The Ontology for Nutritional Studies (ONS) has been developed as part of the ENPADASI European project (http://www.enpadasi.eu/) with the aim to define a common language and building ontologies for nutritional studies.
ENPADASI_WP4
ONS
editor preferred label
editor preferred term
editor preferred term~editor preferred label
The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English)
PERSON:Daniel Schober
example of usage
A phrase describing how a 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.
has curation status
PERSON:Alan Ruttenberg
PERSON:Bill Bug
PERSON:Melanie Courtot
definition
A property representing the English language definitions of what NCI means by the concept. They may also include information about the definition's source and attribution in a form that can easily be interpreted by software.
English language definitions of what NCI means by the concept. These are limited to 1024 characters. They may also include information about the definition's source and attribution in a form that can easily be interpreted by software.
The official OBI definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.
The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.
2012-04-05: Barry Smith The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible. Can you fix to something like: A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property. Alan Ruttenberg Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. On the specifics of the proposed definition: We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with.
editor note
An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology.
term editor
Name of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several people
20110707, MC: label update to term editor and definition modified accordingly. See https://github.com/information-artifact-ontology/IAO/issues/115.
alternative label
A label for a class or property that can be used to refer to the class or property instead of the preferred rdfs:label. Alternative labels should be used to indicate community- or context-specific labels, abbreviations, shorthand forms and the like.
alternative term
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
ontology term requester
The name of the person, project, or organization that motivated inclusion of an ontology term by requesting its addition.
imported from
For external terms/classes, the ontology from which the term was imported
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/>
elucidation
person:Alan Ruttenberg
Person:Barry Smith
Primitive terms in a highest-level ontology such as BFO are terms which are so basic to our understanding of reality that there is no way of defining them in a non-circular fashion. For these, therefore, we can provide only elucidations, supplemented by examples and by axioms
has associated axiom(nl)
Person:Alan Ruttenberg
An axiom associated with a term expressed using natural language
has associated axiom(fol)
An axiom expressed in first order logic using CLIF syntax
term replaced by
Use on obsolete terms, relating the term to another term that can be used as a substitute
term_mapping_to_UMLS
term_mapping_to_NCIT
NIAID GSCID-BRC alternative term
An alternative term used by the National Institute of Allergy and Infectious Diseases (NIAID) Genomic Sequencing Centers for Infectious Diseases (GSCID) and Bioinformatics Resource Centers (BRC).
Super-property collecting all annotation properties assigning classes in ONS to specific subset (i.e. Metadata search). For each subset, there will be an annotation property. To assign a class to a subset, set the annotation property value to "TRUE"
in subset of ONS
Annotation properties assigning a class to the ONS-subset of metadata search classes. Set value to "TRUE" to assign a class.
in minimal requirement ONS subset
A metadata relation between a class and its taxonomic rank (eg species, family)
The present resource may be derived from the Source resource in whole or in part. Recommended best practice is to reference the resource by means of a string or number conforming to a formal identification system.
A reference to a resource from which the present resource is derived.
Source
An account of the content of the resource.
http://www.ebi.ac.uk/efo/MESH_definition_citation is an annotation property that is drawn from MESH
http://www.ebi.ac.uk/efo/MSH_definition_citation is an annotation property that is drawn from MSH
A definition citation is a document, ontology class, person or organization from which the definition of the class is derived. It is used in the same sense as a citation in literature, in that the definition may have been derived from these sources or that this definition is related to these source.
An alternative label for a class or property which has a more general meaning than the preferred name/primary label.
has broad synonym
A property representing a fully qualified synonym, contains the string, term type, source, and an optional source code if appropriate. Each subfield is deliniated to facilitate interpretation by software.
An alternative label for a class or property which has the exact same meaning than the preferred name/primary label.
Fully qualified synonym, contains the string, term type, source, and an optional source code if appropriate. Each subfield is deliniated to facilitate interpretation by software.
has exact synonym
An alternative label for a class or property which has a more specific meaning than the preferred name/primary label.
has narrow synonym
An alternative label for a class or property that has been used synonymously with the primary term name, but the usage is not strictly correct.
has related synonym
has_related_synonym
has synonym
label
is part of
a core relation that holds between a part and its whole
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.
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 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
realizes
Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process
preceded by
x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.
has measurement unit label
is about
A (currently) primitive relation that relates an information artifact to an entity.
Smith, Ceusters, Ruttenberg, 2000 years of philosophy
An information artifact IA mentions an entity E exactly when it has a component/part that denotes E
mentions
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
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
is quality measurement of
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
is quality measured as
The provides_service_consumer_with relation links the service to its primary process it provides for the consumer (as opposed to secondary processual parts of a service process such as payment or documentation). For example, a 'DNA sequencing service' provides_service_consumer_with 'DNA sequencing' as the essential process performed by the provider for the client.
A relation between a service and the primary processual part of the service that is performed by the provider for the consumer.
The relation between a data item and a conclusion where the conclusion is the output of a data interpreting process and the data item is used as an input to that process
The inverse property of is specified input of
has specified input
A relation between a completely executed planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of.
is specified input of
The inverse property of is specified output of
has specified output
A relation between a completely executed planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of.
is specified output of
A relation between continuant instances c1 and c2 where within an experiment/ protocol application, measurement of c1 is used to determine what a measurement of c2 would be.
is_proxy_for
This relation obtains between a planned process and a objective specification when the criteria specified in the objective specification are met at the end of the planned process.
the relation of the cells in the finger of the skin to the finger, in which an indeterminate number of grains are parts of the whole by virtue of being grains in a collective that is part of the whole, and in which removing one granular part does not nec- essarily damage or diminish the whole. Ontological Whether there is a fixed, or nearly fixed number of parts - e.g. fingers of the hand, chambers of the heart, or wheels of a car - such that there can be a notion of a single one being missing, or whether, by contrast, the number of parts is indeterminate - e.g., cells in the skin of the hand, red cells in blood, or rubber molecules in the tread of the tire of the wheel of the car.
Discussion in Karslruhe with, among others, Alan Rector, Stefan Schulz, Marijke Keet, Melanie Courtot, and Alan Ruttenberg. Definition take from the definition of granular parthood in the cited paper. Needs work to put into standard form
PERSON: Alan Ruttenberg
PAPER: Granularity, scale and collectivity: When size does and does not matter, Alan Rector, Jeremy Rogers, Thomas Bittner, Journal of Biomedical Informatics 39 (2006) 333-349
A relation between granular parts and the whole of which they are a part. Granular parts have indeterminate number such that removing one granular part does not necessarily damage or diminish the whole.
Discussion in Karslruhe with, among others, Alan Rector, Stefan Schulz, Marijke Keet, Melanie Courtot, and Alan Ruttenberg. With inspiration from the paper Granularity, scale and collectivity: When size does and does not matter, Alan Recto, Jeremy Rogers, Thomas Bittner, Journal of Biomedical Informatics 39 (2006) 333-349
is grain of
A relation between an organisation or person and a material entity, where the organization or person provides or supplies the material entity for others to use
A relation between a material entity and an organisation or person who owned or has license to the material entity and there was a legal transfer of ownership or licensing of the material entity to the current owner.
This relation obtains between an objective specification and a planned process when the criteria specified in the objective specification are met at the end of the planned process.
Relating a legal person or organization to an organization in the case where the legal person or organization has a role as member of the organization.
has organization member
Relating an organization to a legal person or organization.
A relation between a value specification and an entity which the specification is about.
A relation between an information content entity and a value specification that specifies its value.
has performer
A relation between a planned process and a continuant where the continuant can be a person, organization or device (such as a robot controlled by software workflow management system) that performs the planned process.
is a relationship between a process and a preceding occurrent that directly caused the later one to occur
inheres in
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.
characteristic of
bearer of
Inverse of characteristic_of
has characteristic
participates in
a relation between a continuant and a process, in which the continuant is somehow involved in the process
has participant
a relation between a process and a continuant, in which the continuant is somehow involved in the process
A relationship between a generically dependent continuant and a specifically dependent continuant or process, in which the generically dependent continuant depends on some independent continuant or process in virtue of the fact that the specifically dependent continuant or process also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants or processes.
is concretized as
A relationship between a specifically dependent continuant or process 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 or process also depends on that same independent continuant. Multiple specifically dependent continuants or processes can concretize the same generically dependent continuant.
concretizes
a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence
function of
a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence
quality of
a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence
role of
a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence
has function
a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence
has quality
has role
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
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
derives from
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
derives into
is location of
a relation between two independent continuants, the location and the target, in which the target is entirely within the location
location of
located in
a relation between two independent continuants, the target and the location, in which the target is entirely within the location
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.
immediately preceded by
x overlaps y if and only if there exists some z such that x has part z and z part of y
overlaps
x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed.
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
capable of
x surrounded_by y if and only if (1) x is adjacent to y and for every region r that is adjacent to x, r overlaps y (2) the shared boundary between x and y occupies the majority of the outermost boundary of x
surrounded by
x adjacent to y if and only if x and y share a boundary.
adjacent 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
p has output c iff c is a participant in p, c is present at the end of p, and c is not present in the same state at the beginning of p.
has output
A relationship that holds between a substance and a chemical entity, if the chemical entity is part of the substance, and the chemical entity forms the biologically active component of the substance.
q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w.
characteristic of part of
A relationship that is mediated in some way by the environment or environmental feature (ENVO:00002297)
ecologically related to
A mereological relationship or a topological relationship
mereotopologically related to
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
p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q.
An interaction relationship in which at least one of the partners is an organism and the other is either an organism or an abiotic entity with which the organism interacts.
A biotic interaction where one organism consumes a material entity through a type of mouth or other oral opening.
A relationship between a material entity and a process where the material entity has some causal role that influences the process
p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q.
s determined by f if and only if s is a type of system, and f is a material entity that is part of s, such that f exerts a strong causal influence on the functioning of s, and the removal of f would cause the collapse of s.
A relation that holds between an attribute or a qualifier and another attribute.
participates in a biotic-biotic interaction with
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
is related to
has measurement value
A relation between a value specification and a number that quantifies it.
has specified value
A relation between a value specification and a literal.
A function that processes a set of inputs and results in a set of outputs, or associates arguments (inputs) with values (outputs).
Search or query a data resource and retrieve entries and / or annotation.
Query scientific literature, in search for articles, article data, concepts, named entities, or for statistics.
Search a database (or other data resource) with a supplied query and retrieve entries (or parts of entries) that are similar to the query.
Protein and peptide identification, especially in the study of whole proteomes of organisms.
Whole genomes of one or more organisms, or genomes in general, such as meta-information on genomes, genome projects, gene names etc.
The systematic study of metabolites, the chemical processes they are involved, and the chemical fingerprints of specific cellular processes in a whole cell, tissue, organ or organism.
The study of genetic material recovered from environmental samples, and associated environmental data.
The analysis of transcriptomes, or a set of all the RNA molecules in a specific cell, tissue etc.
Examples of interventions are putting health warnings on cigarette packets, providing free stop smoking services and banning smoking in public places.
A planned process that has the aim of influencing an outcome.
Oral consumption behaviour that involves swallowing a liquid material.
drinking
Oral consumption behaviour that involves chewing and swallowing some solid components
eating
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])
process
disposition
A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances.
realizable entity
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.
role
function
material entity
An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time.
Elucidation: An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time.
immaterial entity
A biological role that may be assigned to a dietary nutritional component based on supporting evidence defined at the levels of molecular interaction, cellular process or physiology.
dietary role
A biological role in humans that may be assigned to a dietary nutritional component based on supporting evidence defined at the levels of molecular interaction, cellular process or physiology.
human dietary role
Aldehydic parent sugars (polyhydroxy aldehydes H[CH(OH)]nC(=O)H, n ≥ 2) and their intramolecular hemiacetals.
A nucleobase-containing molecular entity with a polymeric structure comprised of a linear sequence of 13 or more nucleotide residues.
Any member of the class of organooxygen compounds that is a polyhydroxy-aldehyde or -ketone or a lactol resulting from their intramolecular condensation (monosaccharides); substances derived from these by reduction of the carbonyl group (alditols), by oxidation of one or more hydroxy groups to afford the corresponding aldehydes, ketones, or carboxylic acids, or by replacement of one or more hydroxy group(s) by a hydrogen atom; and polymeric products arising by intermolecular acetal formation between two or more such molecules (disaccharides, polysaccharides and oligosaccharides). Carbohydrates contain only carbon, hydrogen and oxygen atoms; prior to any oxidation or reduction, most have the empirical formula Cm(H2O)n. Compounds obtained from carbohydrates by substitution, etc., are known as carbohydrate derivatives and may contain other elements. Cyclitols are generally not regarded as carbohydrates.
Amide derived from two or more amino carboxylic acid molecules (the same or different) by formation of a covalent bond from the carbonyl carbon of one to the nitrogen atom of another with formal loss of water. The term is usually applied to structures formed from α-amino acids, but it includes those derived from any amino carboxylic acid. X = OH, OR, NH2, NHR, etc.
High molecular weight, linear polymers, composed of nucleotides containing deoxyribose and linked by phosphodiester bonds; DNA contain the genetic information of organisms.
An aldohexose used as a source of energy and metabolic intermediate.
'Lipids' is a loosely defined term for substances of biological origin that are soluble in nonpolar solvents. They consist of saponifiable lipids, such as glycerides (fats and oils) and phospholipids, as well as nonsaponifiable lipids, principally steroids.
Any six-carbon monosaccharide which in its linear form contains either an aldehyde group at position 1 (aldohexose) or a ketone group at position 2 (ketohexose).
Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity.
Any vitamin that dissolves in fats and are stored in body tissues. Unlike the water-soluble vitamins, they are stored in the body for long periods of time and generally pose a greater risk for toxicity when consumed in excess.
fat-soluble vitamin (role)
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 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).
Any polyatomic entity that is an electrically neutral entity consisting of more than one atom.
An oxoacid containing a single carboxy group.
Any fatty acid with one double or triple bond in the fatty acid chain and singly bonded carbon atoms in the rest of the chain. MUFAs have positive effects on the cardiovascular system, and in diabetes treatment.
Any fatty acid containing more than one double bond. Acids in this group are reported to have cardioprotective effects; and levels are lowered in chronic fatigue syndrome.
Any fatty acid containing no carbon to carbon multiple bonds. Known to produce adverse biological effects when ingested to excess.
Any fatty acid containing at least one C=C or C≡C bond.
Any vitamin that dissolves in water and readily absorbed into tissues for immediate use. Unlike the fat-soluble vitamins, they are not stored in the body and need to be replenished regularly in the diet and will rarely accumulate to toxic levels since they are quickly excreted from the body via urine.
water-soluble vitamin (role)
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.
A biochemical role played by any micronutrient that is an organic compound. Vitamins are present in foods in small amounts and are essential to normal metabolism and biochemical functions, usually as coenzymes. The term "vitamines" (from vita + amines) was coined in 1912 by Casimir Funk, who believed that these compounds were amines.
vitamin (role)
A chemical entity constituting the smallest component of an element having the chemical properties of the element.
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 heteroorganic entity is an organic molecular entity in which carbon atoms or organic groups are bonded directly to one or more heteroatoms.
A p-block molecular entity containing any pnictogen.
Any p-block molecular entity containing a chalcogen.
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. Kekulé 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 macromolecule formed by a living organism.
A macromolecule made up of nucleotide units and hydrolysable into certain pyrimidine or purine bases (usually adenine, cytosine, guanine, thymine, uracil), D-ribose or 2-deoxy-D-ribose and phosphoric acid.
High molecular weight, linear polymers, composed of nucleotides containing ribose and linked by phosphodiester bonds; RNA is central to the synthesis of proteins.
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 π-electron system characteristic of aromatic systems and a number of out-of-plane π-electrons corresponding to the Hückel rule (4n+2).
A macromolecule is a molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass.
A hexose with a (potential) aldehyde group at one end.
Any heteroorganic entity containing at least one carbon-nitrogen bond.
Any aliphatic monocarboxylic acid derived from or contained in esterified form in an animal or vegetable fat, oil or wax. Natural fatty acids commonly have a chain of 4 to 28 carbons (usually unbranched and even-numbered), which may be saturated or unsaturated. By extension, the term is sometimes used to embrace all acyclic aliphatic carboxylic acids.
Parent monosaccharides are polyhydroxy aldehydes H[CH(OH)]nC(=O)H or polyhydroxy ketones H‒[CHOH]n‒C(=O)[CHOH]m‒H with three or more carbon atoms. The generic term 'monosaccharide' (as opposed to oligosaccharide or polysaccharide) denotes a single unit, without glycosidic connection to other such units. It includes aldoses, dialdoses, aldoketoses, ketoses and diketoses, as well as deoxy sugars, provided that the parent compound has a (potential) carbonyl group.
A biological macromolecule minimally consisting of one polypeptide chain synthesized at the ribosome.
Any molecular entity consisting of more than one atom.
Any compound containing the carbonyl group, C=O. The term is commonly used in the restricted sense of aldehydes and ketones, although it actually includes carboxylic acids and derivatives.
Organic compounds containing an oxygen atom, =O, doubly bonded to carbon or another element.
An organochalcogen compound is a compound containing at least one carbon-chalcogen bond.
An organochalcogen compound containing at least one carbon-oxygen bond.
A molecular entity consisting of two or more chemical elements.
An amide of a carboxylic acid, having the structure RC(=O)NR2. The term is used as a suffix in systematic name formation to denote the ‒C(=O)NH2 group including its carbon atom.
A compound formally derived from ammonia by replacing one, two or three hydrogen atoms by organyl groups.
Any molecular entity that contains carbon.
A role is particular behaviour which a material entity may exhibit.
A biological role relating to the normal mechanisms and their interactions within a living system.
A cyclic compound having as ring members atoms of at least two different elements.
Any compound that has a nucleobase as a part.
Any organic molecular entity that is acidic and contains carbon in covalent linkage.
Any molecule that consists of at least one carbon atom as part of the electrically neutral entity.
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 organooxygen compound that is a polyhydroxy-aldehyde or -ketone, or a compound derived from one. Carbohydrates contain only carbon, hydrogen and oxygen and usually have an empirical formula Cm(H2O)n; carbohydrate derivatives may contain other elements by substitution or condensation.
carbohydrates and carbohydrate derivatives
A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane.
A cell in vitro that is or has been maintained or propagated as part of a cell culture.
A cell in vitro that has undergone physical changes as a consequence of a deliberate and specific experimental procedure.
A quantitative or qualitative value which is the result of an act of assessing a morphological or physiological state or property in a single individual or sample or a group of individuals or samples, based on direct observation or experimental manipulation.
Morphological measurement involving the entire body of an organism.
The heaviness or degree to which an entire organism's body is drawn to the earth by gravity.
Measurement of the structure or forms of the entire body or parts of the body of an organism.
This is a measurement of the physical form or structure of an organism which has been normalized, adjusted or derived by a mathematical process or computation.
calculated body morphological measurement
A quantification of a parameter of the chemical composition of blood.
Any measurement involving the amount, composition or type of protein, the complex organic compounds containing carbon, hydrogen, oxygen, nitrogen, and sulfur consisting of alpha-amino acids joined by peptide linkages, in blood.
A measurement of the blood, it's contents, cells or other factors contained within the blood.
The level of steroids found in a specific volume of blood.
Any value resulting from the quantification of a morphological or physiological parameter of a blood-derived lipid, any of a structurally diverse group of organic compounds found in blood that are insoluble in water but soluble innonpolar solvents that, among other biological functions, serve as a source of fuel and are an important constituent of cell structure.
Measurement of the entire amount of cholesterol, a eukaryotic sterol that in higher animals is the precursor of bile acids and steroid hormones and a key constituent of cell membranes, without taking into account any association with other molecules such as lipoproteins, in a specified volume of blood, the fluid that circulates through the heart, arteries, capillaries and veins carrying nutrients and oxygen to the body tissues and metabolites away from them.
Measurement of the amount of cholesterol, a eukaryotic sterol that in higher animals is the precursor of bile acids and steroid hormones and a key constituent of cell membranes, carried in high-density lipoprotein (HDL) molecules in a specified volume of blood, the fluid that circulates through the heart, arteries, capillaries and veins carrying nutrients and oxygen to the body tissues and metabolites away from them. HDL is the smallest of the major lipoprotein particles, complex molecules that consist of a protein membrane surrounding a core of lipids. The HDL class of lipoproteins, specifically the subtypes of HDL2 and HDL3, have densities between 1.063 and 1.210 g/ml.
high density lipoprotein cholesterol measurement
blood high density lipoprotein cholesterol level
Measurement of the amount of cholesterol, a eukaryotic sterol that in higher animals is the precursor of bile acids and steroid hormones and a key constituent of cell membranes, carried in low-density lipoprotein (LDL) molecules in a specified volume of blood, the fluid that circulates through the heart, arteries, capillaries and veins carrying nutrients and oxygen to the body tissues and metabolites away from them. LDL constitute a class of relatively large, heterogeneous lipoprotein particles, complex molecules that consist of a protein membrane surrounding a core of lipids. The LDL class of lipoproteins has a density between 1.019 and 1.063 g/ml. In some animal species, such as canine and rodents, this may overlap with the HDL1 class and be designated LDL/HDL1.
low density lipoprotein cholesterol measurement
blood low density lipoprotein cholesterol level
A measurement relating body weight to height in an organism; typically calculated as the weight of an individual divided by the height of that individual squared. For quadrupeds, the square of body height is often replaced by the square of body length.
