The Genomic Epidemiology Ontology aims to provide a comprehensive controlled vocabulary for infectious disease surveillance and outbreak investigations. It is an application ontology that draws on many other ontologies including anatomy, taxonomy, disease, symptoms, environment and food types for foodborn pathogen metadata.
Genomic Epidemiology Ontology
metadata section
term as in existing standard
term source
The user interface label is the label that should be placed on a datum when presented on a form or report
user interface label
user interface definition
A user interface help annotation is a textual phrase to display with an entity on a form or report that provides some detail about what the entity is or how it is being used.
obsolete: user interface help
obsolete: user interface hidden
A user interface feature is a pre-set list of features and their acceptable values that a user interface rendering system should use to display an entity on a form or report
user interface feature
This annotation can be used to select the value specification that a referenced entity or specification component has for data entry. Can be scalar value specification / categorical tree specification etc.
obsolete: user interface value specification
UI regex normalize
user interface regular epression normalize
UI regex validate
user interface regular expression validate
UI regex format
user interface regular expression display format
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.
Allyson Lister 8.10.2019: Although the IAO definition has been included here, we have made a curation decision to allow non-Aristotelian definitions.
editor note
An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology.
definition editor
term editor
Name of editor entering the definition in the file. The definition editor is a point of contact for information regarding the term. The definition editor may be, but is not always, the author of the definition, which may have been worked upon by several people
Name of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several people
20110707, MC: label update to term editor and definition modified accordingly. See https://github.com/information-artifact-ontology/IAO/issues/115.
alternative label
alternative term
A label for a class or property that can be used to refer to the class or property instead of the preferred rdfs:label. Alternative labels should be used to indicate community- or context-specific labels, abbreviations, shorthand forms and the like.
An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent)
Consider re-defing to: An alternative name for a class or property which can mean the same thing as the preferred name (semantically equivalent, narrow, broad or related).
definition source
Formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007
Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w
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
An IRI or similar locator for a request or discussion of an ontology term.
Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg
The 'tracker item' can associate a tracker with a specific ontology term.
imported from
has ID digit count
Relates an ontology used to record id policy to the number of digits in the URI. The URI is: the 'has ID prefix' annotation property value concatenated with an integer in the id range (left padded with '0's to make this many digits)
has ID range allocated
Relates a datatype that encodes a range of integers to the name of the person or organization who can use those ids constructed in that range to define new terms
has ID policy for
Relating an ontology used to record id policy to the ontology namespace whose policy it manages
term replaced by
Add as annotation triples in the granting ontology
Use on obsolete terms, relating the term to another term that can be used as a substitute
Person:Alan Ruttenberg
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).
NIAID GSCID-BRC metadata working group
temporal interpretation
An assertion that holds between an OWL Object Property and a temporal interpretation that elucidates how OWL Class Axioms that use this property are to be interpreted in a temporal context.
relation p is the direct form of relation q iff p is a subPropertyOf q, p does not have the Transitive characteristic, q does have the Transitive characteristic, and for all x, y: x q y -> exists z1, z2, ..., zn such that x p z1 ... z2n y
The general property hierarchy is: "directly P" SubPropertyOf "P" Transitive(P) Where we have an annotation assertion "directly P" "is direct form of" "P"
is direct form of
namespace
contributor
creator
created_by
creation_date
An alternative label for a class or property which has a more general meaning than the preferred name/primary label.
has broad synonym
An annotation property that links an ontology entity or a statement to a prefixed identifier or URI.
Reference database or publication source.
has database cross reference
hasDbXref
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.
An alternative label for a given entity such as a commonly used abbreviation or synonym.
