is the dry weight of a subterranean shoot axis tuber (PO:0004547).
subterranean shoot axis tuber dry weight
A grain weight (TO:0000919) which is the fresh weight of a grain (caryopsis fruit; PO:0030104), including the caryopsis hull (PO:0006000).
A grain weight (TO:0000919) which is the dry weight of a grain (caryopsis fruit; PO:0030104), including the caryopsis hull (PO:0006000).
A 100-grain weight (TO:0000269) which is the fresh weight of a sample of 100 grains (caryopsis fruit; PO:0030104), with the caryopsis hull (PO:0006000).
A grain weight (TO:0000269) which is the dry weight of a sample of 100 grains (caryopsis fruit; PO:0030104), with the caryopsis hull (PO:0006000).
A grain weight (TO:0000382) which is the fresh weight of a sample of 1000 grains (caryopsis fruit; PO:0030104), with the caryopsis hull (PO:0006000).
A grain weight (TO:0000382) which is the dry weight of a sample of 1000 grains (caryopsis fruit; PO:0030104), with the caryopsis hull (PO:0006000).
An infructescence weight trait (TO:0000014) which is the fresh weight of a panicle inflorescence (PO:0030123).
An infructescence weight trait (TO:0000014) which is the dry weight of a panicle inflorescence (PO:0030123).
An ear infructescence weight trait (TO:0000923) that is the fresh weight of an ear infructescence (PO:0025597).
An ear infructescence weight trait (TO:0000923) that is the dry weight of an ear infructescence (PO:0025597).
A cob weight trait (TO:0000922) which is the fresh weight of a cob (ear infructescence axis; PO:0025623).
A cob weight trait (TO:0000922) which is the dry weight of a cob (ear infructescence axis; PO:0025623).
An inflorescence weight (TO:0000803) trait which is the weight of a spike inflorescence (PO:0030117).
A spike weight (TO:0003026) trait which is the fresh weight of a spike inflorescence (PO:0030117).
A spike weight (TO:0003026) trait which is the dry weight of a spike inflorescence (PO:0030117).
A legume fruit weight trait (TO:0001092) which is the dry weight of a legume fruit (PO:0030100).
A legume fruit weight trait (TO:0001092) which is the fresh weight of a legume fruit (PO:0030100).
A pepo fruit morphology trait (TO:0001098) which is the weight of a pepo fruit (PO:0030111).
A pepo fruit weight trait (TO:0003031) which is the fresh weight of a pepo fruit (PO:0030111).
A pepo fruit weight trait (TO:0003031) which is the dry weight of a pepo fruit (PO:0030111).
A moisture content trait (TO:0000228) which is the amount of moisture of a leaf (PO:0025034).
A moisture content trait (TO:0000228) which is the amount of moisture of a stem (PO:0009047).
A moisture content trait (TO:0000228) which is the amount of moisture of a root (PO:0009005).
A moisture content trait (TO:0000228) which is the amount of moisture of the whole plant (PO:0000003).
A moisture content trait (TO:0000228) which is the amount of moisture of the shoot system (PO:0009006).
A moisture content trait (TO:0000228) which is the amount of moisture of a infructescence (PO:0006342).
A moisture content trait (TO:0000228) which is the amount of moisture of a pepo fruit (PO:0030111).
A moisture content trait (TO:0000228) which is the amount of moisture of a second order infructescence (PO:0025241).
second order infructescence moisture content
A moisture content trait (TO:0000228) which is the amount of moisture of a tuberous root tuber (PO:0025476).
A moisture content trait (TO:0000228) which is the amount of moisture of a subterranean shoot axis tuber (PO:0004547).
subterranean shoot axis tuber moisture content
A moisture content trait (TO:0000228) which is the amount of moisture of a legume fruit (PO:0030100).
A moisture content trait (TO:0000228) which is the amount of moisture of a panicle inflorescence (PO:0030123).
A moisture content trait (TO:0000228) which is the amount of moisture of a ear infructescence (PO:0025597).