The amount of lipoproteins, any of a group of conjugated proteins that have at least one lipid component, in a specific volume of blood.
The quantification of any morphological or physiological parameter related to intake or ingestion, especially of food or drink, or a value resulting from such a quantification.
Amount of drink, that is, a liquid that is brought into the mouth and swallowed to quench thirst, for nourishment, etc., consumed per unit time.
The quantification of any parameter related to the process whereby drink, any liquid that is brought into the mouth and swallowed to quench thirst, for nourishment, etc., is taken in for utilization by the body.
The quantification of any parameter related to the process whereby food (i.e. material, usually of plant or animal origin, that contains essential nutrients such as carbohydrates, fats, proteins, vitamins, and/or minerals and that is ingested and assimilated by an organism to produce energy, stimulate growth, and maintain life) is taken in for utilization by the body.
The amount of ethanol, a colorless volatile flammable liquid CH3CH2OH that is the intoxicating agent in liquors, consumed per unit time.
The amount of sterol, any of a group of steroids with a long (8 to 10 carbons) aliphatic side-chain at position 17 and at least one alcoholic group, in a specified sample of blood.
The amount of cholesterol, a eukaryotic sterol that in higher animals is the precursor of bile acids and steroid hormones and a key constituent of cell membranes, in a specified sample of blood. Cholesterol in the blood is generally associated with various lipoproteins.
A value resulting from the quantification of a morphological or physiological parameter of a blood-derived lipoprotein, any of a class of complex molecules found in blood that consist of a protein membrane surrounding a core of lipids.
Measurement of the amount of cholesterol, a eukaryotic sterol that in higher animals is the precursor of bile acids and steroid hormones and a key constituent of cell membranes, carried in lipoprotein molecules in a specified volume of blood. Lipoprotein particles are complexes that consist of protein surrounding a core of lipids.
A material entity that is a maximal functionally integrated unit that develops from a program encoded in a genome
'Maximal functionally integrated unit' is intended to express unity, which Barry considers synonymous with BFO 'object'.
Includes virus - we will later have a class for cellular organisms.
organism
A material entity processed by human activity with an intent to produce it.
In the COB 2024 workshop there was much disagreement about this label.
processed material entity
completely executed planned process
A process that is initiated by an agent who intends to carry out a plan to achieve an objective through one or more actions as described in a plan specification.
planned process
A completely executed planned process that intends to output material entities from input material entities
material processing
characteristic
A processed material entity which is designed to be capable of a process.
device
A political association with effective dominion over a geographic area.
A geographical region whose affairs and population are administered by an authority.
A material part of an astronomical body.
astronomical body part
geophysical entity
A physiological assay of the human body that uses such tools as body mass index, basal metabolic rate, bioelectrical impedance, and dual energy x-ray absorptiometry, along with measurements of skinfold thickness and arm muscle circumference, to assess the structure, form, and composition of the body for purposes of comparison.
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
A food product made of meat, the skeletal muscle and associated fat, and other edible tissues such as organs, livers, skin, brains, bone marrow, kidneys, or lungs, of mammals.
mammalian meat food product
A food product which has as a defining ingredient some plant material.
plant food product
cheese starter culture food product
A seafood product is a vertebrate or invertibrate organism from an aquatic environment.
animal seafood product
A food product which is derived from or produced by an animal that has a vertibrae.
vertebrate food product
A food product made from an avian egg.
avian egg food product
Suidae is a family of artiodactyl mammals which are commonly called pigs, hogs or boars. In addition to numerous fossil species, 17 extant species are currently recognized (or 18 counting domestic pigs and wild boars separately), classified into between four and eight genera. The family includes the domestic pig, Sus scrofa domesticus or Sus domesticus, in addition to numerous species of wild pig, such as babirusas and warthogs. All suids, or swine, are native to the Old World, ranging from Asia to Europe and Africa.
swine food product
bovine meat food product
A food product consisting of an edible fungi or mushroom or yeast.
fungus food product
invertebrate food product
Food product that is 1) ready or nearly ready for consumption; 2) usually a composite of several foods or ingredients that often belong to distinct product types; 3) usually formulated, mixed and partially or fully cooked.
prepared food product
Material which derives from algae (including single-celled microalgae and multicellular macroalgae).
algae material
animal lipid food product
A fish food product includes products made from any fish species (aquatic vertebrate with gills and fins).
fish food product
A food product that is derived from some avian animal.
avian food product
A dairy food product has mammilian milk or a milk component as an ingredient.
dairy product
milk product
dairy food product
milk or milk based food product
A food consisting of a round or oval body laid by the female of many animals, consisting of an ovum surrounded by layers of membranes and an outer casing, which acts to nourish and protect a developing embryo and its nutrient reserves.
egg food product
animal based refined or partially-refined food product
A salad food product with one or more animal products (meat, milk, fat, eggs etc.) as ingredients.
animal based salad food product
animal fat or oil refined food product
animal product based flavoring or seasoning
animal soup food product
Food material which normally exists as an ingredient to another food material, rather than eaten on its own. This includes chemical food components.
food material component
food flavoring or seasoning
human milk based food product
food material by consumer group
refined or partially-refined food product
amphibian or reptile food product
A prepared food product consisting of either a salad or a salad ingredient mixture to which a salad dressing is added.
salad food product
A multi-component food product which is soup.
soup food product
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
food material
A process involving the physical transformation of a food source or food product into some derived organic material or food product
food transformation process
Food material which has been categorized by a characteristic such as granularity or temperature.
food material by characteristic
Game or quarry is any animal hunted for sport or for food. The type and range of animals hunted for food varies in different parts of the world. In some countries, game is classified, including legal classification with respect to licences required, as either "small game" or "large game"
game animal food product
A food product consisting of food material derived from ingredients sourced from multiple organisms.
multi-component food
Food material organized by the process which it results from.
food material by process
A lipid food product is a food product made primarily of plant or animal fat or oil
fats and oils
oils and fats
lipid food product
animal meat food product
A whole animal.
animal
A food product not including meat and animal tissue products (such as gelatin or animal-derived rennet).
vegetarian food
vegetarian food material
A plan specification for making a food product, which may have ingredient, device, action and objective specifications.
food recipe
A food product that is derived from some animal.
animal food product
Anatomical or other piece(s) or substance derived from one or more plants.
plant material
Material which derives from one or more fungai.
fungus material
Material which derives from one or more mammals.
mammal material
Material which derives from one or more vertebrate animals.
vertebrate material
invertebrate material
amphibian material
swine material
Material which is produced by an animal.
animal substance
Milk which is produced by animal lactation.
animal milk
Raw animal milk.
animal milk (raw)
Material that derives from some avian animal.
avian material
animal-derived food
Breast milk is the milk produced by the breasts (or mammary glands) of a human female.
human milk (raw)
processed food
mammalian milk product
Mammals (from Latin mamma "breast") are vertebrate animals constituting the class Mammalia, and characterized by the presence of mammary glands which in females produce milk for feeding (nursing) their young, a neocortex (a region of the brain), fur or hair, and three middle ear bones.
mammal
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
amphibian
Material which is distinguished primarily by the organism(s) it derives from.
organism material
Material that derives from one or more animals
animal material
Food substance or component consisting predominantly of mixed glycerol esters of fatty acids and, in far lesser amounts, of fatty acids, sterols and pigments. A fat is a solid at room temperature, an oil is a liquid at room temperature (20 degrees C.). Excludes essential oils.
fat or oil
A physical-chemical component separated from the food source or its parts by extraction, centrifugation, filtration, heat processing, expressing or a similar process. The separated component may be converted through further processing. If this is done, the final substance is indexed. A water-extracted component may remain in aqueous dispersion. The extract, concentrate or isolate is indexed in preference to the anatomic part from which it is derived. For example, peanut oil is indexed under *PEANUT* combined wih *FAT OR OIL* rather than with *SEED OR KERNEL*. On the other hand, fruit and vegetable juices can be indexed under *FRUIT JUICE OR NECTAR* or *VEGETABLE JUICE* (A. PRODUCT TYPE); therefore the anatomic part of the plant should be indexed.
extract, concentrate or isolate of plant or animal
A state of matter between a solid and a gas, in which a substance has the capacity to flow and conforms to the shape of the container.
food (liquid)
Used to specifically characterize a food product based on the treatment or processes applied to the product or any indexed ingredient. The processes include adding, substituting or removing components or modifying the food or component, e.g., through fermentation.
food treatment process
The methods contributing to the prevention or retardation of microbial, enzymatic or oxidative spoilage and thus to the extension of shelf life. Index all methods for which information is available, even if a corresponding descriptor has already been used in *H. TREATMENT APPLIED*. Preservation descriptors refer to the finished food as a whole with these exceptions: (1) if the components of a multi-component food, such as cream pie, are preservation by different methods, index all methods; (2) if chemical preservatives are declared on the label, always index them even if it is known that the preservative was introduced through or is only present in a component or ingredient of the food; and (3) if the preservation method for an ingredient is declared on the label (such as brie cheese made from pasteurized milk) index it. Also use *INGREDIENT preservation by THERMAL PROCESSING* or *INGREDIENT preservation by IRRADIATION* when ingredients have been pasteurized, ultrapasteurized, sterilized or irradiated.
food preservation process
OBSOLETE. The production of new individuals that contain some portion of genetic material inherited from one or more parent organisms.
A multicellular organismal process carried out by any of the organs or tissues in an organ system. An organ system is a regularly interacting or interdependent group of organs or tissues that work together to carry out a biological objective.
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.
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.
Catalysis of the reaction: ATP + D-fructose-6-phosphate = ADP + D-fructose 1,6-bisphosphate.
Catalysis of the reaction: beta-D-fructose 1,6-bisphosphate = D-glyceraldehyde 3-phosphate + dihydroxyacetone phosphate.
Catalysis of the reaction: alpha-D-glucose 6-phosphate = beta-D-fructose 6-phosphate.
Catalysis of the reaction: D-glyceraldehyde 3-phosphate + phosphate + NAD+ = 3-phospho-D-glyceroyl phosphate + NADH + H+.
glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity
Catalysis of the reaction: lactate + NAD+ = H+ + NADH + pyruvate.
Catalysis of the hydrolysis of any O-glycosyl bond.
hydrolase activity, hydrolyzing O-glycosyl compounds
Catalysis of the hydrolysis of terminal, non-reducing beta-D-galactose residues in beta-D-galactosides.
Catalysis of the reaction: 3-phospho-D-glycerate + ATP = 3-phospho-D-glyceroyl phosphate + ADP + H+.
Catalysis of the reaction: (2R)-2-phosphoglycerate = (2R)-3-phosphoglycerate.
Catalysis of the reaction: 2-phospho-D-glycerate = phosphoenolpyruvate + H2O.
2-phospho-D-glycerate-hydrolase activity
Catalysis of the reaction: D-glyceraldehyde 3-phosphate = dihydroxyacetone phosphate.
The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y.
The chemical reactions and pathways involving monosaccharides, the simplest carbohydrates. They are polyhydric alcohols containing either an aldehyde or a keto group and between three to ten or more carbon atoms. They form the constitutional repeating units of oligo- and polysaccharides.
The chemical reactions and pathways involving glucose, the aldohexose gluco-hexose. D-glucose is dextrorotatory and is sometimes known as dextrose; it is an important source of energy for living organisms and is found free as well as combined in homo- and hetero-oligosaccharides and polysaccharides.
The chemical reactions and pathways resulting in the breakdown of glucose, the aldohexose gluco-hexose.
The chemical reactions and pathways involving organic acids, any acidic compound containing carbon in covalent linkage.
The chemical reactions and pathways involving lactate, the anion of lactic acid.
alpha-hydroxypropionate metabolic process
The chemical reactions and pathways involving pyruvate, 2-oxopropanoate.
The chemical reactions and pathways resulting in the formation of precursor metabolites, substances from which energy is derived, and any process involved in the liberation of energy from these substances.
generation of precursor metabolites and energy
The chemical reactions and pathways resulting in the breakdown of a carbohydrate into pyruvate, with the concomitant production of a small amount of ATP and the reduction of NAD(P) to NAD(P)H. Glycolysis begins with the metabolism of a carbohydrate to generate products that can enter the pathway and ends with the production of pyruvate. Pyruvate may be converted to acetyl-coenzyme A, ethanol, lactate, or other small molecules.
The metabolic process that uses oxidation-reduction reactions of organic compounds and substrate-level phosphorylation for the generation of adenosine triphosphate (ATP), without consuming oxygen and is independent of electron transport chains.
Any cellular metabolic process involving nucleobases, nucleosides, nucleotides and nucleic acids.
cellular nucleobase, nucleoside, nucleotide and nucleic acid metabolic process
cellular nucleobase, nucleoside, nucleotide and nucleic acid metabolism
nucleobase, nucleoside, nucleotide and nucleic acid metabolism
nucleobase-containing compound metabolic process
The chemical reactions and pathways involving a purine nucleotide, a compound consisting of nucleoside (a purine base linked to a deoxyribose or ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.
OBSOLETE. The process of introducing a phosphate group into a nucleoside diphosphate to produce a nucleoside triphosphate.
obsolete nucleoside diphosphate phosphorylation
The chemical reactions and pathways resulting in the breakdown of a purine nucleotide, a compound consisting of nucleoside (a purine base linked to a deoxyribose or ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.
OBSOLETE. The chemical reactions and pathways involving aromatic compounds, any organic compound characterized by one or more planar rings, each of which contains conjugated double bonds and delocalized pi electrons, as carried out by individual cells.
obsolete cellular aromatic compound metabolic process
OBSOLETE. The chemical reactions and pathways involving reduced nicotinamide adenine dinucleotide (NADH), a coenzyme present in most living cells and derived from the B vitamin nicotinic acid.
reduced nicotinamide adenine dinucleotide metabolic process
reduced nicotinamide adenine dinucleotide metabolism
A metabolic process that generates a pool of NADH by the reduction of NAD+.
reduced nicotinamide adenine dinucleotide regeneration
The chemical reactions and pathways involving any phosphorylated nucleoside.
OBSOLETE. The process of introducing a phosphate group into ADP, adenosine diphosphate, to produce ATP.
The chemical reactions and pathways involving the nonmetallic element phosphorus or compounds that contain phosphorus.
The chemical reactions and pathways involving the phosphate group, the anion or salt of any phosphoric acid.
phosphate-containing compound metabolic process
OBSOLETE. The chemical reactions and pathways involving organic or inorganic compounds that contain nitrogen.
obsolete nitrogen compound metabolic process
The whole of the physical, chemical, and biochemical processes carried out by multicellular organisms to break down ingested nutrients into components that may be easily absorbed and directed into metabolism.
The internally coordinated responses (actions or inactions) of animals (individuals or groups) to internal or external stimuli, via a mechanism that involves nervous system activity.
Behavior associated with the intake of food.
A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence.
biological process
A cellular process consisting of the biochemical pathways by which a living organism transforms chemical substances. This includes including anabolism (biosynthetic process) and catabolism (catabolic process). Metabolic processes includes the transformation of small molecules, as well macromolecular processes such as DNA repair and replication, protein synthesis and degradation.
Catalysis of the transfer of a phosphate group, usually from ATP, to a phosphofructose substrate molecule.
A cellular process consisting of the biochemical pathways by which a living organism breaks down substances. This includes the breakdown of carbon compounds with the liberation of energy for use by the cell or organism.
A cellular process consisting of the biochemical pathways by which a living organism synthesizes chemical substances. This typically represents the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones.
The chemical reactions and pathways involving a nucleotide, a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the glycose moiety; may be mono-, di- or triphosphate; this definition includes cyclic nucleotides (nucleoside cyclic phosphates).
The chemical reactions and pathways involving a nucleoside diphosphate, a compound consisting of a nucleobase linked to a deoxyribose or ribose sugar esterified with diphosphate on the sugar.
nucleoside diphosphate metabolic process
The chemical reactions and pathways resulting in the breakdown of a nucleoside diphosphate, a compound consisting of a nucleobase linked to a deoxyribose or ribose sugar esterified with diphosphate on the sugar.
nucleoside diphosphate catabolic process
The chemical reactions and pathways involving purine nucleoside diphosphate, a compound consisting of a purine base linked to a ribose or deoxyribose sugar esterified with diphosphate on the sugar.
purine nucleoside diphosphate metabolism
purine nucleoside diphosphate metabolic process
The chemical reactions and pathways resulting in the breakdown of purine nucleoside diphosphate, a compound consisting of a purine base linked to a ribose or deoxyribose sugar esterified with diphosphate on the sugar.
purine nucleoside diphosphate catabolism
purine nucleoside diphosphate degradation
purine nucleoside diphosphate catabolic process
The chemical reactions and pathways involving a nucleoside triphosphate, a compound consisting of a nucleobase linked to a deoxyribose or ribose sugar esterified with triphosphate on the sugar.
nucleoside triphosphate metabolic process
The chemical reactions and pathways involving purine nucleoside triphosphate, a compound consisting of a purine base linked to a ribose or deoxyribose sugar esterified with triphosphate on the sugar.
purine nucleoside triphosphate metabolism
purine nucleoside triphosphate metabolic process
The chemical reactions and pathways involving a purine ribonucleotide, a compound consisting of ribonucleoside (a purine base linked to a ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.
The chemical reactions and pathways resulting in the breakdown of a purine ribonucleotide, a compound consisting of ribonucleoside (a purine base linked to a ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.
The chemical reactions and pathways resulting in the breakdown of nucleotides, any nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the glycose moiety; may be mono-, di- or triphosphate; this definition includes cyclic-nucleotides (nucleoside cyclic phosphates).
The chemical reactions and pathways involving purine ribonucleoside diphosphate, a compound consisting of a purine base linked to a ribose sugar esterified with diphosphate on the sugar.
purine ribonucleoside diphosphate metabolism
purine ribonucleoside diphosphate metabolic process
The chemical reactions and pathways resulting in the breakdown of purine ribonucleoside diphosphate, a compound consisting of a purine base linked to a ribose sugar esterified with diphosphate on the sugar.
purine ribonucleoside diphosphate breakdown
purine ribonucleoside diphosphate catabolism
purine ribonucleoside diphosphate degradation
purine ribonucleoside diphosphate catabolic process
The chemical reactions and pathways involving a ribonucleoside diphosphate, a compound consisting of a nucleobase linked to a ribose sugar esterified with diphosphate on the sugar.
ribonucleoside diphosphate metabolic process
The chemical reactions and pathways resulting in the breakdown of a ribonucleoside diphosphate, a compound consisting of a nucleobase linked to a ribose sugar esterified with diphosphate on the sugar.
ribonucleoside diphosphate catabolic process
The chemical reactions and pathways involving purine ribonucleoside triphosphate, a compound consisting of a purine base linked to a ribose sugar esterified with triphosphate on the sugar.
purine ribonucleoside triphosphate metabolism
purine ribonucleoside triphosphate metabolic process
The chemical reactions and pathways involving a ribonucleotide, a compound consisting of ribonucleoside (a base linked to a ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.
The chemical reactions and pathways resulting in the breakdown of a ribonucleotide, a compound consisting of ribonucleoside (a base linked to a ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.
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.
Catalysis of the hydrolysis of galactosyl compounds, substances containing a group derived from a cyclic form of galactose or a galactose derivative.
The chemical reactions and pathways by which a cell derives energy from organic compounds; results in the oxidation of the compounds from which energy is released.
energy derivation by oxidation of organic compounds
The chemical reactions and pathways resulting in the breakdown of carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y.
catabolic carbohydrate metabolic process
The chemical reactions and pathways resulting in the formation of organic acids, any acidic compound containing carbon in covalent linkage.
The chemical reactions and pathways resulting in the breakdown of organic acids, any acidic compound containing carbon in covalent linkage.
Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.
Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
Catalysis of an oxidation-reduction (redox) reaction in which a CH-OH group act as a hydrogen or electron donor and reduces a hydrogen or electron acceptor.
oxidoreductase activity, acting on CH-OH group of donors
Catalysis of an oxidation-reduction (redox) reaction in which an aldehyde or ketone (oxo) group acts as a hydrogen or electron donor and reduces NAD or NADP.
oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor
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
Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to an alcohol group (acceptor).
phosphotransferase activity, alcohol group as acceptor
Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to a carboxyl group (acceptor).
phosphotransferase activity, carboxyl group as acceptor
Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc.
Catalysis of the hydrolysis of any glycosyl bond.
hydrolase activity, acting on glycosyl bonds
Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
Catalysis of the cleavage of C-C bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond.
Catalysis of the cleavage of a C-C bond in a molecule containing a hydroxyl group and a carbonyl group to form two smaller molecules, each being an aldehyde or a ketone.
Catalysis of the breakage of a carbon-oxygen bond.
Catalysis of the cleavage of a carbon-oxygen bond by elimination of water.
Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.
Catalysis of an oxidation-reduction (redox) reaction in which the hydrogen donor and acceptor are the same molecule, and no oxidized product appears.
Catalysis of an oxidation-reduction (redox) reaction in which the hydrogen donor and acceptor, which is an aldose or a ketose, are the same molecule, and no oxidized product appears.
intramolecular isomerase activity, interconverting aldoses and ketoses
intramolecular oxidoreductase activity, interconverting aldoses and ketoses
Catalysis of the transfer of a functional group from one position to another within a single molecule.