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 synonym
comment
is defined by
label
A human-readable name for the subject.
see also
backward compatible with
deprecated
incompatible with
prior version
versionInfo
part of
has part
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 http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/
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
Damion comments: In GenEpiO, If an entity has more than one value specification (in a conjunction), then it means the entitiy is a complex entity that can have a value for each specification. Minimum data requirements can be spelled out using some, min 1, max 10 etc. restrictions.
realized in
occurs in
b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t
occurs_in
unfolds in
unfolds_in
Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant
site of
[copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t
Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant
contains process
obsolete has string specification of
T1 after t2 iff:= t2 before_or_simulataneous_with t1 and not (t1 simultaeous_with t2)
Damion Dooley
Damion Dooley's note: Intention is to have it be the inverse of "before". This allows axioms like "B after A" to be placed in class B, rather than having to phrase them as "A before B" in class A. I believe time dependency relations (conditions) don't imply existence by themselves. If B after A, and B exists, this doesn't necessarily mean that A exists, only that if A does exist, it must be before B. To add that extra existence implication probably requires the "causally downstream of" and "immediately causally downstream of" RO relations, in a closed system where B cannot exist any other way.
after
obsolete: has string value specification
obsolete: has categorical specification of
obsolete: has categorical value specification
hasCountryOfOrigin
has unit
has measurement unit label
A (currently) primitive relation that relates an information artifact to an entity.
7/6/2009 Alan Ruttenberg. Following discussion with Jonathan Rees, and introduction of "mentions" relation. Weaken the is_about relationship to be primitive. We will try to build it back up by elaborating the various subproperties that are more precisely defined. Some currently missing phenomena that should be considered "about" are predications - "The only person who knows the answer is sitting beside me" , Allegory, Satire, and other literary forms that can be topical without explicitly mentioning the topic.
person:Alan Ruttenberg
Smith, Ceusters, Ruttenberg, 2000 years of philosophy
is about
An information artifact IA mentions an entity E exactly when it has a component/part that denotes E
7/6/2009 Alan Ruttenberg. P4 RC1 munges our GCI so remove it for now: mentions some entity equivalentTo has_part some ('generically denotes' some entity)
7/6/2009 Alan Ruttenberg: Add this relation following conversation with Jonathan Rees that N&S GCI for is_about was too strong. Really it was simply sufficient. To effect this change we introduce this relation, which is subproperty of is_about, and have previous GCI use this relation "mentions" in it's (logical) definition
PERSON: Jonathan Rees
Person: Alan Ruttenberg
mentions
A primitive, instance-level, relation obtaining between an information content entity and some portion of reality. Denotation is what happens when someone creates an information content entity E in order to specifically refer to something. The only relation between E and the thing is that E can be used to 'pick out' the thing. This relation connects those two together. Freedictionary.com sense 3: To signify directly; refer to specifically
2009-11-10 Alan Ruttenberg. Old definition said the following to emphasize the generic nature of this relation. We no longer have 'specifically denotes', which would have been primitive, so make this relation primitive. g denotes r =def r is a portion of reality there is some c that is a concretization of g every c that is a concretization of g specifically denotes r
Conversations with Barry Smith, Werner Ceusters, Bjoern Peters, Michel Dumontier, Melanie Courtot, James Malone, Bill Hogan
denotes
relates a time stamped measurement datum to the measurement datum that was measured
Alan Ruttenberg
has measurement datum
see is_input_of example_of_usage
The inverse property of is_specified_input_of
8/17/09: specified inputs of one process are not necessarily specified inputs of a larger process that it is part of. This is in contrast to how 'has participant' works.
PERSON: Alan Ruttenberg
has_specified_input
some Autologous EBV(Epstein-Barr virus)-transformed B-LCL (B lymphocyte cell line) is_input_for instance of Chromum Release Assay described at https://wiki.cbil.upenn.edu/obiwiki/index.php/Chromium_Release_assay
A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of.
is_specified_input_of
The inverse property of is_specified_output_of
has_specified_output
is_manufactured_by
http://www.affymetrix.com/products/arrays/specific/hgu133.affx is_manufactered_by http://www.affymetrix.com/ (if we decide to use these URIs for the actual entities)
c is_manufactured_by o means that there was a process p in which c was built in which a person, or set of people or machines did the work(bore the "Manufacturer Role", and those people/and or machines were members or of directed by the organization to do this.