A moisture content trait (TO:0000228) which is the amount of moisture of a ear infructescence axis (PO:0025623).
A moisture content trait (TO:0000228) which is the amount of moisture of a spike inflorescence (PO:0030117).
A potassium content trait (TO:0000609) which is the amount of potassium cation (CHEBI:29103) in a leaf (PO:0025034).
A potassium content trait (TO:0000609) which is the amount of potassium cation (CHEBI:29103) in a stem (PO:0009047).
A potassium content trait (TO:0000609) which is the amount of potassium cation (CHEBI:29103) in an infructescence (PO:0006342).
A potassium content trait (TO:0000609) which is the amount of potassium cation (CHEBI:29103) in a pepo fruit (PO:0030111).
A potassium content trait (TO:0000609) which is the amount of potassium cation (CHEBI:29103) in a second order infructescence (PO:0025241).
second order infructescence potassium content
A potassium content trait (TO:0000609) which is the amount of potassium cation (CHEBI:29103) in a tuberous root tuber (PO:0025476).
A moisture content trait (TO:0000228) which is the amount of potassium cation (CHEBI:29103) in a subterranean shoot axis tuber (PO:0004547).
subterranean shoot axis tuber potassium content
A potassium content trait (TO:0000609) which is the amount of potassium cation (CHEBI:29103) in a caryopsis fruit (PO:0030104).
A potassium content trait (TO:0000609) which is the amount of potassium cation (CHEBI:29103) in a panicle inflorescence (PO:0030123).
A potassium content trait (TO:0000609) which is the amount of potassium cation (CHEBI:29103) in a ear infructescence (PO:0025597).
A potassium content trait (TO:0000609) which is the amount of potassium cation (CHEBI:29103) in a ear infructescence axis (PO:0025623).
A potassium content trait (TO:0000609) which is the amount of potassium cation (CHEBI:29103) in a spike inflorescence (PO:0030117).
A potassium content trait (TO:0000609) which is the amount of potassium cation (CHEBI:29103) in a legume fruit (PO:0030100).
A nitrogen content trait (TO:0020093) which is the amount of nitrogen (CHEBI:51143) in a stem (PO:0009047).
A nitrogen content trait (TO:0020093) which is the amount of nitrogen (CHEBI:51143) in an infructescence (PO:0006342).
A nitrogen content trait (TO:0020093) which is the amount of nitrogen (CHEBI:51143) in a pepo fruit (PO:0030111).
A nitrogen content trait (TO:0020093) which is the amount of nitrogen (CHEBI:51143) in a second order infructescence (PO:0025241).
second order infructescence nitrogen content
A nitrogen content trait (TO:0020093) which is the amount of nitrogen (CHEBI:51143) in a tuberous root tuber (PO:0025476).
A moisture content trait (TO:0000228) which is the amount of nitrogen (CHEBI:51143) in a subterranean shoot axis tuber (PO:0004547).
subterranean shoot axis tuber nitrogen content
A nitrogen content trait (TO:0020093) which is the amount of nitrogen (CHEBI:51143) in a caryopsis fruit (PO:0030104).
A nitrogen content trait (TO:0020093) which is the amount of nitrogen (CHEBI:51143) in a panicle inflorescence (PO:0030123).
A nitrogen content trait (TO:0020093) which is the amount of nitrogen (CHEBI:51143) in a ear infructescence (PO:0025597).
A nitrogen content trait (TO:0020093) which is the amount of nitrogen (CHEBI:51143) in a ear infructescence axis (PO:0025623).
A nitrogen content trait (TO:0020093) which is the amount of nitrogen (CHEBI:51143) in a spike inflorescence (PO:0030117).
A nitrogen content trait (TO:0020093) which is the amount of nitrogen (CHEBI:51143) in a legume fruit (PO:0030100).
A nitrogen content trait (TO:0020093) which is the amount of nitrogen (CHEBI:51143) in a root (PO:0009005).