Catalysis of the transfer of a phosphate group from one position to another within a single molecule.
intramolecular transferase activity, phosphotransferases
phosphotransferase activity, with regeneration of donors, apparently catalyzing intramolecular transfers
intramolecular phosphotransferase activity
Catalysis of an oxidation-reduction (redox) reaction in which an aldehyde or ketone (oxo) group acts as a hydrogen or electron donor and reduces a hydrogen or electron acceptor.
oxidoreductase activity, acting on the aldehyde or oxo group of donors
Catalysis of the transfer of a phosphate group, usually from ATP, to a carbohydrate substrate molecule.
The chemical reactions and pathways resulting in the formation of lactate from other compounds, including pyruvate.
lactate biosynthetic process from pyruvate
The chemical reactions and pathways resulting in the formation of lactate, the anion of lactic acid.
The chemical reactions and pathways involving a hexose, any monosaccharide with a chain of six carbon atoms in the molecule.
The chemical reactions and pathways resulting in the breakdown of hexose, any monosaccharide with a chain of six carbon atoms in the molecule.
The chemical reactions and pathways resulting in the breakdown of a pyridine nucleotide, a nucleotide characterized by a pyridine derivative as a nitrogen base.
The chemical reactions and pathways involving organophosphates, any phosphate-containing organic compound.
The anaerobic enzymatic chemical reactions and pathways resulting in the breakdown of glucose to lactate, and possibly ethanol, yielding energy in the form of adenosine triphosphate (ATP).
The fermentation process resulting in the oxygen-independent conversion of pyruvate to reduced end products (e.g., lactate, ethanol, and acetate), accompanied by the concomitant oxidation of NADH to NAD.
The anaerobic enzymatic chemical reactions and pathways resulting in the breakdown of glucose to lactate, via canonical glycolysis, yielding energy in the form of adenosine triphosphate (ATP).
The chemical reactions and pathways involving nicotinamide adenine dinucleotide (NAD+), a coenzyme that interconverts with its reduced form, NADH, in many redox and catabolic reactions.
nicotinamide adenine dinucleotide metabolic process
nicotinamide adenine dinucleotide metabolism
oxidized nicotinamide adenine dinucleotide metabolic process
oxidized nicotinamide adenine dinucleotide metabolism
The chemical reactions and pathways involving ribose phosphate, any phosphorylated ribose sugar.
The chemical reactions and pathways involving carboxylic acids, any organic acid containing one or more carboxyl (COOH) groups or anions (COO-).
A physical, chemical, or biochemical process carried out by living organisms to break down ingested nutrients into components that may be easily absorbed and directed into metabolism.
The process whose specific outcome is the progression of the myeloid and lymphoid derived organ/tissue systems of the blood and other parts of the body over time, from formation to the mature structure. The site of hemopoiesis is variable during development, but occurs primarily in bone marrow or kidney in many adult vertebrates.
Any biological process, occurring at the level of a multicellular organism, pertinent to its function.
A biological process whose specific outcome is the progression of an integrated living unit: an anatomical structure (which may be a subcellular structure, cell, tissue, or organ), or organism over time from an initial condition to a later condition.
The chemical reactions and pathways involving monocarboxylic acids, any organic acid containing one carboxyl (COOH) group or anion (COO-).
OBSOLETE. The chemical reactions and pathways involving various organic and inorganic nitrogenous compounds, as carried out by individual cells.
obsolete cellular nitrogen compound metabolic process
The chemical reactions and pathways resulting in the breakdown of nucleobases, nucleosides, nucleotides and nucleic acids.
nucleobase, nucleoside, nucleotide and nucleic acid breakdown
nucleobase, nucleoside, nucleotide and nucleic acid catabolism
nucleobase, nucleoside, nucleotide and nucleic acid degradation
nucleobase-containing compound catabolic process
The specific behavior of an organism relating to the intake of food, any substance (usually solid) that can be metabolized by an organism to give energy and build tissue.
The specific behavior of an organism relating to the intake of liquids, especially water.
The chemical reactions and pathways resulting in the breakdown of pyruvate, 2-oxopropanoate.
The chemical reactions and pathways involving any oxoacid; an oxoacid is 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).
Catalysis of the reaction: D-glyceraldehyde 3-phosphate + phosphate + NAD(P)+ = 3-phospho-D-glyceroyl phosphate + NAD(P)H + H+.
D-glyceraldehyde 3-phosphate:NAD(P)+ oxidoreductase (phosphorylating)
glyceraldehyde-3-phosphate dehydrogenase (NAD(P)) (phosphorylating)
glyceraldehyde-3-phosphate dehydrogenase [NAD(P)+] (phosphorylating) activity
OBSOLETE. The chemical reactions and pathways by which individual cells transform chemical substances.
The chemical reactions and pathways involving those compounds which are formed as a part of the normal anabolic and catabolic processes. These processes take place in most, if not all, cells of the organism.
OBSOLETE. The chemical reactions and pathways resulting in the formation of substances, carried out by individual cells.
The chemical reactions and pathways involving small molecules, any low molecular weight, monomeric, non-encoded molecule.
The chemical reactions and pathways resulting in the breakdown of small molecules, any low molecular weight, monomeric, non-encoded molecule.
The chemical reactions and pathways resulting in the formation of small molecules, any low molecular weight, monomeric, non-encoded molecule.
The chemical reactions and pathways involving ADP, adenosine 5'-diphosphate.
The chemical reactions and pathways resulting in the breakdown of ADP, adenosine 5'-diphosphate.
The chemical reactions and pathways involving ATP, adenosine triphosphate, a universally important coenzyme and enzyme regulator.
The chemical reactions and pathways resulting in the breakdown of monosaccharides, polyhydric alcohols containing either an aldehyde or a keto group and between three to ten or more carbon atoms.
The chemical reactions and pathways resulting in the formation of carboxylic acids, any organic acid containing one or more carboxyl (-COOH) groups.
The chemical reactions and pathways resulting in the breakdown of carboxylic acids, any organic acid containing one or more carboxyl (-COOH) groups.
The chemical reactions and pathways resulting in the breakdown of organophosphates, any phosphate-containing organic compound.
OBSOLETE. The chemical reactions and pathways involving heterocyclic compounds, those with a cyclic molecular structure and at least two different atoms in the ring (or rings).
The chemical reactions and pathways involving nicotinamide nucleotides, any nucleotide that contains combined nicotinamide.
nicotinamide nucleotide metabolic process
OBSOLETE. The process of introducing one or more phosphate groups into a nucleotide to produce a phosphorylated nucleoside.
The cellular developmental process in which a specific cell progresses from an immature to a mature state. Cell development start once cell commitment has taken place.
The biological process whose specific outcome is the progression of an anatomical structure from an initial condition to its mature state. This process begins with the formation of the structure and ends with the mature structure, whatever form that may be including its natural destruction. An anatomical structure is any biological entity that occupies space and is distinguished from its surroundings. Anatomical structures can be macroscopic such as a carpel, or microscopic such as an acrosome.
A biological process whose specific outcome is the progression of a cell over time from an initial condition to a later condition.
A process in which nutrients are taken up from the contents of the intestine.
The cellular chemical reactions and pathways involving a nucleobase-containing small molecule: a nucleobase, a nucleoside, or a nucleotide.
nucleobase, nucleoside and nucleotide metabolism
nucleobase-containing small molecule metabolic process
The chemical reactions and pathways resulting in the breakdown of a monosaccharide into pyruvate, occurring through a fructose-6-phosphate intermediate, with the concomitant production of ATP and NADH.
glycolytic process through fructose-6-phosphate
The chemical reactions and pathways resulting in the breakdown of a carbohydrate into pyruvate, occurring through a glucose-6-phosphate intermediate, with the concomitant production of a small amount of ATP.
glycolytic process through glucose-6-phosphate
The glycolytic process that begins with the conversion of glucose to glucose-6-phosphate by glucokinase activity. Glycolytic processes are the chemical reactions and pathways resulting in the breakdown of a carbohydrate into pyruvate, with the concomitant production of a small amount of ATP.
The chemical reactions and pathways resulting in the breakdown of glucose, with the production of pyruvate.
OBSOLETE. The chemical reactions and pathways involving an organic substance, any molecular entity containing carbon.
organic molecular entity metabolic process
obsolete organic substance metabolic process
The chemical reactions and pathways resulting in the breakdown of monocarboxylic acids, any organic acid containing one carboxyl (-COOH) group.
The chemical reactions and pathways resulting in the formation of monocarboxylic acids, any organic acid containing one carboxyl (-COOH) group.
monocarboxylic acid biosynthetic process
The chemical reactions and pathways involving a purine-containing compound, i.e. any compound that contains purine or a formal derivative thereof.
purine-containing compound metabolic process
The chemical reactions and pathways resulting in the breakdown of a purine-containing compound, i.e. any compound that contains purine or a formal derivative thereof.
purine-containing compound catabolic process
The chemical reactions and pathways involving a pyridine-containing compound, i.e. any compound that contains pyridine or a formal derivative thereof.
pyridine and derivative metabolic process
pyridine-containing compound metabolic process
The chemical reactions and pathways resulting in the breakdown of a pyridine-containing compound, i.e. any compound that contains pyridine or a formal derivative thereof.
pyridine and derivative catabolic process
pyridine-containing compound degradation
pyridine-containing compound catabolic process
The chemical reactions and pathways involving carbohydrate derivative.
carbohydrate derivative metabolic process
The chemical reactions and pathways resulting in the breakdown of carbohydrate derivative.
carbohydrate derivative catabolic process
The chemical reactions and pathways resulting in the breakdown of a nucleoside phosphate.
OBSOLETE. The chemical reactions and pathways involving organic cyclic compound.
obsolete organic cyclic compound metabolic process
OBSOLETE. The chemical reactions and pathways involving organonitrogen compound.
obsolete organonitrogen compound metabolic process
OBSOLETE. The chemical reactions and pathways resulting in the breakdown of an organic substance, any molecular entity containing carbon.
organic molecular entity catabolic process
obsolete organic substance catabolic process
OBSOLETE. The chemical reactions and pathways resulting in the formation of an organic substance, any molecular entity containing carbon.
organic molecular entity biosynthetic process
obsolete organic substance biosynthetic process
OBSOLETE. The chemical reactions and pathways involving organic hydroxy compound.
obsolete organic hydroxy compound metabolic process
OBSOLETE. The chemical reactions and pathways resulting in the formation of organic hydroxy compound.
obsolete organic hydroxy compound biosynthetic process
Increased resistance towards insulin, that is, diminished effectiveness of insulin in reducing blood glucose levels.
Impaired ability to absorb one or more nutrients from the intestine.
An abnormality of the intestine. The closely related term enteropathy is used to refer to any disease of the intestine.
Any deviation from the normal concentration of a lipid in the blood circulation.
Abnormal circulating lipid concentration
An abnormality of the gastrointestinal tract.
Abnormality of the gastrointestinal tract
An anomaly in the processes involved in the maintenance of an internal equilibrium.
Abnormal structure of the gastrointestinal tract.
Morphological abnormality of the GI tract
Morphological abnormality of the gastrointestinal tract
Morphological anomaly of the digestive system
Abnormal gastrointestinal tract morphology
A functional anomaly of the digestive system.
Abnormality of digestive system physiology
A structural anomaly of the digestive system.
Abnormality of digestive system morphology
An abnormal level of an analyte measured in the blood.
Abnormal circulating metabolite concentration
Any deviation of the concentration of an orrganic compound from the normal range. An organic compound is defined as any compound that contains a carbon atom.
Abnormal circulating organic compound concentration
conditional specification
A directive information entity that specifies what should happen if the trigger condition is fulfilled.
OBI branch derived
measurement unit label
A measurement unit label is as a label that is part of a scalar measurement datum and denotes a unit of measure.
objective specification
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.
OBI Plan and Planned Process/Roles Branch
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
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.
person:Chris Stoeckert
data item
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.
symbol
An information content entity that is a mark(s) or character(s) used as a conventional representation of another entity.
based on Oxford English Dictionary
information content entity
A generically dependent continuant that is about some thing.
Pier: 'data, information or knowledge'. OR 'representation'
A scalar measurement datum is a measurement datum that is composed of two parts, numerals and a unit label.
scalar measurement datum
directive information entity
An information content entity whose concretizations indicate to their bearer how to realize them in a process.
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.
rule
A rule is an executable which guides, defines, restricts actions.
PRS
algorithm
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.
adapted from discussion on OBI list (Matthew Pocock, Christian Cocos, Alan Ruttenberg)
curation status specification
The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value.
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.
2009-03-16: 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.
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
PERSON: Melanie Courtot
PERSON:Chris Stoeckert
GROUP: OBI
data set
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.
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
A directive information entity with action specifications and objective specifications as parts that, when concretized, is realized in a process in which the bearer tries to achieve the objectives by taking the actions specified.
A directive information entity with action specifications and objective specifications as parts, and that may be concretized as a realizable entity that, if realized, is realized in a process in which the bearer tries to achieve the objectives by taking the actions specified.
measurement datum
A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device.
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.
conclusion textual entity
A textual entity that expresses the results of reasoning about a problem, for instance as typically found towards the end of scientific papers.
textual entity
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.
citation
A textual entity intended to identify a particular publication.
figure
An information content entity consisting of a two dimensional arrangement of information content entities such that the arrangement itself is about something.
diagram
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
PERSON: Lawrence Hunter
publication
A journal article or book
journal article, newspaper story, book, etc.
A document that has been accepted by a publisher
A document that is the output of a publishing process.
PERSON: Chris Stoeckert
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
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
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
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
A scalar measurement datum that is the result of measuring a temporal interval
time measurement datum
email address
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
documenting
A planned process in which a document is created or added to by including the specified input in it.
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
assigning a centrally registered identifier
centrally registered identifier symbol
A symbol that is part of a CRID and that is sufficient to look up a record from the CRID's registry.
Original proposal from Bjoern, discussions at IAO calls
An information content entity that consists of a CRID symbol and additional information about the CRID registry to which it belongs.
centrally registered identifier
A code set of CRID records, each consisting of a CRID symbol and additional information which was recorded in the code set through an assigning a centrally registered identifier process.
centrally registered identifier registry
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.
PERSON: Bill Baumgartner
ethical approval
ethical requirements
ethics
ethics statement
ethical approval textual entity
A textual entity that documents the ethical approval of some study design.
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
identifier
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.
An identifier referring to an individual entity that is ascribed personhood by the user of the identifier.
personal name
An information content entity that is a collection of other information content entities that has been created to identify or annotate things in a specified domain, and where the intention of its creators is that the collection has a one-to-one correspondence with those things.
code set
A document that is intended to be the specified input in a document act. It has a plan specification as a part that specifies the intended socio-legal entities that are created through the document (objective specification) and the way in which the document act is to be performed (by signing, by stamping, etc.) (action specification).
document act input document
A document that explains all relevant information to assist a human being in understanding the expectations and requirements of participation in a process, and is an instrument in obtaining consent and, after having obtained consent, is a record that such a consent has occurred.
A document that explains all relevant study information to assist a human subject in understanding the expectations and requirements of participation in a research study. This form document is presented to and signed by the study subject.
The term definition is adapted from NCIt definition of 'consent form' (C16468) with modification. Compared to the NCIt definition, the ICO definition does not restrict the form to a clinical trial.
NCIt C16468
informed consent form
An informed consent form that has been signed by at least one participant.
signed informed consent form
A person who is the contact for questions about research.
contact person for questions about research
Poeae Chloroplast Group 1 (Aveneae type)
Prunus avium x P. cerasus x P. canescens
Homo sapiens
The collection of subjects that have a common set of parameters defined in the protocol (could be experimental parameters, treatment parameters, or sponsor-defined attributes).
The Trial Master File Reference Model section that contains a collection of documents related to the Institutional Review Board or Independent Ethics Committee decisions for the clinical trial.
Institutional Review Board Independent Ethics Committee Documents
TMF-RM IRB or IEC Trial Approval Section
A 2-oxo monocarboxylic acid anion that is the conjugate base of pyruvic acid, which is an important metabolic product for energy-producing biochemical pathways. Pyruvate is the final product of glycolysis and, when hypoxic conditions arise, can be metabolized anaerobically to form lactate. This chemical is a precursor of both acetyl-coenzyme A and oxaloacetate, which are involved in the citric acid cycle. Additionally, oxaloacetate is a substrate in the gluconeogenesis pathway.
The amount of an individual's total body mass that is fat, expressed as a percent.
The process by which information about the health status of an individual is obtained after a study has officially closed; an activity that continues something that has already begun or that repeats something that has already been done.
A nutritional supplement composed of a fermented milk drink prepared by inoculating cow, goat, or sheep milk with kefir grains, with potential immunomodulating and probiotic activities. Upon oral administration of kefir, the kefir grains may stimulate the proliferation of beneficial bacteria in the gastrointestinal (GI) tract. This modulates the GI flora ecosystem, improves the functions of the intestinal barrier and protects against harmful viruses and bacteria. In addition, this prebiotic modulates the immune system and may inhibit inflammation.
A facility established for research, often designed to promote interactions between faculty, scholars, students, and industry.
An organic or inorganic substance, element, isotope, food or other materials derived from microorganism, plant, or animal sources. They can be used for the prevention, diagnosis, treatment or research of disease states, for industrial purposes, or for the promotion or maintenance of organism viability or health.
Drug, Food, Chemical or Biomedical Material
Substances that are grouped or classified by chemical composition.
Substances introduced into the body by dietary means.
The distinguishing qualities or prominent aspects of an individual person.
Organic acids that have oxygen atoms in the acidic groups. (NCI)
Processed or unprocessed substances obtained from animal, plant, microorganism and mining source that provide nutrients for living organisms to maintain biological processes or functions.
Groups with a focus on clinical or health related studies.
An organizational header for concepts representing mostly abstract entities.
One or more characters used to identify, name, or characterize the nature, properties, or contents of a thing.
The selection and obtaining of small representative quantities of biological, environmental, or other materials for the purpose of analysis.
The street name and building number where a person or organization is located.
The act of abiding by a stated treatment plan or protocol.
A group used as a standard of comparison in a control experiment.
A class of hydrocarbons with an empirical formula of Cm(H20)n (where m and n may be equal) and includes monomers, polymers and derivatives of aldoses, ketoses, saccharides, and alditols.
An organic oxoacid that contains a carboxy moiety (-COOH) as a functional group.
An active process; excludes processes and mechanisms which fulfill biological functions.
Natural or synthetic substances that are used in various industries or in laboratories for a broad range of applications. This group includes, but is not limited to, pharmaceutical excipients, research/diagnostic agents, agricultural agents, and other non-edible products that may have human health implication.
A characteristic of a treatment regimen employed as a comparator against which the study treatment is evaluated.
A method of selecting a sample from a population in such a way that every sample that could be selected has an equal chance of being selected.
A randomly chosen subset of individuals from a larger set.
Units are chosen for inclusion into a sample based on the convenience of accessibility of research.
A collection of web pages and other files.
The name applied to a scientific investigation.
A statistical probability technique that divides a population into subgroups based on shared characteristics. A random sample is then drawn from each subgroup to ensure representation of all groups.
A statistical sampling technique where researchers use their knowledge and expertise to choose participants they believe are most representative and suitable for the study.
A statistical sampling technique where samples are selected in multiple stages, with each subset of the population selected based on the previous stage's selection until the final sample is selected.
Molecule that contains atoms of the element carbon, usually combined with itself and with atoms of one or more other element such as hydrogen, oxygen, nitrogen, sulfur, phosphorus, chlorine, or fluorine. Excludes carbides, carbonates and carbon oxides.
A single serving of a beverage; any liquid suitable for drinking.
Probiotic supplements (pills, liquid, powder; or other probiotics)
The textual representation of the study objective.
The non-unique initials or abbreviated name used for identification of the study protocol document version.
A sequence of letters, numbers, or other characters that uniquely identifies a clinical trial within a clinical trial registry.
A planned process that gathers and measures information on variables of interest, in an established systematic fashion that enables one to answer stated research questions, test hypotheses, and evaluate outcomes. Data collection results in a collection of data.
WEB: http://en.wikipedia.org/wiki/Data_collection
data collection
A data sampling design that uses randomization for sample selection
A data item that is more specifically a rectangular array of numbers, symbols, or expressions, arranged in rows and columns.
WEB: https://en.wikipedia.org/wiki/Matrix_(mathematics)
A data collection process that results in a collection of data from the literature.
data collection from literature
A data item that is produced as the output of a data transformation.
transformed data item
A document editing process in which one or more fields in a form are filled with related information, such as when answering a questionnare.
form filling
A patient questionnaire which has been filled out by a patient.
filled patient questionnaire
A questionnaire that comprises a set of questions about a patient, such as height, weight, race, biological sex, clinical history, etc., which will be filled by the human subject.
A questionnaire that comprises a set of demographic and medical questions about a patient which will be filled by the patient or their legally authorized representative.
patient questionnaire
A time measurement datum which is the end date of a smoking behavior.
smoking end date
A protocol that is a set of step-by-step instructions compiled by an organization for carrying out routine operations.
A textual entity describing a study aim or a sample collection.
sample collection or study aim description
A proper name that designates a study.
study proper name
An objective specification that specifies the total number of individuals who are planned to participate in study.
number of total human study participant objective
obsolete: planned process
a regulatory role involved with making and/or enforcing relevant legislation and governmental orders
OBI
regulator role
biological feature identification objective
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.
regulatory role
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.