Liju Fan
has_make
has_manufacturer
A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of.
is_specified_output_of
A relation between a categorical measurement data item and the categorical label that indicates the value of that data item on the categorical scale.
specifies
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.
inheres in
this fragility is a characteristic of this vase
this red color is a characteristic of this apple
a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence.
inheres_in
Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing.
characteristic of
has participant
this blood coagulation has participant this blood clot
this investigation has participant this investigator
this process has participant this input material (or this output material)
a relation between a process and a continuant, in which the continuant is somehow involved in the process
Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time.
has_participant
this apple has quality this red color
a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence
A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist.
has_quality
has quality
this person has role this investigator role (more colloquially: this person has this role of investigator)
a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence
A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists.
has_role
has role
this cell derives from this parent cell (cell division)
this nucleus derives from this parent nucleus (nuclear division)
a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity
This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'.
derives_from
This relation is taken from the RO2005 version of RO. It may be obsoleted and replaced by relations with different definitions. See also the 'develops from' family of relations.
derives from
this parent cell derives into this cell (cell division)
this parent nucleus derives into this nucleus (nuclear division)
a relation between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity
This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops into'. To avoid making statements about a future that may not come to pass, it is often better to use the backward-looking 'derives from' rather than the forward-looking 'derives into'.
derives_into
derives into
is location of
my head is the location of my brain
this cage is the location of this rat
a relation between two independent continuants, the location and the target, in which the target is entirely within the location
Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/
location_of
location of
located in
my brain is located in my head
this rat is located in this cage
a relation between two independent continuants, the target and the location, in which the target is entirely within the location
Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus
located_in
May be obsoleted, see https://github.com/oborel/obo-relations/issues/260
aligned with
Primitive instance level timing relation between events
before or simultaneous with
x simultaneous with y iff ω(x) = ω(y) and ω(α ) = ω(α), 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 and '=' indicates the same instance in time.
t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2)
simultaneous with
T1 before t2 iff:= t1 before_or_simulataneous_with t2 and not (t1 simultaeous_with t2)
before
X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y)
immediately preceded by
X immediately_precedes_Y iff: end(X) simultaneous_with start(Y)
immediately precedes
X starts_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (start(X) before_or_simultaneous_with end(Y))
starts during
X happens_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (end(X) before_or_simultaneous_with end(Y))
happens during
w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type.
The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity.
For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit.
has component
A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts.
The epidermis layer of a vertebrate is adjacent to the dermis.
The plasma membrane of a cell is adjacent to the cytoplasm, and also to the cell lumen which the cytoplasm occupies.
The skin of the forelimb is adjacent to the skin of the torso if these are considered anatomical subdivisions with a defined border. Otherwise a relation such as continuous_with would be used.
x adjacent to y if and only if x and y share a boundary.
This relation acts as a join point with BSPO
adjacent to
Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor
x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.
starts with
x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.
ends with
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
An organism that is a member of a population of organisms
is member of is a mereological relation between a item and a collection.
member of
has member is a mereological relation between a collection and an item.
has member
input of
output of
causally downstream of
p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q.
causally upstream of
all dengue disease transmitted by some mosquito
A relationship that holds between a disease and organism
a produced_by b iff some process that occurs_in b has_output a.
produced by
the relationship between a fraction and the number above the line
AGB
the relationship between a fraction and the number below the line (or divisor)
link two concepts, indicating a high degree of confidence that the concepts can be used interchangeably across a wide range of information retrieval applications. skos:exactMatch is a transitive property, and is a sub-property of skos:closeMatch.
exactMatch
An object relation between a LinkML SlotDefinition to a LocalName.
obsolete: has primitive data type
has specified value
A relation between a value specification and a literal.
This is not an RDF/OWL object property. It is intended to link a value found in e.g. a database column of 'M' (the literal) to an instance of a value specification class, which can then be linked to indicate that this is about the biological gender of a human subject.
An abstract class is a high level class or slot that is typically used to group common slots together and cannot be directly instantiated.
Notes and comments about an element intended for external consumption.
Date/time at which the element was created.
Not Applicable; Missing; Not Collected; Not Provided; Restricted Access
A value (string or URI) indicating the data collection state an instance of a slot has.
A description of the element's purpose and use
A list of terms from different schemas or terminology systems that have identical meaning.