A phosphorus content trait (TO:0001024) which is the amount of phosphorus cation (CHEBI:33467) in a stem (PO:0009047).
A phosphorus content trait (TO:0001024) which is the amount of phosphorus cation (CHEBI:33467) in an infructescence (PO:0006342).
A phosphorus content trait (TO:0001024) which is the amount of phosphorus cation (CHEBI:33467) in a pepo fruit (PO:0030111).
banana finger phosphorus content (exact)
A phosphorus content trait (TO:0001024) which is the amount of phosphorus cation (CHEBI:33467) in a second order infructescence (PO:0025241).
second order infructescence phosphorus content
A phosphorus content trait (TO:0001024) which is the amount of phosphorus cation (CHEBI:33467) in a tuberous root tuber (PO:0025476).
A moisture content trait (TO:0000228) which is the amount of phosphorus cation (CHEBI:33467) in a subterranean shoot axis tuber (PO:0004547).
subterranean shoot axis tuber phosphorus content
A phosphorus content trait (TO:0001024) which is the amount of phosphorus cation (CHEBI:33467) in a caryopsis fruit (PO:0030104).
A phosphorus content trait (TO:0001024) which is the amount of phosphorus cation (CHEBI:33467) in a panicle inflorescence (PO:0030123).
A phosphorus content trait (TO:0001024) which is the amount of phosphorus cation (CHEBI:33467) in a ear infructescence (PO:0025597).
A phosphorus content trait (TO:0001024) which is the amount of phosphorus cation (CHEBI:33467) in a ear infructescence axis (PO:0025623).
A phosphorus content trait (TO:0001024) which is the amount of phosphorus cation (CHEBI:33467) in a spike inflorescence (PO:0030117).
A phosphorus content trait (TO:0001024) which is the amount of phosphorus cation (CHEBI:33467) in a legume fruit (PO:0030100).
A carbon content trait (TO:0000466) which is the amount of carbon (CHEBI:27594) in a leaf (PO:0025034).
A carbon content trait (TO:0000466) which is the amount of carbon (CHEBI:27594) in a stem (PO:0009047).
A carbon content trait (TO:0000466) which is the amount of carbon (CHEBI:27594) in a root (PO:0009005).
A carbon content trait (TO:0000466) which is the amount of carbon (CHEBI:27594) in an infructescence (PO:0006342).
A carbon content trait (TO:0000466) which is the amount of carbon (CHEBI:27594) in a pepo fruit (PO:0030111).
A carbon content trait (TO:0000466) which is the amount of carbon (CHEBI:27594) in a second order infructescence (PO:0025241).
second order infructescence carbon content
A carbon content trait (TO:0000466) which is the amount of carbon (CHEBI:27594) in a tuberous root tuber (PO:0025476).
A moisture content trait (TO:0000228) which is the amount of carbon (CHEBI:27594) in a subterranean shoot axis tuber (PO:0004547).
subterranean shoot axis tuber carbon content
A carbon content trait (TO:0000466) which is the amount of carbon (CHEBI:27594) in a caryopsis fruit (PO:0030104).
A carbon content trait (TO:0000466) which is the amount of carbon (CHEBI:27594) in a panicle inflorescence (PO:0030123).
A carbon content trait (TO:0000466) which is the amount of carbon (CHEBI:27594) in a ear infructescence (PO:0025597).
A carbon content trait (TO:0000466) which is the amount of carbon (CHEBI:27594) in a ear infructescence axis (PO:0025623).
A carbon content trait (TO:0000466) which is the amount of carbon (CHEBI:27594) in a spike inflorescence (PO:0030117).
A carbon content trait (TO:0000466) which is the amount of carbon (CHEBI:27594) in a legume fruit (PO:0030100).
A megasporophyll morphology trait (TO:0000867) which is a quality of a carpel (PO:0009030).
A carpel morphology trait (TO:0006012) which is the number of carpels (PO:0009030) in the gynoecium (PO:0009062).