OBI, CDISC
a role realized through the process of supplying materials such as animal subjects, reagents or other materials used in an investigation.
material supplier role
processed material
Is a material entity that is created or changed during material processing.
chromatography device
A device that facilitates the separation of mixtures. The function of a chromatography device involves passing a mixture dissolved in a "mobile phase" through a stationary phase, which separates the analyte to be measured from other molecules in the mixture and allows it to be isolated.
Frank Gibson
chromatography instrument
open tracker https://sourceforge.net/tracker/index.php?func=detail&aid=2881353&group_id=177891&atid=886178
A mass spectrometer is an instrument which is used to measure the mass to charge ratio of ions. All mass spectrometers consist of three basic parts: an ion source, a mass analyzer, and a detector system. The stages within the mass spectrometer are: 1. Production of ions from the sample 2. Separation of ions with different masses 3. Detection of the number of ions of each mass produced 4.Collection of data to generate the mass spectrum
investigation
a planned process that consists of parts: planning, study design execution, documentation and which produce conclusion(s).
evaluant role
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
assay
Assay the wavelength of light emitted by excited Neon atoms. Count of geese flying over a house.
A planned process that has the objective to produce information about a material entity (the evaluant) by examining it.
A planned process with the objective to produce information about the material entity that is the evaluant, by physically examining it or its proxies.
12/3/12: BP: the reference to the 'physical examination' is included to point out that a prediction is not an assay, as that does not require physical examiniation.
PlanAndPlannedProcess Branch
measuring
scientific observation
sample preparation for assay
A sample_preparation_for_assay is a protocol_application including material_enrollments and biomaterial_transformations. definition_source: OBI.
diagnosis textual entity
diagnosis is an assessment of a disease or injury, its likely prognosis and treatment.
a processed material that provides the needed nourishment for microorganisms or cells grown in vitro.
culture medium
A role inhering in a biological or chemical entity that is intended to be applied in a scientific technique to participate (or have molecular components that participate) in a chemical reaction that facilitates the generation of data about some entity distinct from the bearer, or the generation of some specified material output distinct from the bearer.
reagent role
a role which inheres in a person and is realized by the process of being under the care of a physician or health care provider
patient role
protocol testing objective
Protocol_testing_objective is a methodology_testing_objective role describing a study designed to examine the effects of using different protocols.
study subject role
A role that is realized through the execution of a study design in which the bearer of the role participates and in which data about that bearer is collected.
participant under investigation role
responsible party role
he THERAPIST has the ability to print a separate statement for the patient and each responsible party. http://www.beaverlog.com/therapist/ez_support/billing/responsible_party_statements.htm
a study personnel role played by a party who is accountable for the execution of a study component and can make decisions about the conduct of the study
Person: Jennifer Fostel
a responsible party role played by a person responsible for the overall conduct of a study
principal investigator role
A role borne by a material entity that is obtained during a specimen collection process and that can be realized by performing measurements or observations on the specimen.
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 reference participant role which is realized by making the reference to qualities at the start of the study or intervention
baseline participant role
filter paper
A device manufacture with the intent to provide a porous unsized paper used for filtering.
a role realized when a participant serves as reference to itself
crossover population role
a study population role where the bearer is a population of material entities and the role is realized in the implementation of a study design wherein the entities bearing the study population role are observed or subjected to intervention according to the study design and are biological replicates, i.e. they receive the same treatment under the protocol
study group role
population
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
adapted from Oxford English Dictionnary
a reference participant role realized by equivalent treatment of participants
biological replicate role
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.
methodology testing objective
Methodology_testing_objective is an objective role carried out by a proposition defining the aim of the study is to examine the effect of using different methodologies.
a reference subject role which inheres in an organism or entity of organismal origin so that the characteristics or responses of the participant playing the reference participant role are used for comparison or reference
reference subject role
organization
An entity that can bear roles, has members, and has a set of organization rules. Members of organizations are either organizations themselves or individual people. Members can bear specific organization member roles that are determined in the organization rules. The organization rules also determine how decisions are made on behalf of the organization by the organization members.
technical replicate role is realized when two portions from one evaluant are used in replicate runs of an assay
technical replicate role
a cohort role is a biological replicate role played by a group of study participants who share a common characteristic of interest to the study.
WEB:http://www.sceoc.com/glossaryofterms/ # a group of individuals having a statistical factor (as age or class membership) in common in a demographic study, such as a cohort of students.
WEB:http://www.thebody.org/content/treat/art2612.html # a group of individuals in a study who share a demographic, clinical, or other statistical characteristic (eg, age, study site).
WEB:http://www.uhhospitals.org/tabid/591/Default.aspx # A cohort is a group of people with a common characteristic that is studied over a period of time as part of a scientific or medical investigation.
cohort role
plan
A plan is a realizable entity that is the inheres in a bearer who is committed to realizing it as a completely executed planned process.
branch derived
protocol
A plan specification which has sufficient level of detail and quantitative information to communicate it between investigation agents, so that different investigation agents will reliably be able to independently reproduce the process.
OBI branch derived + wikipedia (http://en.wikipedia.org/wiki/Protocol_%28natural_sciences%29)
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
A measurand role borne by a molecular entity or an atom and realized in an analyte assay which achieves the objective to measure the magnitude/concentration/amount of the analyte in the entity bearing evaluant role.
analyte role
A role of a material entity that is realized in an "adding a material entity into a target" process where the bearer of the role is added into another material entity (the target).
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
mass analyzer
The mass analyzer of the Voyager-DE(tm) STR Biospectrometry Workstation
A Mass analyzer is a device that separates ions according to their mass-to-charge ratio. All mass spectrometers are based on dynamics of charged particles in electric and magnetic fields in vacuum where the two laws of Lorentz force law and Newton's second law of motion apply.
An ion source is a device that is part of a mass spectrometer that ionizes the material under analysis. The ions are then transported by magnetic or electric fields to the mass analyzer. Techniques for ionization have been key to determining what types of samples can be analyzed by mass spectrometry. Electron ionization and chemical ionization are used for gases and vapors. In chemical ionization sources, the material is ionized by chemical ion-molecule reactions during collisions in the source. Two techniques often used with liquid and solid biological samples include electrospray ionization (due to John Fenn PMID 2675315.) and matrix-assisted laser desorption/ionization (MALDI, due to M. Karas and F. Hillenkamp (Measuring Mass: From Positive Rays to Proteins by Michael A. Grayson (Editor) (ISBN 0-941901-31-9))).
ion detector
The ion detector of the Voyager-DE(tm) STR Biospectrometry Workstation
An ion detector is a device that measures and records the charge induced or current produced when an ion passes by or hits a surface. Example: In a scanning instrument the signal produced in the detector during the course of the scan versus where the instrument is in the scan (at what m/Q) will produce a mass spectrum, a record of ions as a function of m/Q.
contain function
A contain function is a function to constrain a material entities location in space
heat function
A heat function is a function that increases the internal kinetic energy of a material
material separation function
A material separation function is a function that increases the resolution between two or more material entities. The to distinction between the entities is usually based on some associated physical quality.
filter function
A filter function is a function to prevent the flow of certain entities based on a quality or qualities of the entity while allowing entities which have different qualities to pass through
ionization function
An ionization function is a function to physically convert an atom or molecule into an ion by adding or removing charged particles such as electrons or other ions.
cool function
A cool function is a function to decrease the internal kinetic energy of a material below the initial kinetic energy of that type of material.
environment control function
An environmental control function is a function that regulates a contained environment within specified parameter ranges. For example the control of light exposure, humidity and temperature.
measuring glucose concentration in blood serum
measuring glucose concentration in blood serum assay
An assay that determines the concentration of glucose molecules in a blood serum sample
extract
an extract is a material entity which results from an extraction process
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 assay objective to determine the presence or concentration of an analyte in the evaluant
analyte measurement objective
an objective specification to determine a specified type of information about an evaluated entity (the material entity bearing evaluant role)
assay objective
analyte assay
example of usage: In lab test for blood glucose, the test is the assay, the blood bears evaluant_role and glucose bears the analyte role. The evaluant is considered an input to the assay and the information entity that records the measurement of glucose concentration the output
An assay with the objective to capture information about the presence, concentration, or amount of an analyte in an evaluant.
Note: is_realization of some analyte role isn't always true, for example when there is none of the analyte in the evaluant. For the moment we are writing it this way, but when the information ontology is further worked out this will be replaced with a condition discussing the measurement.
logical def modified to remove expression below, as some analyte assays report below the level of detection, and therefore not a scalar measurement datum, replaced by measurement datum and ('has measurement unit label' some 'measurement unit label') and ('is quality measurement of' some 'molecular concentration'))
PERSON:Bjoern Peters, Helen Parkinson, Philippe Rocca-Serra, Alan Ruttenberg
PERSON:Bjoern Peters PERSON:Helen Parkinson PERSON:Philippe Rocca-Serra PERSON:Alan Ruttenberg GROUP:OBI Planned process branch
A role of a material entity that is realized in an "adding a material entity into a target" process where the bearer of the role (the target) receives the addition of another material entity.
target of material addition role
A data set that is produced as the output of a normalization data transformation.
normalized data set
measure function
Measure function is a function that is borne by a processed material and realized in a process in which information about some entity is expressed relative to some reference.
an objective specifiction that creates an specific output object from input materials.
material transformation objective
A planned process with the objective to produce a processed material which will have a function for future use.
manufacturing
is the objective to manufacture a material of a certain function (device)
manufacturing objective
a planned process that carries out a study design
An analyte assay which uses analytical methods to produce measurements and data on the concentration of chemical parameters (analytes) present in a bodily fluid collected from an organism.
Manufacturer role is a role which inheres in a person or organization and which is realized by a manufacturing process.
a material entity that consists of all the molecules of a specific type that are located in some bounded region and which is part of a more massive material entity that has parts that are other such aggregates
scattered molecular aggregate
Co-associations between insulin sensitivity and measures of liver function, subclinical inflammation, and hematology. Godsland IF, Johnston DG. Metabolism. 2008 Sep;57(9):1190-7. PMID: 18702943
An assay that studies phenotypes of an organism involving its blood and blood producing organs using a variety of techniques and instruments
hematology is a process studying blood and blood producing organs relying on a variety of techniques and instruments
is an objective to transform a material entity into spatially separated components.
a portion of urine collected from an organism
is a material processing with the objective to combine two or more material entities as input into a single material entity as output.
a quality inheres_in some device and is concretization of some (device_setting_specification and is_about a quality of the device
a material entity derived from a portion of blood collected from an organism
A planned process with the objective to obtain a material entity for potential use as an input upon which measurements or observations are performed.
a material obtained from an organism in order to be a representative of the whole
A material separation objective aiming to separate material into multiple portions, each of which contains a similar composition of the input material.
separation into different composition objective
A material separation objective aiming to separate a material entity that has parts of different types, and end with at least one output that is a material with parts of fewer types (modulo impurities).
A objective specification that is fulfilled by obtaining a material entity for potential use as an input upon which measurements or observations are performed.
is an objective to obtain an output material that contains several input materials.
PMID: 19527607 Using the 100-g Oral Glucose Tolerance Test to Predict Fetal and Maternal Outcomes in Women with Gestational Diabetes Mellitus. Lin CH, Wen SF, Wu YH, Huang MJ. Chang Gung Med J. 2009 May-Jun;32(3):283-9.
An assay that measures glucose clearance from blood over time by repeated glucose measurement in blood serum or plasma after the administration of a glucose bolus in-vivo. This assay can be used to evaluate the severity of insulin resistance or the efficiency of glucose clearance.
is a process in which following administration of a bolus a glucose in-vivo, glucose clearance from blood plasma is monitored over time by repeated glucose measurement in blood serum. the output of a process is a measure which can be used to evaluate the severity of insulin resistance or the efficiency of glucose clearance.
30-10-2013:[author: PRS] removing "realizes some (concretizes some 'time series design')" axiom as it causes 'gtt' to be classified under study design execution instead of assay
host role is a role played by an organism and realized by providing nourishment, shelter or a means of reproduction to another organism within the organism playing the host role
A material sample role is a specimen role borne by a material entity that is the output of a material sampling process.
A material entity that has the material sample role
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
Web: http://en.wikipedia.org/wiki/Dependent_and_independent_variables
study design independent variable
dependent variable specification is part of a study design. The dependent variable is the event studied and expected to change when the independent variable varies.
study design dependent variable
An objective specification maintains some or all of the qualities of a material over time.
A planned process with the objective to inform a person or their legal representative of legally and ethically relevant facts about a process that the person in question is asked to participate in, and which results in a documented decision as to whether the person in question will participate.
to be treated with active ingredient role
A study subject role which begins to exist when a subject is assigned to be one of those who will receive active ingredient, and is realized in a study execution in which they receive the active ingredient
A study subject role which begins to exist when a subject is assigned to be one of those who will receive a placebo, and realized in a study execution in which they receive the placebo
An organization formed with a goal to have its members conduct investigations
A device in which a measure function inheres.
A planned process with the objective to maintain some or all of the characteristics of an input material over time.
A planned process that is the part of the execution of an intervention design study which is varied between two or more subjects in the study.
A device with a separation function realized in a planed process
a role which inheres in a person who uses a service
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
an intervention design in which the treatment is the administration of a compound
A specimen that has been intentionally physically modified.
A device that can be used to restrict the location of material entities over time
a directive information entity that describes the dose that will be administered to a target
A data item that representing the primary structure of a macromolecule(it's sequence) sometimes associated with an indicator of confidence of that measurement.
sequence data
A measurement datum that measures the quantity of something that may be administered to an organism or that an organism may be exposed to. Quantities of nutrients, drugs, vaccines and toxins are referred to as doses.
The directed combination of a material entity with a specimen.
A document with a set of printed or written questions with a choice of answers, devised for the purposes of a survey or statistical study.
JT: It plays a role in collecting data that could be fleshed out more; but I'm thinking it is, in itself, an edited document. JZ: based on textual definition of edited document, it can be defined as N&S. I prefer to leave questionnaire as a document now. We can add more restrictions in the future and use that to determine it is an edited document or not.
Need to clarify if this is a document or a directive information entity (or what their connection is))
PERSON: Jessica Turner
Merriam-Webster
An extract that is the output of an extraction process in which nucleic acid molecules are isolated from a specimen.
An environmental control device is a device which has the function to control some aspect of the environment such as temperature, or humidity.
high performance liquid chromatography instrument
A liquid chromatography instrument that consists of a reservoir of mobile phase, a pump, an injector, a separation column, and a detector. The pump (rather than gravity) provides the higher pressure required to propel the mobile phase and analyte through the densely packed column.
An device that is used to determine the order of nucleotides in nucleic acid sequences.
An device that is used to determine the order of amino acids in protein sequences.
A chromatography device that dissolves a mixture in liquid mobile phase to separate the analyte to be measured from other molecules in the mixture and allows it to be isolated
A planned process in which a service provider performs a task (i.e. a planned process) for a service consumer.
A study design in which some aspects of the experiment is quality controlled for the purposes of quality assurance.
A study design that examines the relationship between the size of the administered dose and the extent of the response.
A specimen that derives from an anatomical part or substance arising from an organism. Examples of tissue specimen include tissue, organ, physiological system, blood, or body location (arm).
A material processing service in which a service provider makes physical modifications to a specified input material, such that at least one of the specified outputs of this process is a modified version of a specified input material.
A service which has a material entity as specified input and/or specified output.
A service in which a service consumer provides some input material and a service provider performs some analysis of this material to generate data that is returned to the service consumer.
A storage service in which a service consumer provides some material as input which a service provider stores and returns as output.
investigation description
A textual entity that describes an investigation.
NIAID GSCID-BRC metadata working group
project description
specimen identifier
A CRID symbol denotes a specimen and used to distinguish one specimen from another in an investigation.
Person: Chris Stoeckert, Jie Zheng
specimen ID
PubMed ID
A CRID symbol that is sufficient to look up a citation from the PubMed, a literature database of life sciences and biomedical information.
Edits was made on Aug 24, 2016 based on OBI dev call, details see tracker: https://sourceforge.net/p/obi/obi-terms/819/
PMID
PubMed Identifier
Website: http://en.wikipedia.org/wiki/Wikipedia:PMID
investigation title
A textual entity that denotes an investigation.
project title
Bioinformatics Resource Center
An organization that is one of the Internet-based research centers established and funded by NIAID (the National Institute of Allergy and Infectious Diseases). The Bioinformatics Resource Centers (BRCs) were formed in response to the threats posed by emerging and re-emerging pathogens, particularly CDC Category A, B, and C pathogens, and their potential use in bioterrorism. The intention of NIAID in funding these bioinformatics centers is to assist researchers involved in the experimental characterization of such pathogens and the formation of drugs, vaccines, or diagnostic tools to combat them.
Website: http://en.wikipedia.org/wiki/Bioinformatics_Resource_Centers
country name
A textual entity that denotes a geographic location that is a site or part of a site that is identified as a country in the political geography.
Website: http://en.wikipedia.org/wiki/Country
investigation identifier
A CRID symbol used to identify an investigation.
Person: Chris Stoeckert, Jie Zhneg
project ID
grant identifier
A CRID symbol used to identify a grant.
grant ID
An analyte assay that uses a biomaterial's preferential affinity for either the mobile phase or the stationary phase to separate it from other materials and thereby detect its presence in an input material.
grant
A plan specification of organization A to give money to organization B so that B conducts investigations. Organization A has funder role and Organization B has research organization role.
contact representative role
A role inhering in a person who represents an institution, organization, or service provider and realized when communication is directed at them about the entity they represent.
selection criterion
A directive information entity which defines and states a principle of standard by which selection process may take place.
OBI discussion summarized under the following tracker item : http://sourceforge.net/p/obi/obi-terms/678/
specimen collector role
An Investigation agent role borne by a person or organization which is realized in a specimen collection process.
A planned process in which new information is inferred from existing information.
organization of specimen provider principal investigator
An organization that is the affiliation of the principal investigator providing the specimens for the investigation
organization of Bioinformatics Resource Center contact person
An organization that is the affiliation of the person who is contact representative of a Bioinformatics Resource Center
Bioinformatics Resource Center Contact's Institution
specimen-based scope of investigation specification
A plan specification which specifies the scope of an investigation based on the heterogeneity of organisms or type of material that are the specified input of specimen collection.
specimen repository organization
An organization that provides a service to store and distribute specimens
email address of Bioinformatics Resource Center contact person
An email address of the person who is contact representative of a Bioinformatics Resource Center
Bioinformatics Resource Center Contact's email
email address of specimen collector
An email address of the person collecting the specimen
sequencing facility organization
An organization that provides sequence determination service
organization of specimen collector
An organization that is the affiliation of the person collecting the specimen
email address of sequencing facility contact person
An email address of the contact representative at the sequencing facility
investigation assay specification
A plan specification which indicates the assay type used to obtain data.
organization of sequencing facility contact person
An organization that is the affiliation of the contact representative at the sequencing facility
Sequencing Facility Contact's Institution
comment on investigation
A textual entity that is about any of the aspects of an investigation worth noting
specimen identifier assigned by specimen repository
A specimen identifier which is assigned by a specimen repository
specimen identifier assigned by sequencing facility
A specimen identifier which is assigned by a sequencing facility
sample preparation for sequencing assay
A sample preparation for assay that preparation of nucleic acids for a sequencing assay
email address of specimen provider principal investigator
An email address of the principal investigator providing the specimens for the investigation
sequencing service
A service provides sequencing service which is the realization of some sequencing such as RNA and DNA sequencing in which the service provider role is realized.
An information content entity that expresses an assertion that is intended to be tested.
An information content entity that is inferred from data.
A processed material that serves as a liquid vehicle for freezing cells for long term quiescent stroage, which contains chemicls needed to sustain cell viability across freeze-thaw cycles.
cell freezing medium
selection
A planned process with the objective to create a group of entities by applying a predefined criteria to a larger group of entities.
A value specification that consists of two parts: a numeral and a unit label
A planned process in which predicted values for some thing are compared to measured values for that thing.
An information content entity that specifies a value within a classification scheme or on a quantitative scale.
an information content entity that has been generated by a prediction process in which an estimate of a value of an entity is made which can be measured but without performing such a measurement. The value specification is intended to be close to the value a measurement process would produce modulo a prediction error.
grant agency
An organization that provides funding support for projects such as investigations.
collection of specimens
A material entity that has two or more specimens as its parts.
specimen set collection process
A specimen collection process that generates multiple specimens from one source (e.g. one organism) during a time period which for the purpose of the study can be considered to be taken at the same sampling time.
OBIB, OBI
specimens collected in one encounter
A collection of specimens that is collected from one source (e.g. one organism) during a time period which for the purpose of the study can be considered to be taken at the same sampling time.
human specimen set
A specimen set that is collected from one person during a time period which for the purpose of the study can be considered to be taken at the same sampling time.
Duke Biobank, OBIB, OBI
specimens collected longitudinally
A collection of specimens that was derived from the same source material entity at different time points in order to observe changes in that entity.
Bjoern Peters, OBI
physical store
a freezer. a humidity controlled box.
A container with an environmental control function.
For details see tracker item: http://sourceforge.net/p/obi/obi-terms/793/
Chris Stoeckert
Duke Biobank, OBIB
Biobank
digital object identifier
The doi symbol: "10.1109/5.771073" resolves to ieee website: http://ieeexplore.ieee.org/xpl/articleDetails.jsp?reload=true&arnumber=771073
A centrally registered identifier symbol used to uniquely identify objects given by International DOI Foundation. The DOI system is particularly used for electronic documents such as journal articles.