Id of the schema that defined the element.
The imports entry that this element was derived from. Empty means primary source
The ncname of the source of the name.
local_name_source
A name assigned to an element in a given ontology.
For slots with ranges of type number, the value must be equal to or lowe than this
For slots with ranges of type number, the value must be equal to or higher than this
true means that slot can have more than one value
The unique name of the element within the context of the schema. Name is combined with the default prefix to form the globally unique subject of the target class.
The string value of the slot must conform to this regular expression
A list of possible values for a slot range.
true if this slot is not required, but is recommended.
true means that the slot must be present in the loaded definition.
A reference.
IAO:0000122 ('ready for release')
status of the element.
The uri that defines the possible values for the type definition
URI is typically drawn from the set of URI's defined in OWL (https://www.w3.org/TR/2012/REC-owl2-syntax-20121211/#Datatype_Maps)
Description of what the value is doing.
The identifier of a "value set" -- a set of identifiers that form the possible values for the range of a slot
A persistent, unique identifier of a molecular sequence database entry.
sequence accession
The name of a field in a database.
database field name
animal - laboratory
Animals considered to be wild or feral or not adapted for domestic use. It does not include wild animals in zoos for which ANIMALS, ZOO is available.
animal - wild
the relative amounts of the purines and pyrimidines in a nucleic acid.
base composition base compositions base ratio base ratios gc composition gc compositions gc content gc contents gc g+c composition g+c compositions g+c content g+c contents guanine + cytosine composition guanine + cytosine content
base composition
Animals kept by humans for companionship and enjoyment, as opposed to DOMESTIC ANIMALS such as livestock or farm animals, which are kept for economic reasons.
animal - pet
Domesticated farm animals raised for home use or profit but excluding POULTRY. Typically livestock includes CATTLE; SHEEP; HORSES; SWINE; GOATS; and others.
livestock
A generically dependent continuant which derives its existence and its entire endowment from an intending experience of consciousness (an "act") that is laden with determinate, uniformily structured content.
MB: Right now we represent 'purely intentional entities' as siblings to 'information content entities'. Given their nature I am not entirly sure that this is correct. It seems that both 'information content entity' and 'simulation' are subclass to 'purely intentional entity'.
purely intentional entity
A duration of the parts of an infection during which the host bears an infectious disposition in a population of hosts.
MB: In order to get the temporal occupation relations I added properties that I renamed with BFO2 URIs.
infectious period duration
A duration of the time interval between the host acquiring an infection and the host bearing a contagiousness disposition during the same disease course within a population of hosts.
The duration of the period between when an organism becomes infected and when it becomes infectious.
latent period duration
count of simulated exposed population
count of simulated contagious population
count of simulated resistant population
The count of (simulated organisms) in a simulated population.
MW: I know this causes problems with our set-theoretic definition. Unfortunately the compartmental models produce fractional counts at each of their time steps, including the final step. Any ideas? I’ve considered and rejected allowing individual organisms to be fractional. Perhaps if we just replace the term “cardinality” in the definition with ‘computed size’
count of simulated population
A simulation of a population or populations of organisms of a particular biological taxon that simulates a particular type of event or types of event that occur in a specified time interval.
simulated population
A measurement datum that is the output of counting.
count
The planned process of finding the number of elements in a finite set of objects.
counting
Mathias Brochhausen
Motivating use case is to cover Synthia data, and possibly configuration/output of the MRSA simulator in the MIDAS community (CA-MRSA Repast).
hospital patient population census
A purely intentional entity that simulates an entity and its properties.
simulation
The count of individuals in a contagious population (empirical or virtual).
count of contagious population
The count of individuals in a resistant population (empirical or virtual).
count of resistant population
The biological process of pathogen organism(s) of a particular biological taxon entering (the tissues of the body of) a host organism of another taxon from a contagious host or a contaminated thing and reproducing using host resources
Apollo-SV defines infection acquisition rather than infection transmission, which is the direction of movement of a pathogen in current use. The Apollo-SV conceptualization is simpler when accounting for infections acquired from contaminated things. The likelihood of acquisition is expressed by parameters such as the basic reproduction rate and transmission coefficient. An infection is acquired from an infectious organism or a contaminated thing.