An inflorescence morphology trait (TO:0000373) which is the variation in size of inflorescence (PO:0009049).
A panicle inflorescence morphology trait (TO:0000847) which is the variation in size of panicle inflorescence (PO:0030123).
The average width of a plant measured across an axis such as the main stem/stalk.
Leaf Area Index (LAI) is the ratio of total upper leaf surface of vegetation divided by the surface area of the land on which the vegetation grows.
A chlorophyll content trait (TO:0000495) which is the chlorophyll content of a leaf (PO:0025034).
A grain yield trait (TO:0000396) which is the ratio of grain weight (TO:0000919) to panicle weight (TO:0000014).
A potassium content trait (TO:0000609) which is the potassium cation (CHEBI:29103) composition in a shoot system (PO:0009006).
The trait takes into account energy losses occurring in the animal in faeces, urine and CH4 and estimates how much energy (in calories or joules) a given unit of ground stover is actually available for meat and milk production . Value derived from chemical and in vitro analysis of dried and ground stover.
A trait to measure percent nitrogen concentration in the stover sample used for predicting crude protein (CP) content of stover by multiplication with a factor of 6.25 (CP = N x 6.25). This concentration is one of the criteria to assess the quality of fodder. Value derived from the analysis of stover using Near Infrared Reflectance Spectrophotometry (NIRS).
A mineral and ion content trait (TO:0000465) which is the amount of nitrogen (CHEBI:51143) in a plant structure (PO:0009011).
A plant cell morphology trait (TO:0002683) which is the length of a plant cell (PO:0009002).
A phosphorus content trait (TO:0001024) which is the phosphorus cation (CHEBI:33467) composition in a shoot system (PO:0009006).
A trait to measure the ethanol yield from the industrial processing of feedstock (biomass).
A tuber morphology trait (TO:0000741) which is the quality of a tuberous root tuber (PO:0025476).
A whole plant morphology trait (TO:0000398) which is the size of a whole plant (PO:0000003).
A potassium content trait (TO:0000609) which is the potassium cation (CHEBI:29103) composition in a root system (PO:0025025).
A phosphorus content trait TO:0001024 which is the phosphorus cation (CHEBI:33467) composition in a root system (PO:0025025).
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.
Multicellular, connected anatomical structure that has multiple organs as parts and whose parts work together to achieve some shared function.
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.
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.
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.
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 structure that overlaps the outer epithelial layer and is adjacent to the space surrounding the organism.
An anatomical structure that develops (entirely or partially) from the ectoderm.
A portion of tissue that is part of an embryo.
A 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 unit which is a standard measure of the distance between two points.
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 dimension in which events occur in sequence.
t/ha
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
A state of being, an external or environmental factor or a treatment observed or administered prior to or concurrent with an investigative procedure such as an assessment of a morphological or physiological state or property in a single individual or sample or in a group of individuals or samples, especially a state, factor or treatment which has the potential to influence the outcome of such an assessment.
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.
Core is an instance of a grouping of terms from an ontology or ontologies. It is used by the ontology to identify main classes.
obsolete_core
placeholder removed
terms merged
An editor note should explain what were the merged terms and the reason for the merge.
term imported
This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use.
term split
This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split and indicate the URIs of the new terms created.
This is to be used if none of the existing instances cover the reason for obsolescence. An editor note should indicate this new reason.
We expect to be able to mine these new reasons and add instances as required.
obsolete_other
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.
A reference to a place on the Earth, by its name or by its geographical location.
microeinstein per square meter per second
kg/ha
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'
This rule is dubious: added as a quick fix for expected inference in GO-CAM. The problem is most acute for transmembrane proteins, such as receptors or cell adhesion molecules, which have some subfunctions inside the cell (e.g. kinase activity) and some subfunctions outside (e.g. ligand binding). Correct annotation of where these functions occurs leads to incorrect inference about the location of the whole protein. This should probably be weakened to "... -> overlaps"
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).