Discussed on Aug 22, 2016 OBI dev call. Details see tracker: https://sourceforge.net/p/obi/obi-terms/818/
https://en.wikipedia.org/wiki/Digital_object_identifier https://www.doi.org/
high performance liquid chromotography assay
On-line coupled immunoaffinity chromatography-reversed-phase high-performance liquid chromatography (IAC-HPLC) with detection by quadrupole ion trap mass spectrometry using a particle beam interface has been developed for the determination of the steroids, dexamethasone and flumethasone. HEMA (polyhydroxyethylmethacrylate) was evaluated as a support material for the anti-dexamethasone antibodies used in IAC. Antibody cross-reactivity and non-specific binding have been investigated for the HEMA bound anti-dexamethasone IAC column. The on-line IAC-HPLC-MS determination of dexamethasone and flumethasone in post-administration equine urine samples showed precisions (R.S.D.) of 8.0 and 7.1%, respectively, with limits of detection in the range 3-4 ng/ml.
An analytical chromatography assay that utilizes a high performance liquid chromatography instrument for separation of compounts in a solution.
molecular analysis facility organization
An organization that provides molecular analysis service.
measurand role
A role borne by a material entity and realized in an assay which achieves the objective to measure the magnitude/concentration/amount of the measurand in the entity bearing evaluant role.
A specimen that is derived from bile.
A specimen that is derived from feces.
digestive system fluid or secretion specimen
A specimen that is derived from digestive system fluid or secretion.
A specimen that is derived from milk.
A specimen that is derived from saliva.
A specimen that is derived from sputum.
A specimen that is derived from sweat.
An assay that has a blood specimen as evaulant.
reactant role
A role borne by a biological or chemical entity that participates or has molecular components that participate in a chemical reaction.
a material entity which corresponds to the liquid component of blood, in which the blood cells are suspended.
WEB: http://en.wikipedia.org/wiki/Blood_plasma
A material entity which derives from blood and corresponds to blood plasma without fibrinogen or the other clotting factors.
specimen
A material entity that is collected for potential use as an input upon which measurements or observations are performed.
GROUP: OBI Biomaterial Branch
A processed material comprised of a collection of cultured cells that has been continuously maintained together in culture and shares a common propagation history.
A scattered aggregate of glucose molecules in a liquid
data transformation
A completely executed planned process that produces output data from input data.
Branch editors
data transformation objective
An objective specification to transformation input data into output data
PERSON: James Malone
data normalization objective
A normalization objective is a data transformation objective where the aim is to remove systematic sources of variation to put the data on equal footing in order to create a common base for comparisons.
normalization data transformation
A normalization data transformation is a data transformation that has objective normalization.
scaling objective
is a data transformation objective where all, or some of a data set is adjusted by some data transformation according to some scale, for example a user defined minimum or maximum
Any design in which the decision as to whether to enroll the next patient, pair of patients, or block of patients is determined by whether the cumulative treatment difference for all previous patients is within specified limits. Enrollment is continued if the difference does not exceed the limits. It is terminated if it does
observation design is a study design in which subjects are monitored in the absence of any active intervention by experimentalists.
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.
an information content entity which results from a validation process aimed at confirming a claim, a finding or a predicted information entity about a material entity or a process by experimental means.
validated information
An information content entity that has undergone a digital curation performed by a curator for accuracy checks and compliance with curation requirements. Information which has been assessed for accuracy by domain experts.
curated information
a role that borne by an organism and realized by some group randomization process
randomized group participant role
A material separation in which a desired component of an input material is separated from the remainder
extraction
filtration is a process which separates components suspended in a fluid based on granularity properties relying on a filter device
OBI-Branch: adapted from wikipedia and wordnet
filtration
centrifugation
PMID: 18428461.Purification of oligodendrocytes and their progenitors using immunomagnetic separation and Percoll gradient centrifugation. Curr Protoc Neurosci. 2001 May;Chapter 3:Unit 3.12.
centrifugation is a process separating molecules by size or density using centrifugal forces generated by a spinning rotor. G-forces of several hundred thousand times gravity are generated in ultracentrifugation
adapted from http://www.fao.org/DOCREP/003/X3910E/X3910E06.htm
A planned process with the objective to preserve and protect material entities by placing them in an identified location which may have a controlled environment.
storage
A group assignment which relies on chance to assign materials to a group of materials in order to avoid bias in experimental set up.
adapted from wikipedia [http://en.wikipedia.org/wiki/Randomization]
group randomization
is a planned process with specified input original document and specified output edited document
document editing
a planned process with objective to check that the accuracy or the quality of a claim or prediction satisfies some criteria and which is assessed by comparing with independent results
validation
Digital curation is the process of establishing and developing long term repositories of digital assets for current and future reference by researchers, scientists, and historians, and scholars generally.
digital curation
A DNA sequencer is an instrument that determines the order of deoxynucleotides in deoxyribonucleic acid sequences.
centrifuge
A device with a rapidly rotating container that applies centrifugal force to its contents
Melanie Courtot
Trish Whetzel
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.
Plan for the precise procedure to be followed in a clinical trial, including planned and actual timing of events, choice of control group, method of allocating treatments, blinding methods; assigns a subject to pass through one or more epochs in the course of a trial. Specific design elements, e.g., crossover, parallel; dose-escalation [Modified from Pocock, Clinical Trials: A Practical Approach]
Clinical Research Glossary Version 4.0 CDICS glossary group
a study design which use the same individuals and exposure them to a set of conditions. The effect of order and practice can be confounding factor in such designs
a repeated measure design which ensures that experimental units receive, in sequence, the treatment (or the control), and then, after a specified time interval (aka *wash-out periods*), switch to the control (or treatment). In this design, subjects (patients in human context) serve as their own controls, and randomization may be used to determine the ordering which a subject receives the treatment and control
(source: http://www.sbu.se/Filer/Content0/publikationer/1/literaturesearching_1993/glossary.html)
N-of-1 design is a cross-over design in which the same patient is repeatedly randomised to receive either the experimental treatment or its control (Senn, 1993).
Adapted from http://www.childrens-mercy.org/stats/definitions/crossover.htm and source:http://symptomresearch.nih.gov/chapter_6/sec1/csss1pg1.htm)
A matched pair design is a study design which use groups of individuals associated (hence matched) to each other based on a set of criteria, one member going to one treatment, the other member receiving the other treatment.
A parallel group design or independent measure design is a study design which uses unique experimental unit each experimental group, in other word no two individuals are shared between experimental groups, hence also known as parallel group design. Subjects of a treatment group receive a unique combination of independent variable values making up a treatment
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.
balanced incomplete block design is a kind of factorial design where all treatment pairs occur together within a block an equal number ?? times. ??ii' is the number of times treatment i occurs with i'
http://en.wikipedia.org/wiki/Block_design and http://www.stat.psu.edu/~jglenn/stat503/05_factorial/02_factorial_IBD.html
A loop experiment design is where labeled extracts are compared in consecutive pairs. synonym: circular design
A reference experiment design type is where all samples are compared to a common reference.
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.
Adapted from: http://www.itl.nist.gov/div898/handbook/pri/section3/pri3321.htm and
Greco-Latin square design is a study design which relates to Latin square design
PRS to do
factorial design is_a study design which is used to evaluate two or more factors simultaneously. The treatments are combinations of levels of the factors. The advantages of factorial designs over one-factor-at-a-time experiments is that they are more efficient and they allow interactions to be detected. In statistics, a factorial design experiment is an experiment whose design consists of 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. Such an experiment allows studying the effect of each factor on the response variable, as well as the effects of interactions between factors on the response variable.
http://www.stats.gla.ac.uk/steps/glossary/anova.html#facdes And from wikipedia (01/03/2007): http://en.wikipedia.org/wiki/Factorial_experiment)
a factorial design which has 2 experimental factors (aka independent variables) and 2 factor levels per experimental factors
A fractional factorial design is_a study design in which only an adequately chosen fraction of the treatment combinations required for the complete factorial experiment is selected to be run
http://www.itl.nist.gov/div898/handbook/pri/section3/pri334.htm From ASQC (1983) Glossary & Tables for Statistical Quality Control
An experiment design type where the label orientations are reversed. exact synonym: flip dye, dye flip
A replicate experimental design type is where a series of replicates are performed to evaluate reproducibility or as a pilot study to determine the appropriate number of replicates for a subsequent experiments.
A study design that investigates variance and error estimates in the experimental system, and is where the same extract is compared.
Groups of assays that are related as part of a time series.
stopping rule
a stopping rule (criterion) is_a *rule* which causes a *stopping process* to happen
compliance rule
a compliance rule is a rule which ensures a compliance process occurs
standard compliance rule
a standard compliance rule is a compliance rule which defines conformity to a representation standard
ethical standard compliance rule
an ethical standard compliance rule is_a *compliance rule* which enable a *ethical compliance process* to occur
eligibility criterion
an eligibility criterion (rule) is_a selection criterion which defines and states the requirements (positive or negative) for an entity to be considered as suitable for a given task or participation in a process.
Adapted from Clinical Research Glossary Version 4.0 CDICS glossary group
inclusion criterion
an inclusion criterion (rule) is_a *eligibility criterion* which defines and states a condition which, if met, makes an entity suitable for a given task or participation in a given process. For instance, in a study protocol, inclusion criteria indicate the conditions that prospective subjects MUST meet to be eligible for participation in a study.
exclusion rule
an exclusion criterion (rule) is_a *eligibility criterion* which defines and states a condition which, if met, makes an entity unsuitable for a given task or participation in a given process. For instance, in a study protocol, exclusion criteria indicate the conditions that prospective subjects SHOULD NOT meet to be eligible for participation in a study
exclusion criterion
human subject enrollment
A planned process with the objective to obtain a population of human subjects to participate in an investigation by determining eligibility of subjects and obtaining informed consent.
IEDB
collecting specimen from organism
a process with the objective to obtain a material entity that was part of an organism for potential future use in an investigation
administering substance in vivo
A process by which a substance is intentionally given to an organism resulting in exposure of the organism to that substance.
material component separation
a material processing in which components of an input material become segregated in space
group assignment
group assignment is a process which has an organism as specified input and during which a role is assigned
OBI Plan
maintaining cell culture
A planned process with the objective to keep cells alive in a defined environment outside of an organism.
a process through which a new type of cell culture or cell line is created, either through the isolation and culture of one or more cells from a fresh source, or the deliberate experimental modification of an existing cell culture (e.g passaging a primary culture to become a secondary culture or line, or the immortalization or stable genetic modification of an existing culture or line).
sequencing assay
The use of the Sanger method of DNA sequencing to determine the order of the nucleotides in a DNA template
An assay the uses chemical or biochemical means to infer the sequence of a biomaterial
the use of a chemical or biochemical means to infer the sequence of a biomaterial
has_output should be sequence of input; we don't have sequence well defined yet
dialysis
the use of a dialysis bag of select pore size to remove salt from collagen isolated from mouse cartilage
a protocol application that uses diffusion through a semi-permeable membrane to separate an input material into two fractions of different composition
PERSON:Kevin Clancy
nucleic acid extraction
a material separation to recover the nucleic acid fraction of an input material
disposition to cause an allergic reaction
The role borne by a material entity that is realized when it is recognized by the immune system and results in the occurrence of an allergic disease.
an allergic reaction is an pathologic immune response by an organism to a non-self entity that is normally harmless(the allergen)
allergic reaction
The process of an allergic disease occurring in an organism.
occurrence of allergy
is a disease caused by an infectious agent
infectious disease
is a disease in which an abnormally strong inflammatory immune response is triggered against non-self entities, and the immune response has no protective effect
allergy
A disease characterized by abnormal and uncontrolled cell division
cancer
Is a disease characterized by an immune response of an organism against parts of itself
autoimmune disease
A specimen collection in which blood is collected from an organism.
blood specimen collection
abnormal, harmful processes caused by or associated with a disease
pathologic process
A material entity bearing the disposition to cause an allergic reaction
A specimen that is derived from some bodily fluid
Christian Stoeckert ORCID:0000-0002-5714-991X
An analyte assay that measures the abundance of glucose
A representation that is either the output of a clinical history taking or a physical examination or an image finding, or some combination thereof.
A series of statements representing health-relevant qualities of a patient and of a patient's family.
A representation of a quality of a specimen that is the output of a laboratory test and that can support an inference to an assertion about some quality of the patient.
A (combination of) quality(ies) of an organism determined by the interaction of its genetic make-up and environment that differentiates specific instances of a species from other instances of the same species.
A disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism.
A measurement assay that has as input a patient-derived specimen and as output a data item that is about a quality of the specimen.
A sequence of acts of observing and measuring qualities of a patient performed by a clinician; measurements may occur with and without elicitation.
The totality of all processes through which a given disease instance is realized.
The representation of a conclusion of a diagnostic process.
A planned process whose completion is hypothesized by a health care provider to eliminate, prevent, or alleviate a disorder, the signs and symptoms of a disorder, or a pathological process
A hypothesis about some future part of a disease course.
A planned process with the objective to improve the health status of a patient that directly involves the treatment, diagnosis, or prevention of disease or injury of a patient
A health care process with the objective to produce information about the material entity that is the evaluant, by physically examining it or its proxies.
A data item that is about a patient and is the specified output of a health care process assay or diagnostic process
clinical data item
human microbiome
A biome that consists of a collection of microorganisms (i.e., microbiota) and the surrounding environment where the microorganisms reside.
microbiome
a human microbiome that is located in a human gastrointestinal system
microbiome in human gastrointestinal system
human gut microbiome
The observable manifestation of the genotype of a microbial cell or group of cells in an environment.
A population growth range phenotype related to how growth of a microbial population is affected by the temperature of the environment.
temperature effects on population growth phenotype
A population growth phenotype relating to how the rate and/or extent of growth of a microbial population is affected by the pH of the environment.
pH effects on population growth phenotype
A population growth range phenotype related to how growth of a microbial population is affected by the concentration of solutes (water activity) in the environment.
solute and water activity effects on population growth phenotype
A microbial phenotype where the phenotype is observed at the level of a microbial population.
A microbial phenotype that is altered in some way relative to a designated control.
A population growth phenotype where the rate and/or extent of growth of a microbial population at a specified pH is altered relative to a designated control.
altered effects of pH on population growth
A population growth phenotype where the rate and/or extent of growth of a microbial population is altered relative to a designated control.
A microbial phenotype relating to the growth of a microbial population, i.e. an increase in the size of the population resulting from reproduction of individual microbes in the population.
A population growth phenotype related to how non-nutrient environmental factors affect growth of a microbial population.
effect of non-nutrient environmental factors on population growth phenotype
A microbial phenotype that affects a biological process.
A biological process phenotype where the rate, frequency, timing, or extent of a biological process is altered relative to a designated control.
A population growth phenotype relating to the vegetative growth of a microbial population in conditions of high osmolarity, which refers to osmotic conditions where the osmolarity of the environment is higher than the osmolarity that allows for optimal population growth. Population growth may refer to growth rate, growth yield, or both.
population growth in high osmolarity phenotype
A population growth phenotype where the growth of a microbial population in conditions of high osmolarity is altered relative to a designated control.
altered population growth in high osmolarity
A population growth range phenotype where the rate and/or extent of growth of a microbial population in a specified environmental condition is altered relative to a designated control.
A microbial population phenotype where the phenotype of a microbial population is altered in some way relative to a designated control.
A population growth phenotype where the rate and/or extent of growth of a microbial population at a temperature that is towards the upper end of the organism's temperature growth range is altered relative to a designated control.
altered population growth at high temperature
A role borne by a human individual or by a collection of humans regarded as possessing rights and duties enforeable at law.
Malcolm N. Shaw: International Law. Cambridge University Press, Cambridge, 2008.
legal person role
Partecipants' identification number
Aphanumeric string (1 to 8 digits) which univocally identify a partecipant/subject.
participants' identification number
Month of anthropometry assessment
Month of anthropometry assessment counted from 1900; e.g. May 2011=1337 (2011-1900=111; 111x12 months/y= 1332; 1332 + 5 (May=05)= 1337)
month of anthropometry assessment
For past smokers: time in years since quitting smoking
Time since quitting smoking
Month of physical activity assessment by questionnaire counted from 1900; e.g. May 2011=1337 (2011-1900=111; 111x12 months/y= 1332; 1332 + 5 (May=05)= 1337)
Month of physical activity assessment by questionnaire
Categories of physical activity level 1=low; 2= Medium; 3= High
categories of physical activity level
Total physical activity in MET-hours/day (without sedentary or sleeping time) derived from questionnaire data
total physical activity by questionnaire
Physical activity from recreational or leisure-time activities in MET-hours/day derived from questionnaire data
physical activity from recreational or leisure-time activities by questionnaire
time spent in light physical activity in minutes/day derived from questionnaire data
light physical activity by questionnaire
Time spent in moderate physical activity in minutes/day derived from questionnaire data
moderate physical activity by questionnaire
Time spent in vigorous physical activity in minutes/day derived from questionnaire data
vigorous physical activity by questionnaire
Time spent sedentary (PC use, TV watching) in minutes/day derived from questionnaire data
sedentary time by questionnaire
Number of physical activity bouts of moderate or vigorous physical activity of at least 10 minutes per day
number of bouts by questionnaire
Month of physical activity assessment by accelerometer counted from 1900; e.g. May 2011=1337 (2011-1900=111; 111x12 months/y= 1332; 1332 + 5 (May=05)= 1337)
Month of physical activity assessment by accelerometer
Time spent in light physical activity in minutes/day derived from accelerometer data
light physical activity by accelerometer
Time spent in moderate physical activity in minutes/day derived from accelerometer data
moderate physical activity by accelerometer
Time spent in vigorous physical activity in minutes/day derived from accelerometer data
vigorous physical activity by accelerometer
Time spent sedentary in minutes/day derived from accelerometer data
sedentary time by accelerometer
Number of bouts of moderate or vigorous physical activity per day
number of bouts by accelerometer
Average minutes per bout of moderate or vigorous physical activity per day
average duration of bouts
Dietary assessment used for uploaded dietary variables 1=24-hour recall; 2=FFQ; 3=Food record; 4=other
obsolete Dietary assessment method
Month of dietary assessment counted from 1900; e.g. May 2011=1337 (2011-1900=111; 111x12 months/y= 1332; 1332 + 5 (May=05)= 1337)
month of dietary assessment
Carbohydrate intake per unit time
calculated carbohydrate intake
Fiber intake per unit time
calculated fiber intake
Total fat intake per unit time
calculated total fat intake
Saturated fatty acid intake per unit time
calculated saturated fatty acid intake
Monounsaturated fatty acid intake per unit time
calculated monounsaturated fatty acid intake
Polyunsaturated fatty acid intake per unit time
calculated polyunsaturated fatty acid intake
Protein intake in per unit time
calculated protein intake
Month of blood draw counted from 1900; e.g. May 2011=1337 (2011-1900=111; 111x12 = 1332; 1332 + 5 = 1337)
month of blood draw
Fasting status before blood draw (measured in hours of fasting before blood draw) 1=less than 9 hours; 2=9 hours or more
fasting status
The process of collecting information on the diet/eating habits of a subject using a questionnaire.
Dietary assessment
Anthropometric and habits information of the subject. This class should not be used as an ontology term, it is included as a superclass for the purpose to give a better organization to the ontology.
subject informations
A study short name is a short alphanumeric string used to abbreviate a study proper name (OMIABIS_0000037)
short study name
Name of the consortium which the study refers to
consortium
The name of the method used for randomization (OBCS_0000089), if any randomization was adopted.
randomization method
Indicate whether blinded experiment were conducted or not
blinding
If blinded experiment were conducted, indicate the method used for blinding
blinding method
Indicated whether the study is terminated or not
study terminated
Indicate whethet the compliance was assessed or not
compliance assessment
The ration between the circumference of the waist to that of the hips
waist:hip ratio
A (short) alphanumeric string which identify the event/tretment
event identifier name
An alphanumeric string which identify and describe the event/tretment
treatment descriptive name
A long description of the sampling method used
Sampling method description
Long text describing the assay used.
assay description
Platform used for the assay
Assay platform
The unique sampling event identifier for the sample collection producing the sample
sampling identifier
This field is usually 0 for the overall intervention but may be several time points for challenges, e.g. at 0 and 12 weeks.
absolute start times
This class should not be used as an ontology term, it is included as a superclass for the purpose to give a better organization to the ontology of the terms pertinent to physical activity assessment assay
Physical activity assessment
This class should not be used as an ontology term, it is included as a superclass for the purpose to give a better organization to the ontology pertinent to blood analystics assay
blood analytics
START TAB. This class should not be used as an ontology term, it is included as a superclass for the purpose to give a better organization to the ontology.
obsolete Start tab
SUBJECT TAB. This class should not be used as an ontology term, it is included as a superclass for the purpose to give a better organization to the ontology.
Subject tab
EVENTS TAB. This class should not be used as an ontology term, it is included as a superclass for the purpose to give a better organization to the ontology.