Cannot acquire from colonized host directly - contamination results from colonized or contaminated thing and new host picks it up from contaminated thing
infection acquisition
A census that is the outcome of a population survey.
population census
Motivating use case is Synthia synthetic population data.
nursery school student population census
primary school student population census
secondary school student population census
A data set of a specific entity in a specified region at a specified time.
census
school student population census
The probability of the occurence of an infection acquisition from one infected organism to another when in contact.
transmission probability
asymptomatic host
An organism of a particular biological taxon that is the site of reproduction of an organism of a different taxon.
host organism
A information content entity that specifies the date of a census.
census reference date
A measurement datum that quantifies a temporal region that is occupied by a processual entity.
duration
The duration between the appearance of symptoms of a disease and the start of a treatment.
delay from symptoms to treatment
An infection acquisition whereby a susceptible host acquires an infection from an infectious host.
William R. Hogan
infection acquisition from infectious host
The duration from the time an organism satisfies a case definition until a process or system detects the organism as satisfying that case definition
time delay to case detection
A duration that measures the temporal interval occupied by a treatment course.
duration of treatment course
The count of the number of doses that are part of a treatment course.
number of doses in a treatment course
The duration from the time an individual receives a treatment until the time a system designed to detect that the treatment occurred detects it in a population
time delay of treatment detection
A data item that is about a proposition and has a numeric value between 0 and 1, inclusive, that is the output of some process of inference, such that 1) logical falsehoods and logical truths are assigned a value of 0 and 1, respectively, while contingent propositions are assigned some intermediate value; and 2) the process of inference conforms with rules for the calculation of probabilities, and that any interpretation of probability must specify the extent to which probabilities might be used to constrain the degrees of belief of rational agents.
The first criterion is derived from Kolmogorov's Probability Calculus, while the second is derived from Salmon's Admissibility and Applicability Criteria of Adequacy. Salmon's ascertainability criterion is subsumed by the definition for 'data item'.
probability
A count of individuals in a population who meet the criteria of some case definition during some time interval.
count of disease cases
A count of disease cases in an infected population that meet the case definition criteria within a particular epidemic interval.
count of cases in an epidemic
A population census about the organisms specific to that population that were the host in some colonization acquisition.
population colonization census
An infection acquistion from infectious host that is causally downstream of some potentially infectious sexual contacting
Note that infections that are acquired in this manner do not fall within the class of sexually transmitted infections (STI's), ipso facto. This type of transmission can also occur with non-STI pathogens--such as meningitis and Zika.
infection acquisition through sexual activity with infectious host
A count of simulated or physical individuals in a population.
Matthew Diller
population count
Qualitative description of a microbial response to antimicrobial agents and the expected clinical outcome. Bacteria may be susceptible or resistant to a broad range of antibiotic drugs or drug classes, with several intermediate states or phases.
intermediate
Intermediate sensitivity of a bacterial strain to a given antibiotic occurs when it is inhibited by a concentration of the drug that is associated with uncertain therapeutic effect. The elimination of intermediate phenotype bacteria may depend on the site of infection and/or the concentration of the administered drug. Definition from https://clsi.org.
resistant
A bacterial strain is said to be resistant to a given antibiotic when it is inhibited in vitro by a concentration of this drug that is associated with a high likelihood of therapeutic failure.
susceptible
A bacterial strain is said to be susceptible to a given antibiotic when it is inhibited in vitro by a concentration of a drug that is associated with a high likelihood of therapeutic success.
sensitive
nonsusceptible
A bacterial strain is said to be nonsusceptible to a given antibiotic drug if it demonstrates either an intermediate or resistant phenotype when exposed to a concentration of a drug that is associated with a high likelihood of therapeutic failure, i.e. if the bacterial strain is not susceptible to the antibiotic drug but not necessarily totally resistant under all conditions. Definition from https://clsi.org.
nonsensitive
susceptible - dose dependent
A bacterial strain is said to be susceptible-dose dependent (SDD) to a given antibiotic when growth is inhibited with a high likelihood of therapeutic success, but when multiple approved dosing options exist. When a higher or more frequent dose is used, the predicted therapeutic result is the same as for susceptible individuals.