Event tab
SAMPLING TAB. This class should not be used as an ontology term, it is included as a superclass for the purpose to give a better organization to the ontology.
obsolete: Sampling tab
PHYSIOLOGY ASSAY TAB. This class should not be used as an ontology term, it is included as a superclass for the purpose to give a better organization to the ontology.
obsolete physiology assay tab
INFORMATIONS TAB. This class should not be used as an ontology term, it is included as a superclass for the purpose to give a better organization to the ontology.
obsolete: Information tab
The process of collecting various chemical-biological data (e.g. blood analytics)
Chemical-biological assay
The process of collecting data from a sample using 'omic' technologies
Omics technology assay
Type of omic assay performed (i.e. targeted metabolomics, untargeted metabolomics)
Type of omics
Assay type (i.e. Clinical chemistry assay: Standard kit #34567 from 'vendor' assayed on a Cobas Mira analyzer)
Assay type
A short text identifying the question
short question name
Type of question or question variable code
question type
Type of physiology assay performed
obsolete Physiology assay type
An assay which purpose is to collect all the general information (e.g. anthropometric measurement) available on the subjects of nutritional studies
Subject Information collection
The subject (Human) participating in a nutritional study.
subject of a nutritional study
An experimental comparison study in which participants are allocated to treatment/intervention or control/placebo groups using a random mechanism (see randomisation). Best for study the effect of an intervention.
A controlled trial where each study participant has both therapies, e.g, is randomised to treatment A first, at the crossover point they then start treatment B. Only relevant if the outcome is reversible with time, e.g, symptoms.
Data are obtained from groups who have been exposed, or not exposed, to the new technology or factor of interest (eg from databases). No allocation of exposure is made by the researcher. Best for study the effect of predictive risk factors on an outcome.
Patients with a certain outcome or disease and an appropriate group of controls without the outcome or disease are selected (usually with careful consideration of appropriate choice of controls, matching, etc) and then information is obtained on whether the subjects have been exposed to the factor under investigation.
A study that examines the relationship between diseases (or other health-related characteristics) and other variables of interest as they exist in a defined population at one particular time (ie exposure and outcomes are both measured at the same time). Best for quantifying the prevalence of a disease or risk factor, and for quantifying the accuracy of a diagnostic test.
Any substance that is distributed in foodstuffs. It includes materials derived from plants or animals, such as vitamins or minerals, as well as environmental con-taminants. Concept of food component can be viewer both as a role and as a material entity. This class, for convenience, represents the material entity "food component", including all those material entity having the role of "Food Component"
food component entity
Component added to food to improve or preserve it
additive
Unwanted food component that makes the food no longer suitable for use
contaminant
A food bioactive is a food component other than those needed to meet basic human nutritional needs (nutrients). Food bioactives modulates one or more metabolic processes, possibly resulting in the promotion of better health. The daily required intake for food bioactives is not established yet, and there is no demonstration that malnutrition occurs when the right amount is not provided
food bioactive
A nutrient is a food component used by the body for normal physiologic functions that guarantee survival and growth. It must be supplied in adequate and defined amounts from foods consumed within a diet. Malnutrition occurs when the right amount of nutrient is not provided
nutrient
An ingredient is a material entity used as part for the preparatio of food. Recipes specify which ingredients are used to prepare a specific food
Ingredient
The food is a complex matrix that is consumed by a person through the process of eating or drinking. Food are bearer of the nutrients, bioactives and sometimes other food components. Food consumption, through the meal consumption, follows a certain dietary pattern, which define the diet. Nutrients and bioactives contained in food can be exploited by the human organism thanks to the process of digestion, absorption, metabolization, or through the intervention of the gut microflora
A descriptive diet which is the regular course of eating and drinking adopted by an organism.
individual regular diet
A diet administered during an intervention study. It usually comprises the adoption of a certain nutritional intervention, intended as the prescription of consuming or not consuming certain food, and follows a precise study design. Intervention studies usually compare at least two subgroups of a population, one control group receiving a null nutritional intervention, and one or more test groups receiving the intervention
study intervention diet
A diet prescribed by a physician/ nutritionist to meet specific nutritional needs of a person.
clinical treatment protocol
diet therapy
dietetic diet
medically proscribed diet
clinically prescribed diet
A descriptive diet consumed by a population in a certain geographical area, or in a certain cultural setting, or following certain common eating behaviour.
usual diet
population regular diet
Cook role is the role of the person responsible for food prepraration
cook role
A meal is an eating/drinking occasion which usually occurs at certain time during the day.
The consumption of liquids. Not for drinking alcohol or alcohol consumption ( = ALCOHOL DRINKING); differentiate from DRINKING BEHAVIOR.
obsolete drinking
The consumption of edible substances. The act of eating: do not confuse with FOOD (the substance eaten) or EATING BEHAVIOR (the manner of eating).
obsolete eating
A class which groups the data item collected as results from the subject information collection assay
subject information collection data
A class which groups the data item collected as results from the dietary assessment assay
dietary assessment data
A class which groups the data item collected as results from the chemical biological assay
chemical biological data
A class which groups the data item collected as results from the analysis performed with an omics platform
omics data
A class which groups the data item collected as results from the physical activity assay
physical activity assessment data
The process in which food is made.
food preparation
A descriptive diet pertaining to an individual organism.
eating pattern
obsolete: individual dietary pattern
An objective measurement to assess the exposure (including food intake), effect, or succeptibility of the human organism (or an animal etc.)
biomarker
An exposure biomarker reflects the level of extrinsic variables that humans are exposed to, such as diets or food compounds, including nutrients and non-nutrients.
Intake Biomarker
exposure biomarker
An effect biomarker reflects the funciontal response of the human body to an exposure.
effect biomarker
Measurable indicator including genetic or acquired host factors and intrinsic factors, influencing the response of an individual to a (dietary) exposure.
susceptibility biomarker
A raw food is an uncooked, unprocessed food that is consumed in its natural state
raw food
A processed food is the result of the process of home or industrial food preparation
Digestion is the breakdown of large food molecules into small water-soluble food molecules. The breakdown is both mechanical and chemical (enzymatic digestion). During digestion, food components are released from the food matrix and may become bioaccessible.
Should break the definition down into separate terms, e.g. bioaccessable should be defined separately.
food digestion
Process mainly occurring in the small intestine and allowing the passage of the biaoccessible food components from the gastro-intestinal lumen into the blood vessels. Absorption occurs through either diffusion or active transport. The degree and rate at which a substance is absorbed and is made available at the site of physiological activity is called bioavailability
food component absorption
Sum of the chemical changes occurring to nutrients and food component within the body. Changes can be anabolic (constructive) or catabolic (destructive). Anabolism converts simpler compounds into organized substances that the body can use. Catabolism converts more organized substances into simpler compounds. In the oxidative or energetic catabolism, this is coupled with the production of ATP
food component metabolization
Finite list of foods and beverages with response categories to indicate usual frequency of consumption over the time period queried. The time period can vary (from 1 week to 1 year and over). To assess the total diet, the number of foods and beverages queried typically ranges from 80 to 120. Usual portion size can be asked separately for each food and beverage. Alternatively, portion size can be combined with frequency information by asking respondents to translate usual consumption amount to number of specified units (e.g., spoon, cup, glass, etc). Some questionnaires include portion size images in an attempt to enhance reporting accuracy. In addition to foods and beverages, FFQs often ask about the frequency of intake and dosages of dietary supplements.
A structured interview intended to capture detailed information about all foods and beverages (and possibly, dietary supplements) consumed by the respondent in the past 24 hours, most commonly, from midnight to midnight the previous day. A key feature of the 24HR is that, when appropriate, the respondent is asked for more detailed information than first reported. For example, a respondent reporting chicken for dinner or a sandwich for lunch would be asked about the preparation method and type of bread. This open-ended response structure is designed to prompt respondents to provide a comprehensive and detailed report of all foods and beverages consumed. A 24h can also be filled at home by the responder, and be checked during an interview to further improve it with additional details
A food diary is a record of eaten foods on a meal-by-meal, daily, or weekly basis. It is directly filled by the investigated subject, and it can include nutritional or other dietary information, organize and track foods by food group, and allows monitoring what, when, and how often the filling subject eats.
Nutritional researcher role is the role of a researcher with specific training and expertise in the nutritional science field
any type of assay that can be performed in the context of a nutritional study
Francesco Vitali
nutritional research assay
an assay that is aimed at discovering new potential metabolites as food consumption biomarkers, or to measure/validate known food consumption biomarkers in a biological sample (e.g. urine, blood, serum, feces).
food biomarker analysis assay
An assay that is aimed at measuring the quantity (or presence) of food intake biomarkers in a biological sample (e.g. urine, blood, serum, feces) in order to evaluate the consumption of defined foods
Food biomarker validation assay
An assay that is aimed at measuring the quantity (or presence) of food related metabolites in a biological sample (e.g. urine, blood, serum, feces) in order to identify/discover new food intake biomarkers
food biomarker discovery assay
A data item which is a quantitative estimate of nutrient intake to be used as a reference value for planning and assessing diets for healthy people.
Damion Dooley
DRI
dietary reference intake
A dietary reference intake which is an average of daily nutrient intake values to be used as a reference for planning and assessing diets for healthy people.
average daily nutrient intake level
daily dietary intake level
An average daily nutrient intake level which is sufficient to meet the nutrient requirement of nearly all (97 to 98 percent) healthy individuals in a group.
RDA
recommended dietary allowance
An average daily nutrient intake level which is recommended based on observed or experimentally determined approximations or estimates of nutrient intake by a group (or groups) of apparently healthy people that are assumed to be adequate with respect to deficiency or disease criteria.
Adequate intake is used when an RDA cannot be determined.
adequate intake
An average daily nutrient intake level which is the highest level that is likely to pose no risk of adverse health effects to almost all individuals in the general population.
As intake increases above the UL, the potential risk of adverse effects may increase.
tolerable upper intake level
If a specified group is at the EAR threshold of a nutrient intake, then half of the individuals in the specified group are not having their nutritional needs met.
An average daily nutrient intake level which is estimated to meet the requirement of half the healthy individuals in a particular life stage and gender group.
EAR
estimated average requirement
An average daily nutrient intake level which is predicted to maintain energy balance in healthy, normal weight individuals of a defined age, gender, weight, height, and level of physical activity consistent with good health.
EER
In children and pregnant and lactating women, the EER includes the needs associated with growth or secretion of milk at rates consistent with good health. • Relative body weight (i.e. loss, stable, gain) is the preferred indicator of energy adequacy
estimated energy requirement
A dietary reference intake data item which is a range of intake for a particular energy source (protein, fat, or carbohydrate), expressed as a percentage of total energy (kcal), that is associated with reduced risk of chronic disease while providing adequate intakes of essential nutrients.
AMDR
Relative body weight (i.e. loss, stable, gain) is the preferred indicator of energy adequacy
acceptable macronutrient distribution range
unselected, autochthonous microbial consortia that initiates the fermentation
natural starter culture
microorganisms selected for specific technological and sensory properties that are inoculated directly into food materials used to initiate the fermentation process and in order to bring about desired and predictable changes in the finished product
commercial starter cultures
microorganisms naturally present in the raw food or processing environment
autochthonous food microbiota
the role of a material entity that is the vehicle for introduction of one or more microorganisms (representing starter culture) into a suitable substrate to initiate the fermentation process
microbial inoculum
a complex matrix composed of a polysaccharide (kefiran) in association with bacteria and yeasts formed during kefir fermentation
kefir grains
the addition of a small amount of a previously fermented batch to the raw food, with the aim of initiating a new fermentation process
bakslopping
the food choice management process refers to the complex decision-making process an organism carry out to realize choices about which food to be consumed, and to the choices regarding quantity and mode of consumption of foods.
food choice management process
wine consumption is part of the Mediterranean diet; as opposed to the "mismanagement of food choice" an healthy management food choice of red wine consumption in the context of mediterranean diet dietary pattern, would be that of limit consumption to a maximum of 2 glasses per day during meals (https://www.health.harvard.edu/blog/a-practical-guide-to-the-mediterranean-diet-2019032116194)
a food choice management process resulting in healthy food choice
healthy management of food choice
Wine consumption is part of the Mediterranean diet, which can be regarded as a healthy dietary pattern. A mismanagement of red wine, which might be related to alcohol addiction, leads to unhealthy food choice about the number of red wine servings consumed per day (> 2). This produces a specific dietary pattern and diet, with unfavourable health consequences, even though all the other requirements to adhere to a Mediterranean diet are met
a food choice management process resulting in unhealthy food choice
mismanagement of food choice
a determinant of diet is any factor that drive the food choices of an organism
evaluate if it is more convenient to use the determinant of diet as superclass of a series of factor, or else to define the various factor as separate classes (i.e. palatabiliyt) with a "determinant of diet" role. Could be convenient in case of determinants imported from other ontologies, to avoid changing the original superclass assertion
determinant of diet
food choice refers to any decision an organism makes regarding food and diet. It both refers to the selection of specific foods to be consumed by an organism, from a variety of available options, and to the choices regarding quantity and mode of consumption of foods. Food choice are direct consequence of the food management process, and depends on a variety of determinants of diet
food selection
food choice
"Food choices" [ONS:0000132] are driven by the "food choice management process" [ONS:0000128], which in turn is influenced by a multitude of factors defined as "determinant of diet" [ONS:0000131]. Among these, there is the appeal to eat very tasty foods because of the positive effect they exert on the dopamine reward circuitry. In this way, foods rich in highly palatable ingredients such as simple sugars and fats might be preferred to healthier nutrient-dense alternatives.
the palatability of a food refers to its capacity of triggering a reward (i.e. hedonic reward, or pleasure, via a stimulation of the dopamine reward pathway) upon consumption. This property can be related to various aspects of food, usually related to fats and sugars content.
palatability
microbial culture responsible for the beginning of the fermentation process
starter culture for food fermentation
microbial cultures that do not take part to the fermentation process but contribute to the development of flavours, aroma and organoleptic properties during maturation/ripening through other metabolic pathways
non starter culture for food fermentation
This is a high-level term with the purpose of organization of more granular children term. Should not be used in annotation, favoring more specific sub-classes
technological processes during dairy food fermentation
biological process during dairy food fermentation
microbiota in finished or semi-finished fermented products and in the entire food-chain
a process in the cheese-making consisting of the storage of cheese in controlled temperature and condition, for defined amount of time. The process is associated to microbial activities such as proteases and lipases which change the morphology and physical texture of the cheese as well as develop taste and flavor of the final product
fermented food ripening
the set of reactions leading to the conversion of fats (triglycerides) into free fatty acids, monoacylglycerol, diacylglycerol, and glycerol during the fermentation process
lipolysis during food fermentation
the set of reactions leading to the hydrolysis of milk proteins into peptides during the food fermentation process
proteolysis during food fermentation
the set of reactions leading to the conversion of glucose into pyruvic acid, which is substrate for the fermentation processes
glucose metabolism during food fermentation
Water-soluble exopolisaccharide produced by Lactobacillus kefiranofaciens during kefir fermentation. It is present in kefir grains
kefiran
consortium of living microorganisms present in kefir, characterized by bacteria and yeast components (has part)
kefir microbiota
The set of reactions leading to the conversion of carbohydrates into organic acids, ethanol and CO2 by the enzymatic activity of kefir microbiota
kefir fermentation
vital biomass containing microorganisms added to start the fermentation process
inoculum for fermentation
complex matrix composed of an exopolysaccharide in association with bacteria and yeast cells added to milk for kefir production
kefir grain as inoculum
the procedure in which a small amount of the finished or intermediate fermentation product is used to inoculate a new batch with the aim of starting a new fermentation process
backslopping
kefir recipe includes and defines the set of ingredients and procedures that should be employed to obtain kefir
kefir recipe
consortium of living microrganisms present in whey, characterized by bacteria and yeast components (has part)
whey microbiota
mixture of milk originating from different animal species or from different milking times
mixed milk
the process of destabilization of casein micelles, which flocculate and aggregate to form a gel enclosing the soluble milk components. It is caused by acidification, by enzymatic activities or by the combination of the two processes
milk coagulation
the set of reactions leading to the conversion of carbohydrates into organic acids by the enzymatic activity of starter microbes in the production of Parmigiano Reggiano. It can also be extended to the proteolitic and lipolytic reactions characterizing maturation and ripening steps.
parmigiano reggiano fermentation
Parmigiano Reggiano recipe includes and defines the set of ingredients and procedures that must be employed to obtain Parmigiano Reggiano cheese
parmigiano reggiano recipe
the result of moulding and final pressing of Parmigiano Reggiano mass retrieved from cauldron
shaped parmigiano reggiano
the set of reactions leading to the conversion of carbohydrates into organic acids, ethanol and CO2 by the enzymatic activity in the absence of oxygen
fermentation ons
foods or beverages produced through controlled microbial growth, and the conversion of food components through enzymatic action
fermented food
starter culture
a chemical and/or physical factor that exerts selection pressure and brings about natural selection within microbiota components
agent for physico-chemical selection of microbiota
the process in which the cheese is placed in a mould giving rise to it its final shape, and immersed in a saturated solution of water and salt
cheese shaping and salting
a heating process in which the curd is cooked at defined temperature for a defined amount of time. As a result the curd sink to the bottom of the cauldron forming a single mass
curd cooking
the microbial consortium associated to curd
curd microbiota
a hard, cooked, brittle cheese with a long ripening time (minimum of 12 months), produced using raw semiskim high-quality cow milk, natural fermented whey, calf rennet and sodium chloride, designed as PDO
parmigiano reggiano
a heating process were curd is cooked at 55 °C for 12 minutes, after which the cheesy granules sink to the bottom of the cauldron forming a single mass
parmigiano reggiano curd cooking
the process in which the shaped cheese is stored in controlled temperature condition and for defined amount of time to give rise to the ripened cheese
cheese maturation
the process during which the parmigiano reggiano cheese wheels are stored at 18-20 °C for a minimum of 12 months giving rise to the ripened parmigiano reggiano
parmigiano reggiano maturation
the microbial consortium associated to parmigiano reggiano cheese
parmigiano reggiano microbiota
the process in which the cheese, wrapped in typical linen cloth, is placed in a mould that gives it its final shape and immersed in a saturated solution of water and salt.
parmigiano reggiano shaping and salting
the result of moulding and final pressing in cheese-making
shaped cheese
mixture obtained by combining milk from morning milking with milk from previous evening milking and used as initial ingredient in Parmigiano Reggiano making
starting milk mixture
consortium of living microrganisms present in milk before processing, characterized by bacteria and yeast components (has part)
starting milk mixture microbiota
the role of a material entity, generally a chemical compound, such as the material entity is not suitable for consumption by a defined group of individuals. This role has a causal relation (is determined by) with another material entity such that it exerts a strong causal influence on the role, and its removal cause the termination of the existence of the role
suitable for consumption
the role of a material entity, generally a chemical compound, such as the material entity is unfit for consumption by a defined group of individuals. This role has a causal relation (is determined by) with another material entity such that it exerts a strong causal influence on the role, and its removal cause the termination of the existence of the role
unfit for consumption
the ratio between the vapor pressure of the food, when in a completely undisturbed balance with the surrounding air media, and the vapor pressure of distilled water under identical conditions
water activity in food
whey from the previous day manufacture containing the consortium of living microorganisms, added to start the fermentation process
whey as inoculum
the procedure in which a small amount of the finished or intermediate kefir is used to inoculate a new batch with the aim of starting a new fermentation process
backslopping in kefir fermentation
the procedure in which a small amount of whey product of the parmigiano reggiano milk coagulation is used to inoculate a new batch with the aim of starting a new fermentation process
backslopping in parmigiano reggiano fermentation
nutritional study
An assay that investigates food and nutrient intake or dietary pattern of an individual or individuals
dietary assessment method
A dietary assessment method that relies on participants recalling and reporting their food and beverage intake over a defined period
retrospective dietary assessment method
A dietary assessment method that involves recording the diet when the foods or drinks are being consumed
prospective dietary assessment method
A retrospective dietary assessment method that assesses the number of different foods, drinks and/or food groups consumed over a specified reference period
Dietary Diversity Score (DDS)
retrospective method to assess dietary diversity
A retrospective dietary assessment method in which respondents recall and report all foods and beverages consumed in the past 24 hours, typically through an interview conducted by a trained professional
24-hour dietary recall method
A retrospective dietary assessment method that is a detailed assessment of usual food intake and its variation over a long period of time
dietary history method
A retrospective dietary survey method that estimates usual food intake by assessing the frequency and, in some cases, portion size of foods and/or food groups consumed over a specified time period
FFQ
food frequency questionnaire method
A prospective dietary assessment method where participants set aside duplicate portions of all foods and beverages consumed throughout a specific time period. These duplicate portions are weighed and then sent to a laboratory for chemical analysis to determine chemical composition
duplicate diet method
A dietary assessment method that prospectively collects data about foods and beverages consumed over a previously specified period of time
dietary record method
food dairies
A retrospective method to assess dietary diversity in infants and young children
retrospective method to assess dietary diversity of infant and young children
IYCDDS
Infant and Young Child Dietary Diversity Score
A retrospective method for assessing dietary diversity in women. Minimum Dietary Diversity-Women is a dichotomous indicator of whether or not women of 15–49 years of age have consumed at least five out of ten predefined food groups during the previous 24 hours.
retrospective method to assess dietary diversity of women
MDD-W
Minimum Dietary Diversity–Women
A food frequency questionnaire method that uses a brief questionnaires to asses frequency categories and number of foods or food groups consumed
screener method
A food frequency questionnaire method that collects only the frequency of food or drink intake without assessing portion sizes
non-quantitative FFQ method
A food frequency questionnaire method that collects information on both the frequency and the portion sizes or quantities of food or drink consumed
semi-quantitative FFQ method
A dietary record method where respondents are asked to weigh foods or drinks using weighing scales
weighed food records method
A dietary record method where respondents document all foods and beverages consumed during a predefined period
estimated food records method
An information content entity that specifies the quality of a dietary survey.
quality indicator of a dietary assessment
quality of a dietary assessment
A quality indicator of a dietary survey that describes the quality of a diet recall method.
quality indicator of a dietary recall method
A quality indicator of a dietary questionnaire that describes the quality of dietary survey
quality indicator of a diet assessment questionnaire
quality of a data collection instrument
A quality indicator of a dietary survey that specifies the representativeness of the assessment
quality indicator of representativeness of days of a dietary assessment
A quality indicator of a dietary survey that specifies the accuracy of a food quantification process
quality indicator of a food quantification method
A quality indicator of a dietary recall method that specifies the administration type
administration type of a dietary recall method
A quality indicator of a dietary recall method that specifies when the dietary intake was recorded
time of dietary record
A quality indicator of a diet survey questionnaire that specifies how the questionnaire was developed
Chen Yang
origin of a diet assessment questionnaire
A quality indicator of a diet survey questionnaire that specifies the content validity of a diet survey questionnaire in another comparable population in terms of both age and dietary habits.
content validity of a diet assessment questionnaire
A quality indicator of a food quantification method that indicates whether a food quantification method is tailored to the characteristics of the assessed population.
customized food quantification
A quality indicator of a food quantification method that indicates how the measured food intake data are matched to food composition data.
referred food composition data for quantification
A quality indicator of representativeness of days of a dietary survey that specifies if data collection was seasonality representative
representativeness of seasons of a dietary assessment
A quality indicator of representativeness of days of a dietary assessment that specifies the representativeness of week/weekend days when conducting a dietary survey
representativeness of week/weekend days of a dietary assessment
A quality indicator of representativeness of days of a dietary survey that specifies the number of days of a dietary recall/measurement per individual
number of days of a dietary assessment
A quality indicator of representativeness of days of a dietary assessment that specifies how the recall/measurement days of a dietary survey were selected
selection of recall/measurement days of a dietary assessment
A quality indicator of a food quantification method that specifies how the quantity of the portion sizes is estimated
quantification of a food portion size
A quality indicator of a food quantification method that specifies how food intake data are expressed into units of weights or volume
quantification of food intake data
A quality indicator of a food quantification method that indicates whether a food quantification method is geography matched to the area where the food is measured
geographically specific food quantification
An abstract of a nutrition that describes the dietary or nutritional assessment method
abstract of a nutrition study
A results section that reports the number of individuals excluded based on missing, incomplete or implausible dietary/nutritional data.