SSD
Sensitive dose dependent antimicrobial phenotype
sensitive - dose dependent
susceptible dose dependent antimicrobial phenotype
Multidrug-resistant organisms are defined as bacterial strains that have become resistant to multiple classes of antibacterial drugs or other agents. The phenotype of these organisms is defined by the spectrum of antibiotic drug classes to which that organism is resistant. Often, these organisms are susceptible to a narrow range of available drugs, making treatment difficult and urgent.
multidrug resistance antimicrobial phenotype
Uses breakpoints to create standards for interpreting the clinical outcome of an MIC value for a particular microbial species and antimicrobial agent.
antimicrobial resistance testing reference standard
BSAC is a British inter-professional organisation involved in antibiotic education, research and leadership. Baquero F. found that the BSAC system recommends lower breakpoints than the consensus standard of all systems for antimicrobial susceptibility testing used in Europe (BSAC, DIN, SFM, SIR, NCCLS and WRG).
British Society for Antimicrobial Chemotherapy (BSAC)
The Clinical and Laboratory Standards Institute develops and implements clinical laboratory testing standards.
NCCLS
National Committee on Clinical Laboratory Standards (NCCLS)
On January 1, 2005 the National Committee on Clinical Laboratory Standards (NCCLS) changed its name to CLSI
Clinical and Laboratory Standards Institute (CLSI)
DIN is recognized by the Federal Government of Germany as the competent standards organization for Germany and as the national standards body representing Germany in non-governmental international standards organizations. Baquero F. found that the DIN system recommends lower breakpoints than the consensus standard of all systems for antimicrobial susceptibility testing used in Europe (BSAC, DIN, SFM, SIR, NCCLS and WRG).
EUCAST is a standing committee jointly organized by ESCMID, ECDC and European national breakpoint committees; it deals with breakpoints and technical aspects of phenotypic in-vitro antimicrobial susceptibility testing.
European Committee on Antimicrobial Susceptibility Testing (EUCAST)
The French Society of Microbiology (SFM) is a non-profit association which aims to bring together microbiologists from French-speaking countries, working in the domains of bacteria, viruses, Fungi and parasites, and related medical, industrial and environmental microbiology, physiology, genetics, taxonomy, hygiene, and antimicrobial agents. Baquero F. found that the SFM system recommends higher breakpoints than the consensus standard of all systems for antimicrobial susceptibility testing used in Europe (BSAC, DIN, SFM, SIR, NCCLS and WRG).
Société Française de Microbiologie (SFM)
Unit for measurement of minimum inhibitory concentration (MIC).
An experimental test conducted outside of a living organism, usually in a tube or plate.
System of analysis for determining antimicrobial susceptibility.
Microbial species are inoculated in a growth medium onto which antimicrobial agents are transferred by diffusion.
Components of complex mixtures such as plant extracts are separated across a TLC plate and tested for anti-microbial activity.
thin-layer chromatography (TLC)-bioautography
Allows for time-dependent or concentration-dependent analysis of antimicrobial effects. Several tubes of broth culture medium containing a suspension of the test microbe are treated with varying concentrations of the antimicrobial agent and the percentage of dead cells determined at various time points.
Relies on the indirect measurement of microbe populations by quantifying microbial ATP production.
Microbes exposed to antimicrobial agents are then stained with the intercalating agent propidium iodide. Damaged cells emit a positive signal that is detected by flow cytometry analysis. Flow cytometry can also be used to discriminate between dead, damaged and live cells.
Test that directly detect the presence of a particular resistance mechanism.
The microbial species are inoculated in liquid growth medium containing incremental dilutions (usually 2-fold) of the antimicrobial agent.
Automated system of analysis for determining antimicrobial susceptibility.
Non-automated system of analysis for determining antimicrobial susceptibility.
Specific automated system of analysis for determining antimicrobial susceptibility developed by Omron.