Carl Lachat
participants result section
A methods section of a nutrition study that describes the characteristics of dietary or nutrition assessment
methods section of a nutrition study
A results section of a nutrition study that describes the findings of the study
results section of a nutrition study
A discussion of a nutrition study that discusses the findings of the study
discussion of a nutrition study
An ethical approval section of a nutrition study that describes the ethical aspects related to participation in nutrition research
ethics approval section of a nutrition study
A discussion section nutrition study that describes the main limitations of the data sources and assessment methods used the interpretation of the findings
limitation section
Supplementary material of a nutrition study that provides data collection tools and data as online material for dietary surveys or nutrition studies .
Lachat C, Hawwash D, Ocké MC, Berg C, Forsum E, Hörnell A, Larsson C, Sonestedt E, Wirfält E, Åkesson A, Kolsteren P, Byrnes G, De Keyzer W, Van Camp J, Cade JE, Slimani N, Cevallos M, Egger M, Huybrechts I. Strengthening the Reporting of Observational Studies in Epidemiology-Nutritional Epidemiology (STROBE-nut): An Extension of the STROBE Statement. PLoS Med. 2016 Jun 7;13(6):e1002036. doi: 10.1371/journal.pmed.1002036.
supplementary material of a nutrition study
A methods section that describes any characteristics of the study settings that might affect the dietary intake or nutritional status of the participants, if applicable.
settings section
A methods section that reports particular dietary, physiological or nutritional characteristics that were considered when selecting the target population.
participants section
A methods section that a) clearly defines foods, food groups, nutrients, or other food components.b) when using dietary patterns or indices, describes the methods to obtain them and their nutritional properties.
variables section
A methods section of a dietary survey that includes elements for the description of data measurements conducted in the survey.
data measurements section
A method section of a dietary survey that reports how bias in dietary or nutritional assessment was addressed.
An example can include misreporting, changes in habits as a result of being measured, or data imputation from other sources.
bias section
A methods section that explains categorization of dietary/nutritional data (e.g., use of N-tiles and handling of nonconsumers) and the choice of reference category, if applicable.
quantitative variables section
A statistical analysis section of a nutrition study that describes the statistical method used to combine dietary or nutritional data and statistical analysis of nutrition or dietary data
statistical analysis section of a nutrition study
A data measurements section that describes the dietary assessment method(s), e.g., portion size estimation, number of days and items recorded, how it was developed and administered, and how quality was assured, and report if and how supplement intake was assessed.
dietary assessment method(s) section
A data measurements section that describes and justifies food composition data used. (e.g. explain the procedure to match food composition with consumption data and describe the use of conversion factors, if applicable.)
food composition data section
A data measurements section that describes the nutrient requirements, recommendations, or dietary guidelines and the evaluation approach used to compare intake with the dietary reference values, if applicable.
dietary reference values section
A data measurements section that reports the type of biomarkers used and their usefulness as dietary exposure markers. When using nutritional biomarkers, additionally use the STROBE Extension for Molecular Epidemiology (STROBE-ME).
biomarkers section
A data measurements section that describes the assessment of nondietary data (e.g., nutritional status and influencing factors) and timing of the assessment of these variables in relation to dietary assessment.
nondietary data section
A data measurements section that reports on the validity of the dietary or nutritional assessment methods and any internal or external validation used in the study, if applicable.
study validation section
A results section that gives the distribution of participant characteristics across the exposure variables if applicable, specifies if food consumption of total population or consumers only were used to obtain results.
descriptive data section
A result section that specifies if nutrient intakes are reported with or without inclusion of dietary supplement intake, if applicable.
main results section
A results section that reports any sensitivity analysis (e.g., exclusion of misreporters or outliers) and data imputation, if applicable.
other analyses section
A discussion section of nutrition study that interprets the nutritional relevance of the findings, given the complexity of diet or nutrition as an exposure
interpretation section
A food-based dietary guideline that provides advice about diversity in diets and food intake
food-based dietary guideline regarding food diversity
dietary guideline regarding food diversity
dietary recommendation regarding food diversity
A publication that provides science-based dietary advice to promote healthy eating for the general public
SYSTEMIC WP5
food-based dietary guideline
FBDG
dietary guideline
dietary recommendation
healthy eating plan
A food-based dietary guideline that provides qualitative advice about diets
qualitative food-based dietary guideline
qualitative FBDG
qualitative dietary guideline
qualitative dietary recommendation
A food-based dietary guideline that provides quantitative advice about diets
quantitative food-based dietary guideline
quantitative FBDG
quantitative dietary guideline
quantitative dietary recommendation
A food-based dietary guideline that provides advice about diets of infants
food-based dietary guideline for infants
FBDG for infants
dietary guideline for infants
dietary recommendation for infants
A food-based dietary guideline that provides advice about diets of children
food-based dietary guideline for children
FBDG for children
dietary guideline for children
dietary recommendation for children
A food-based dietary guideline that provides advice about diets of adolescents
food-based dietary guideline for adolescents
FBDG for adolescents
dietary guideline for adolescents
dietary recommendation for adolescents
A food-based dietary guideline that provides advice about diets of adults
food-based dietary guideline for adults
FBDG for adults
dietary guideline for adults
dietary recommendation for adults
A food-based dietary guideline that provides advice about diets of older people
food-based dietary guideline for older people
FBDG for older people
dietary guideline for older people
dietary recommendation for older people
A collection of food types or items which have organoleptic, nutritional, availability, safety, meal time, or socially relevant characteristics with respect to a consuming individual or population.
OLD definition: In nutrition, diet is the sum of food consumed by a person or other organism
diet
A feline biologically and anatomically follows a carnivorous diet; Homo sapiens biologically and anatomically follow an omnivorous diet
A diet that is defined by the biological, anatomical, and evolutionistic digestive capabilities of a given organism.
diet by digestive capability
A diet that is defined by characteristics of ingested food.
diet by type of food
A diet which involves food produced under certain agricultural conditions.
diet by agricultural treatment
A diet defined by the nutritional presence or absence of types of food bioactive compounds.
diet by nutritional composition
An eating pattern that excludes a given diet.
restrictive diet
A diet which is prescribed to meet some dietary pattern objective for an individual organism or group.
prescribed diet
A diet which represents food types or items consumed in the regular course of eating and drinking by an individual or population over some duration of time.
The food entities in a descriptive diet may be characterized by kind of diet as well as other (food survey or log) parameters such as quantity, time, frequency or duration of aggregate consumption, meal type and/or setting.
descriptive diet
An eating pattern pertaining to a single organism (an instance of organism). This can be used descriptively or prescriptively.
obsolete individual dietary pattern
Pregnant women should not drink more than 2 glasses of wine a day.
A prescribed diet which pertains to a population or sub-population of organism.
Was labeled "population dietary pattern", but semantics are now reserved for proscriptive use. For descriptive use see "population regular diet".
recommended diet
A food consumption process in which the timing of food and/or liquid ingestion is limited.
fasting process
Intermittent fasting is a broad term that encompasses a variety of programs that manipulate the timing of eating occasions by utilizing short-term fasts with the intention of modulating body composition and/or overall health.
intermittent fasting
involving fasting periods that are longer than a normal overnight fast of 8–12 hours. A form of time restricted eating, typically 16 h fasting and 8 h eating.
A type of intermittent fasting process which allows ad libitum energy intake within controlled time frames, generally a 3-12 hour range each day.
TRE
time-restricted feeding
The fasting protocol indicated fasting for 16 hrs per 24 hrs for a duration of 3 months.
A protocol that specifies the timing of food consumption.
fasting schedule
fasting protocol
The process of ingesting food during a single eating and/or drinking session. This does not include the digestion process.
episodic food intake process
A diet of a carnivore, which focuses almost exclusively on the consumption of animal food sources.
carnivorous diet
A diet of an omivore, which includes both plant and animal food sources.
omnivorous diet
A diet of a herbivore, which focuses almost exclusively on the consumption of plants, fungi and/or lichen.
herbivorous diet
A diet defined by the food source organisms it allows or excludes.
diet by food organism
A diet which focuses almost exclusively on the consumption of plants, fungi and/or lichen.
A diet that excludes all animal products (including fish and seafood).
vegan diet
A diet that includes vegetarian and milk-derived food.
lacto-vegetarian diet
A diet that includes vegetarian and avian egg derived food.
ovo-vegetarian diet
A diet that includes vegetarian, avian egg, and milk derived food.
lacto-ovo vegetarian diet
primarily a plant-based diet but includes meat, dairy, eggs, poultry and fish on occasion or in small quantities
flexitarian diet
semi-vegetarian diet
A diet which includes vegetarian food as well as fish and seafood.
pescetarian diet
A diet that excludes food containing beef food products.
non-beef diet
A diet that excludes food containing swine food products.
non-pork diet
A diet consisting entirely of breast milk.
infant breast milk diet
A diet involving formula milk.
formula milk diet
infant formula milk diet
A diet defined by the texture of prepared food.
diet by food texture
A soft textured diet was the most often prescribed followed by pureed texture and then minced texture.
A diet containing carefully selected foods of an appropriate consistency which can be more easily chewed and managed by a person with dysphagia.
texture modified diet
A full liquid diet is made up only of fluids and foods that are normally liquid and foods that turn to liquid when they are at room temperature. A full liquid diet excludes solid foods.
liquid diet
A diet consisting of food produced from organic agriculture (food that is grown without the use of synthetic fertilizers, sewage sludge, irradiation, genetic engineering, pesticides, or drugs.)
biological agriculture diet
organic agriculture diet
A diet consisting of food that may have been reared with the use of pesticides, herbicides or chemical fertilizers.
non-organic agriculture diet
A ketogenic diet is a high-fat, low-carbohydrate, adequate-protein diet that mimics a fasting state, resulting in the substitution of ketone bodies as a source of energy. The ketogenic diet can be used to reduce recurrent epileptic seizures in individuals with intractable epilepsy. Intractable epilepsy is defined as epilepsy that failed to respond to three or more antiepileptic drugs. A high-fat, adequate-protein, low-carbohydrate diet. It is primarily used in medicine to treat difficult-to-control epilepsy in children
Modified Atkins diet
ketogenic diet
Dietary Approaches to Stop Hypertension (DASH) trial, which demonstrated that consuming a diet rich in fruits, vegetables, and low-fat dairy products and reduced in saturated fat and cholesterol
DASH diet
A moderate-fat, restricted-calorie, Mediterranean diet is rich in vegetables and low in red meat, with poultry and fish replacing beef and lamb.
mediterranean diet
A diet which provides > 60% of total dietary energy from carbohydrates. It consists predominantly of high glycemic carbohydrates have detrimental metabolic effects
high-carbohydrate diet
Low-carbohydrate diets restrict carbohydrate consumption relative to the average diet. Foods high in carbohydrates (e.g., sugar, bread, pasta) are limited, and replaced with foods containing a higher percentage of fat and protein (e.g., meat, poultry, fish, shellfish, eggs, cheese, nuts, and seeds), as well as low carbohydrate foods (e.g. spinach, kale, chard, collards, and other fibrous vegetables).
Low carbohydrate diet
low-carbohydrate, high-protien, high fat diet
A diet involving the a larger proportion of fat than normal.
high fat diet
A restricted-energy diet with less than 30% of energy from fat.
low fat diet
A diet which minimises or eliminates the consumption of gluten.
gluten free diet
A diet that an individual organism has chosen as an objective.
self-prescribed diet
A diet prescribed to a group in a research study.
research prescribed diet
A dietairy pattern adhered to by a study control group. (possibly a placebo).
null nutritional diet
study null nutritional diet
A diet designed to reduce the symptoms of Coeliac disease which is caused by a reaction to gliadin (a gluten protein found in wheat) and similar proteins found in other crops.
celiac diet
coeliac diet
A diet involving the avoidance of Fermentable Oligo-Di-Monosaccharides and Polyols.
FODMAP diet
A diet designed to reduce the presence of fat in an organism.
weight loss diet
A diet which has an athletic performance objective
performance diet
A cultural or religious eating pattern.
ethnographic diet
A diet consisting of halal approved food.
halal diet
A diet consisting of kosher approved food.
kosher diet
An ingested food data set which is subjectively recorded or recalled by an individual consuming the food.
diet record
self-reported diet
A descriptive diet which is observed by a researcher to have been consumed by a subject organism or population of organisms.
objectively-reported diet
A descriptive diet which contains a list of foods that an individual organism has ingested over some period of time.
ingested food data set
A population regular diet which is a long-term average daily intake of nutrients and/or foods calculated according to a National Cancer Institute statistical model.
NCI usual diet
An ingested food data set of food consumption events detailing food ingested and the time of ingestion.
This may include the mass or quantity of a food item, and other details such as its preparation process.'
ingested food log
A descriptive diet containing food types or items pertinent to an average day or a given day which are ingested by an individual or organism population. The collection may indicate quantities or counts of food material.
daily food intake
A descriptive diet containing nutrient classes and their average daily intake quantity for an individual or organism population.
daily average nutritional intake
The whole of the processes by which food components released by food digestion are able to reach bloodstream
food component absorption process
A set of restrictions on food type ingestion and/or timing of food ingestion.
dietary protocol
dietary regimen
The process an organism has which achieves a dietary pattern and involves food availability, physiological or psychological motivation, selection, episodic consumption, and digestion.
organism food management process
A data item recording data about a dietary pattern
dietary pattern data item
the diet resulting from the lifestyle adaptation following the industrial revolution. It is often associated with western countries, but is increasingly becoming adopted also in other geographic areas. It is known to be rich in red and processed meats, sweets, fried foods, and refined grains while being poor in fruits, vegetables, legumes, fish, poultry, and whole grains. In terms of micronutrients, this diet is usually rich in salt, yet poor in other minerals and vitamins, whereas in terms of fats, it is high in saturated and trans-fatty acids, and low in mono- and polyunsaturated fatty acids. Its fibre and complex carbohydrates contents are also very low due to the high consumption of refined sugars instead of whole-grain foods.
"Western diet" synonym of this concept has a wider use in the literature, nevertheless it imply a misleading association to specific geographic location, even though it has a broader distribution. Another possible synonym, taking into consideration that this lifestyle is considered the result of the Industrial Revolution, is "industrialized diet"
industrialized diet
urban diet
western diet
globalized diet
the diet characteristic of the lifestyle in isolated/rural areas, commonly in developing countries. It is mainly composed of naturally available food products, including fresh animal protein and vegetables while excluding industrially processed foods. Nevertheless, it is common to use traditional food processing methods to improve nutrient availability, digestibility or to increase conservation time to avoid scarcity. These methods include soaking, fermentation, cooking, pounding, and sprouting.
local agrarian diet
traditional diet
rural diet
The temporal aspect of a dietary pattern that details meal frequency or fasting as a daily or episodic activity.
This should be placed under BCIO "consumption behaviour pattern" BCIO:050210
timing of food intake
A dietary pattern that define the quantity, variety or combination of different food in a diet by digestive capabilities.
obsolete: dietary pattern by digestive capability
A dietary pattern that define the quantity, variety or combination of different food in a diet by type of food
obsolete: dietary pattern by type of food
A dietary pattern that define the quantity, variety or combination of different food in a diet by agriculture treatment
obsolete: dietary pattern by agriculture treatment
A dietary pattern that define the quantity, variety or combination of different food in a diet by nutritional composition
obsolete: dietary pattern by nutritional composition
A dietary pattern that define the quantity, variety or combination of different food in a proscribed diet
obsolete proscribed dietary pattern
A dietary pattern that define the quantity, variety or combination of different food in a prescribed diet
obsolete prescribed dietary pattern
A dietary pattern that define the quantity, variety or combination of different food in descriptive diet
obsolete descriptive dietary pattern
A dietary pattern that define the quantity, variety or combination of different food in a diet by food organism
obsolete: dietary pattern by food organism
A dietary pattern that define the quantity, variety or combination of different food in a vegetarian diet
obsolete: vegetarian dietary pattern
A dietary pattern that define the quantity, variety or combination of different food in a vegan diet
obsolete: vegan dietary pattern
A dietary pattern that define the quantity, variety or combination of different food in a lacto-vegetarian diet
obsolete: lacto-vegetarian dietary pattern
A dietary pattern that define the quantity, variety or combination of different food in a ovo-vegetarian diet
obsolete: ovo-vegetarian dietary pattern
A dietary pattern that define the quantity, variety or combination of different food in a lacto-ovo vegetarian diet
obsolete: lacto-ovo vegetarian dietary pattern
A dietary pattern that define the quantity, variety or combination of different food in a semi-vegetarian diet
obsolete: semi-vegetarian dietary pattern
A dietary pattern that define the quantity, variety or combination of different food in a pescetarian diet
obsolete: pescetarian dietary pattern
A dietary pattern that define the quantity, variety or combination of different food in a ketogenic diet
obsolete: ketogenic diet dietary pattern
A dietary pattern that define the quantity, variety or combination of different food in a DASH diet
obsolete: DASH diet dietary pattern
A dietary pattern that define the quantity, variety or combination of different food in a Mediterranean diet
obsolete: meditteranean diet dietary pattern
A dietary pattern that define the quantity, variety or combination of different food in a high-carbohydrate diet
obsolete: high-carbohydrate diet dietary pattern
A dietary pattern that define the quantity, variety or combination of different food in a low-carbohydrate, high-protien, high fat diet
obsolete: low-carbohydrate, high-protien, high fat diet dietary pattern
A dietary pattern that define the quantity, variety or combination of different food in a high fat diet
obsolete: high fat diet dietary pattern
A dietary pattern that define the quantity, variety or combination of different food in a low fat diet
obsolete: low fat diet dietary pattern
A dietary pattern that define the quantity, variety or combination of different food in a gluten free diet
obsolete: gluten free dietary pattern
a dietary pattern that define the quantity, variety or combination of different food in a globalized diet
obsolete: globalized diet dietary pattern
a dietary pattern that define the quantity, variety or combination of different food in a rural diet
obsolete: rural diet dietary pattern
A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities
A time quality inhering in a bearer by virtue of how long the bearer has existed.
A 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.
An organismal quality inhering in a bearer by virtue of the bearer's ability to undergo sexual reproduction in order to differentiate the individuals or types involved.
A physical quality inhering in a bearer by virtue of the bearer's resistance to pressure, being broken, or pierced
A quality of a single physical entity inhering in the bearer by virtue of the bearer's size or shape or structure.
A quality of an entity that is descriptive or observational, typically not represented numerically.
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 morphology quality inhering in a bearer by virtue of the bearer's physical magnitude.
A 1-D extent quality which is equal to the distance between two points.
A physical quality that inheres in a bearer by virtue of the proportion of the bearer's amount of matter.
A 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 quality in which events occur in sequence.
An organismal quality inhering in a bearer by virtue of the bearer's behavior aggregate of the responses or reactions or movements in a given situation.
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 color hue with low wavelength of that portion of the visible spectrum lying between green and indigo, evoked in the human observer by radiant energy with wavelengths of approximately 420 to 490 nanometers.
A color consisting of green and blue hue.
A color hue with medium-low wavelength of that portion of the visible spectrum lying between yellow and blue, evoked in the human observer by radiant energy with wavelengths of approximately 490 to 570 nanometers.
A color consisting of red and blue hues.
A color hue with high wavelength of the long-wave end of the visible spectrum, evoked in the human observer by radiant energy with wavelengths of approximately 630 to 750 nanometers.
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 color quality inhering in a bearer by virtue of the bearer's having color.
A biological sex quality inhering in an individual or a population that only produces gametes that can be fertilised by male gametes.
A biological sex quality inhering in an individual or a population whose sex organs contain only male gametes.
A hardness quality of being rigid and resistant to pressure.
A hardness quality of giving little resistance to pressure.
A maturity quality inhering in a bearer by virtue of the bearer's having arrived at the onset of puberty (the age at which sex glands become functional) but not yet fully mature.
A quality inhering in a bearer by virtue of the bearer's deviation from normal or average.
A quality inhering in a bearer by virtue of the bearer's existence.
A size quality which is relatively high.
A 3-D extent quality inhering in a bearer by virtue of the bearer's amount of 3-dimensional space it occupies.
A color that falls about midway between red and blue in hue.
A color consisting of dark orange, red, of very low intensity.
A color hue with high-medium wavelength that of that portion of the visible spectrum lying between red and yellow, evoked in the human observer by radiant energy with wavelengths of approximately 585 to 620 nanometers.
Red color having medium to high brightness and low to moderate saturation.
A physical quality of a fluid inhering in a bearer by virtue of the bearer's disposition to internal resistance to flow.
A viscosity quality inhering in a bearer by virtue of the bearer's having viscosity.
A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities.
A physical quality that inheres in a bearer by virtue of the bearer's amount of force per unit area it exerts.
A concentration quality inhering in a bearer by virtue of the bearer's exhibiting concentration.
A concentration which is higher relative to the normal or average.
A concentration which is lower relative to the normal or average.
A maturity quality inhering in a bearer by virtue of the bearer's indirect development, undergoing metamorphosis.
A maturity quality inhering in a bearer by virtue of the bearer's being at the age immediately before puberty.
A maturity quality inhering in a insect by virtue of the bearer's being in the chrysalis (cocoon) or post larval stage.
A maturity quality inhering in a bearer by virtue of the bearer's being in an inactive stage in the development of some insects, between the larval and the pupal stages.
A maturity quality inhering in a bearer by virtue of the bearer's being between the onset of puberty and maturity.
A maturity quality inhering in a bearer by virtue the bearer's being not fully grown or developed.
quality of a single physical entity
A physical object quality which inheres in a single-bearer.
obsolete quality of a single physical entity
A quality which inheres in a continuant.
multiply inhering quality of a physical entity
A color consisting of blue hue and high brightness.
A color consisting of blue hue and low brightness.
A color consisting of brown hue and low brightness.
A color consisting of brown hue and high brightness.
A color consisting of cyan hue and high brightness.
A color consisting of cyan hue and low brightness.
A color consisting of green hue and low brightness.
A color consisting of green hue and high brightness.
A color consisting of grey color and low brightness.
A color consisting of grey color and high brightness.
A color consisting of magenta color and high brightness.
A color consisting of magenta with low brightness.
A color consisting of orange hue and high brightness.
A color consisting of orange color and low brightness.
Pink color having high brightness and moderate saturation.
Pink color having medium brightness and moderate saturation.
A color consisting of purple color and low brightness.
A color consisting of purple color and high brightness.
A color consisting of red hue and low brightness.
A color consisting of red hue and high brightness.
A color consisting of yellow hue and low brightness.
A color consisting of yellow hue and high brightness.
A color consisting of blue hue and high saturation.
A color consisting of blue hue and low saturation.
A color consisting of brown hue and high saturation.
A color consisting of brown hue and low saturation.
A color consisting of cyan colour and high saturation.
A color consisting of cyan colour and low saturation.
A color consisting of green hue and high saturation.
A color consisting of green hue and low saturation.
A color consisting of magenta color and high saturation.
A color consisting of magenta color and low saturation.
A color consisting of orange hue and high saturation.
A color consisting of orange hue and low saturation.
Pink color having medium brightness and low saturation.
A color consisting of purple color and high saturation.
A color consisting of purple color and low saturation.
A color consisting of red hue and high saturation.
A color consisting of red hue and low saturation.
A color consisting of yellow hue and high saturation.
A color consisting of yellow hue and low saturation.
A color consisting of red and brown hue.
A color consisting of red and brown hue and low brightness.
A color consisting of red and brown hue and high brightness.
An EM radiation quality in which the EM radiation is within the fiat range of the spectrum visible deemed to be light.
A color consisting of red and orange hue with a slight amount of gray.
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 temperature which is increased by a low degree.
A temperature which is increased by a medium degree.
A temperature which is increased by a high degree.
A biological sex quality inhering in a population of multiple sexes.
A biological sex quality inhering in an organism or a population with both male and female sexual organs in one individual.
A color hue with very low wavelength of that portion of the visible spectrum lying between reddish blue or bluish purple, evoked in the human observer by radiant energy with wavelengths of approximately 420 to 380 nanometers.
A color hue consisting of red hue and yellow hue and high brightness.
A color consisting of purple and brown hue.
A quality inhering in a bearer by virtue of the bearer's lacking complete growth, differentiation, or development.
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 ability of 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 an entity exhibiting the physical characteristics of an amorphous (non-crystalline) form of matter between a gas and a solid that has a definite volume, but no definite shape.
A quality inhering in a bearer by virtue of the bearer's exhibiting complete growth, differentiation, or development.
A color consisting of violet hue and high saturation.
A color consisting of violet hue and low saturation.
A color consisting of violet hue and high brightness.
A color consisting of violet hue and low brightness.
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 three dimensions.
A physical quality inhering in a bearer by virtue of the bearer's parts having the arrangement which exhibits characteristics of liquids.
A physical quality inhering in a bearer by virtue of the bearer's parts having the arrangement which exhibits characteristics of solids.
A composition quality inhering in an bearer by virtue of the quantities or relative ratios of water of the inhering entity.
A composition quality inhering in an bearer by virtue of the reduction in amount of water the bearer contains.
A biological sex quality inhering in an individual or a population by virtue of having internal reproductive organs of one sex and external sexual characteristics of the other sex.
A biological sex quality inhering in an individual or a population by virtue of having internal reproductive organs of male and external sexual characteristics of female.
A biological sex quality inhering in an individual or a population by virtue of having internal reproductive organs of female and external sexual characteristics of male.
A quality of a liquid inhering in a bearer by virtue of the bearer's ability to mix with (dissolve in) another liquid.
An organismal quality inhering in a bearer by virtue of the bearer's physical expression of sexual characteristics.
A color consisting of yellow and green hues.
A color consisting of brown and green hues.
A purple color which has low saturation and low brightness.
A color consisting of yellow and orange hue.
A moderate yellow-orange to orange color.
A quality inhering in a bearer by virtue of the bearer's being kept below its freezing point.
A quality that inheres in an entire organism or part of an organism.
A quality that inheres in an entire population or part of a population.
Pink color having high brightness and low saturation.
A solid configuration inhering in a material entity by virtue of its constituent atoms, molecules, or ions being arranged in an orderly repeating pattern extending in all three spatial dimensions.
A hardness quality of being rigid and resistant to pressure and fibrous.
A physical quality inhering in a bearer by virtue of the bearer's disposition to being fit to be eaten.
A physical quality inhering in a bearer by virtue of the bearer being suitable for use as food.
A physical quality inhering in a bearer by virtue of the bearer not being suitable for use as food.
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 maturity quality inhering to a bearer by virtue of the bearer's being at the point or short after birth.
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 medium brown color with a metallic sheen, resembles the actual alloy bronze.
Female quality of having complete, unaltered reproductive organs
Male quality of having complete, unaltered reproductive organs.
Male quality of being incapable to reproduce because of functional loss of the testicles from surgical removal or chemical means.
A colour that is very pale yellowish brown.
A color consisting of yellow and brown hue.
A color consisting of yellow and brown hue and low brightness.
A color consisting of yellow and brown hue and high brightness.
A hardness quality of giving significant resistance to pressure.
Female quality of being incapable to reproduce because of functional loss of the ovaries and/or uterus from surgical removal.
A biological sex quality inhering in an individual or a population who are otherwise male of a non-hermaphroditic species who has ambiguous or atypical congenital development of the reproductive system.
male with differences of sexual differentiation
male with disorder of sexual development
A phenotypic sex quality inhering in a plant organism or a population of plants in which the flowers have two stamens.
A phenotypic sex quality inhering in a plant organism or a population of plants in which the flowers have only one stamen.
A sequential hermaphroditic quality whereby organisms start out as female and change to male at a later life stage.
A sequential hermaphroditic quality whereby organisms start out as male and change to female at a later life stage.
A protogynous quality whereby organisms start out as female and change to hermaphrodite at a later life stage.
A protandrous quality whereby organisms start out as male and change to hermaphrodite at a later life stage.
A biological sex quality inhering in an individual or a population who are otherwise female of a non-hermaphroditic species who has ambiguous or atypical congenital development of the reproductive system.
female with differences of sexual differentiation
female with disorder of sexual development
A quality of an object that has a value that is normal or average.
A flexibility which is relatively normal or average.
A temperature which is relatively normal or average
A viscosity which is relatively normal or average
A hermaphroditic quality that inheres in a population or organism where an organism changes is a different sexes during different life stages.
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 quality of an entity that can be represented numerically, including anything that can be counted, measured, or given a numerical value.
A material entity that consists of two or more organisms, viruses, or viroids.
collection of organisms
A plant structure (PO:0005679) which is a whole organism.
A plant anatomical entity (PO:0025131) that is, or was, part of a plant, or was derived from a part of a plant.
An anatomical entity that is or was part of a plant.
entidad anat&#243mica vegetal (Spanish, exact)
A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids.
stratification is a planned process which executes a stratification rule using as input a population and assign it member to mutually exclusive subpopulation based on the values defined by the stratification rule
PRS+AGB adapted from wikipedia: http://en.wikipedia.org/wiki/Stratified_sampling polled on June 7th,2013
population stratification prior to sampling
a stratification rule/criteria is a criteria used to determine population strata so that a stratification process implementing the rule can result in any member of the total population being assigned to one and only one stratum
STATO
adapted from wikipedia: http://en.wikipedia.org/wiki/Stratified_sampling polled on June 7th,2013
stratification rule
a stratum population is a population resulting from a population stratification prior to sampling process which aims to produce homogenous subpopulations from an heterogeneous population by applying one or more stratification criteria
statistical sampling is a planned process which aims at assembling a population of observation units (samples) in as an unbiaised manner as possible in order to obtain or infer information about the actual population these samples have been drawn.
Simple random sampling is a statistical sampling process which creates a sample of a size n entirely by chance. In such process, each unit has the same probability of being selected. Depending on the size of the population being sampled, the sampling process may be done with or without replacement
simple random sampling
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].
A multicellular structure that is a part of an organ.
Segment of the alimentary canal extending from the stomach to the anus and, in humans and other mammals, consists of two segments, the small intestine and the large intestine.
The proximal portion of the digestive tract, containing the oral cavity and bounded by the oral opening. In vertebrates, this extends to the pharynx and includes gums, lips, tongue and parts of the palate. Typically also includes the teeth, except where these occur elsewhere (e.g. pharyngeal jaws) or protrude from the mouth (tusks).
A portion of organism substance that is the product of an excretion process that will be eliminated from the body. An excretion process is elimination by an organism of the waste products that arise as a result of metabolic activity.
A fluid that is composed of blood plasma and erythrocytes.
Circulating fluid that is part of the hemolymphoid system. Blood, lymph, interstitial fluid or its analogs.
A portion of organism substance that is produced by exocrine glands.
Material anatomical entity in a gaseous, liquid, semisolid or solid state; produced by anatomical structures or derived from inhaled and ingested substances that have been modified by anatomical structures as they pass through the body.
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 group whose component anatomical structures lie in close proximity to each other.
Multicellular anatomical structure that consists of many cells of one or a few types, arranged in an extracellular matrix such that their long-range organisation is at least partly a repetition of their short-range organisation.
An expanded region of the vertebrate alimentary tract that serves as a food storage compartment and digestive organ. A stomach is lined, in whole or in part by a glandular epithelium.
Anatomical system that has as its parts the organs devoted to the ingestion, digestion, and assimilation of food and the discharge of residual wastes.
Portion of connective tissue composed of adipocytes enmeshed in areolar 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.
Excretion that is the output of a kidney.
A portion of the large intestine before it becomes the rectum. In mammals, the colon is the most part of the large intestine, excluding the vermiform appendix, the rectum and the anal canal.
A fluid produced in the oral cavity by salivary glands, typically used in predigestion, but also in other functions.
An emulsion of fat globules within a fluid that is secreted by the mammary gland during lactation.
mammal milk
Vital aqueous secretion of the liver that is formed by hepatocytes and modified down stream by absorptive and secretory properties of the bile duct epithelium.
Portion of semisolid bodily waste discharged through the anus[MW,modified].
Tissue with cells that deposit non-polarized extracellular matrix including connective tissue fibers and ground substance.
Gonochoristic organism that can produce female gametes.
A proximal-distal subdivision of the digestive tract.
The part of the digestive system that excludes the hepatobiliary system.
alimentary part of gastrointestinal system
Liquid components of living organisms. includes fluids that are excreted or secreted from the body as well as body water that normally is not.
A portion of organism substance that secreted_by a respiratory system.
A substance that is secreted by a mammary gland. The substance may differ depending on phase, with colostrum produced during pregancy/early lactation, and milk produced afterwards.
A multicellular organism that existence_ends_with a post-juvenile adult stage and existence_starts_with a post-juvenile adult stage.
Matter ejected from the lungs, bronchi, and trachea, through the mouth.
An anatomical structure that has more than one cell as a part.
An organ of the digestive tract that is capable of retaining and storing food.
Connective tissue, which consists of a population of connective tissue cells, the intercellular matrix of which contains an irregular network of collagen and elastic fiber bundles. Examples: areolar tissue, mucoid tissue, connective tissue of peritoneum, connective tissue of fibrous pericardium.
Irregular connective tissue is an irregular connective tissue, the intercellular matrix of which contains a dense irregular network of collagen and elastic fiber bundles. Examples: connective tissue of peritoneum, connective tissue of fibrous pericardium.
typus irregularis (textus connectivus collagenosus compactus)
Dense connective tissue is mainly composed of collagen type I. Crowded between the collagen fibers are rows of fibroblasts, fiber-forming cells, that manufacture the fibers. Dense connective tissue forms strong, rope-like structures such as tendons and ligaments. Tendons attach skeletal muscles to bones; ligaments connect bones to bones at joints. Ligaments are more stretchy and contain more elastic fibers than tendons. Dense connective tissue also make up the lower layers of the skin (dermis), where it is arranged in sheets.
A substance that is consumed by the organism for food.
Any of the organs or elements that are part of the digestive system. Examples: tongue, esophagus, spleen, crop, lunge feeding organ, tooth elements.
Material anatomical entity consisting of multiple anatomical structures that are not connected to each other.
A unit of measurement is a standardized quantity of a physical quality.
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.
A unit which is a standard measure of the average kinetic energy of the particles in a sample of matter.
A unit which is a standardised quantity of an element or compound with uniform composition.
A unit which is one of a particular measure to which all measures of that type can be related.
A unit which represents a standard measurement of how much of a given substance there is mixed with another substance.
A unit which is a standard measure of the amount of space occupied by any substance, whether solid, liquid, or gas.
A unit which is a standard measure of the number of repetitive actions in a particular time.
A unit which is a standard measure of the force applied to a given area.
A unit which is a standard measure of the volume of fluid which passes through a given surface per unit time .
A unit which represents a standard measurement occurrence of a process per unit time.
Material entity that is manufactured to realize the vaccine function.
Process of administering a vaccine in vivo to a recipient (e.g., a human), with the intent to invoke a protective or therapeutic adaptive immune response.
start date
quantity
measurement value
question
sentence
dimensional quantity
number
time measurement
study group
time instant
biological quality
geometric entity
point
endpoint
terminal point
country
start time
end time
ethnicity
control group
obsolete body height
obsolete waist circumfrence
obsolete hip circumference
Temporal Instant
Time extent; duration of a time interval separate from its particular start position
Temporal Duration
example to be eventually removed
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.
to be replaced with external ontology term
Terms with this status should eventually replaced with a term from another ontology.
Alan Ruttenberg
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.
lactose concentration in starting milk mixture
lactose concentration in parmigiano reggiano
temperature of parmigiano reggiano curd cooking
duration of parmigiano reggiano curd cooking
duration of parmigiano reggiano maturation
axiom holds for all times
## Elucidation This is used when the statement/axiom is assumed to hold true 'eternally' ## How to interpret (informal) First the "atemporal" FOL is derived from the OWL using the standard interpretation. This axiom is temporalized by embedding the axiom within a for-all-times quantified sentence. The t argument is added to all instantiation predicates and predicates that use this relation. ## Example Class: nucleus SubClassOf: part_of some cell forall t : forall n : instance_of(n,Nucleus,t) implies exists c : instance_of(c,Cell,t) part_of(n,c,t) ## Notes This interpretation is *not* the same as an at-all-times relation
A length unit which is equal to the length of the path traveled by light in vacuum during a time interval of 1/299 792 458 of a second.
A time unit which is equal to the duration of 9 192 631 770 periods of the radiation corresponding to the transition between the two hyperfine levels of the ground state of the caesium 133 atom.
A length unit which is equal to one hundredth of a meter or 10^[-2] m.
A length unit which is equal to one thousandth of a meter or 10^[-3] m.
A length unit which is equal to one millionth of a meter or 10^[-6] m.
A length unit which is equal to one thousandth of one millionth of a meter or 10^[-9] m.
A length unit which is equal to 10 [-10] m.
A mass unit which is equal to one thousandth of a gram or 10^[-3] g.
A mass unit which is equal to one millionth of a gram or 10^[-6] g.
A mass unit which is equal to one thousandth of one millionth of a gram or 10^[-9] g.
A mass unit which is equal to 10^[-12] g.
A temperature unit which is equal to one kelvin degree. However, they have their zeros at different points. The centigrade scale has its zero at 273.15 K.
A time unit which is approximately equal to the length of time of one of cycle of the moon's phases which in science is taken to be equal to 30 days.
A substance unit equal to a millionth of a mol or 10^[-6] mol.
A substance unit equal to one thousandth of one millionth of a mole or 10^[-9] mol.
A unit of concentration which expresses a concentration of 1 mole of solute per liter of solution (mol/L).
A unit of molarity which is equal to one thousandth of a molar or 10^[-3] M.
A unit of molarity which is equal to one millionth of a molar or 10^[-6] M.
A unit of molarity which is equal to one thousandth of one millionth of a molar or 10^[-9] M.
A unit of molarity which is equal to 10^[-12] M.
A volume unit which is equal to one millionth of a cubic meter or 10^[-9] m^[3], or to 1 ml.
A volume unit which is equal to one thousandth of a liter or 10^[-3] L, or to 1 cubic centimeter.
A volume unit which is equal to one thousandth of a cubic meter or 10^[-3] m^[3], or to 1 decimeter.
A volume unit which is equal to one thousand of a cubic meter or 10^[-3] m^[3], or to 1 L.
A volume unit which is equal to one millionth of a liter or 10^[-6] L.
A volume unit which is equal to one thousandth of one millionth of a liter or 10^[-9] L.
A volume unit which is equal to 10^[-12] L.
A frequency unit which is equal to 1 complete cycle of a recurring phenomenon in 1 second.
A dimensionless concentration unit which denotes the mass of a substance in a mixture as a percentage of the mass of the entire mixture.
A dimensionless concentration unit which denotes the mass of the substance in a mixture as a percentage of the volume of the entire mixture.
A dimensionless concentration unit which denotes the volume of the solute in mL per 100 mL of the resulting solution.
A mass unit density which is equal to mass of an object in grams divided by the volume in liters.
A mass unit density which is equal to mass of an object in milligrams divided by the volume in milliliters.
A dimensionless concentration notation which denotes the acidity of a solution in terms of activity of hydrogen ions (H+).
A volume per unit volume unit which is equal to one millionth of a liter of solute in one liter of solution.
A mass density unit which is equal to mass of an object in grams divided by the volume in deciliters.
A concentration unit which a measure of viable bacterial numbers in a given volume.
A volumetric flow rate unit which is equal to one microliter volume through a given surface in one minute.
A rate unit which is equal to one over one nanomolar second.
A rate unit which is equal to one over one molar second.
A rate unit which is equal to one over one nanomolar.
A rate unit which is equal to one over one molar.
A mass unit density which is equal to mass of an object in micrograms divided by the volume in liters.
A mass unit which is equal to the mass of the International Prototype Kilogram kept by the BIPM at Svres, France.
A mass unit which is equal to one thousandth of a kilogram or 10^[-3] kg.
A time unit which is equal to 60 seconds.
A time unit which is equal to 3600 seconds or 60 minutes.
A time unit which is equal to 12 months which in science is taken to be equal to 365.25 days.