Specific automated system of analysis for determining antimicrobial susceptibility developed by Becton Dickinson.
Specific automated system of analysis for determining antimicrobial susceptibility developed by Trek, Thermo Fisher Scientific.
Specific automated system of analysis for determining antimicrobial susceptibility developed by bioMérieux.
Vendor of automated system of analysis for determining antimicrobial susceptibility.
Specific vendor of automated system of analysis for determining antimicrobial susceptibility headquartered in New Jersey, USA. Becton Dickinson is the developer of the Phoenix automated testing platform.
Specific vendor of automated system of analysis for determining antimicrobial susceptibility headquartered in France. bioMérieux is the developer of the Vitek automated testing platform.
Specific vendor of automated system of analysis for determining antimicrobial susceptibility headquartered in Berlin and Munich.
Specific vendor of automated system of analysis for determining antimicrobial susceptibility based in Japan. Omron is the developer of the MicroScan automated testing platform.
Specific vendor of automated system of analysis for determining antimicrobial susceptibility that was acquired by Thermo Fisher Scientific Inc. Thermo Fisher Scienfiic Inc. is headquartered in Massachusetts, USA. Trek is the developer of the Sensitire automated testing platform.
Broth dilution conducted on 96-well microtiter plates (≤200 µL per well).
This test is a common method of evaluating the antimicrobial activity of plants or microbial extracts. In this method, bacteria are inoculated onto agar plates and the antimicrobial agent is injected into the plate and allowed to diffuse.
This method is commonly used to study the antagonism between microorganisms. The first bacterial strain is inoculated onto agar plates in tight streaks. The bacteria will secrete molecules that diffuse in the agar medium; this medium is cut and placed on another agar plate inoculated with another microorganism.
This method is commonly used to study the antagonism between microorganisms. The microbial strain of interest is seeded by a single streak in the center of the agar plate. After incubation, the plate is seeded with the second microorganism by single streak perpendicular to the central streak.
The antimicrobial agent is transferred from a chromatogram to an agar plate previously inoculated with the test microorganism.
A developed TLC plate is dipped into or sprayed with a microbial suspension and then incubated. Live microbial cells are visualized using tetrazolium salts.
The TLC plate is covered with a molten agar medium seeded with the test microbe and the antimicrobial compounds are allowed to diffuse onto the agar medium. Tetrazolium dye staining allows for visualization.
Commercial colorimetric assay for detection of chloramphenicol modifying enzyme chloramphenicol acetyltransferase.
chloramphenicol acetyltransferase assay (CAT)
The tissue type used to select breakpoints from a particular standard, for the interpretation of MIC results.
antimicrobial resistance tissue specificity
Qualitative description of a microbial response to antimicrobial agents as described by EUCAST using breakpoints determined through in-vitro testing. These breakpoints are determined irrespective of tissue specificity of infection.
A microbe whose susceptibility to antibiotics is comparable to that of a reference susceptible microbe, meaning that the microbe is sensitive to the particular antibiotic.
A microbe whose susceptibility to antibiotics differs from that of a reference susceptible microbe, meaning that the microbe is resistant to the particular antibiotic.
order: ARO:3004303 # nonsensitive ARO:3004300 # intermediate ARO:3004302 # sensitive ARO:3004304 # sensitive - dose dependant ARO:3004301 # resistant
Qualitative description of a microbial response to antimicrobial agents as described by CLSI using breakpoints that take into consideration tissue specificity of infection.
A method to determine microbial susceptibility to antibiotics in which test bacteria is inoculated onto an agar plate that contains a concentration gradient of antibiotic. The minimum inhibitory concentration of antibiotic is assessed.
The National Committee for Clinical Laboratory Standards is an American organization responsible for developing accredited consensus clinical laboratory standards.
National Committee for Clinical Laboratory Standards (NCCLS)
SIR is a revised system for antibiotic sensitivity testing in Sweden that was proposed in 1977. The SIR system included two main changes: three sensitivity groups instead of the previous four and new breakpoints for the sensitivity groups.
Swedish Reference Group for Antibiotics (SIR)
The WRG is a standardized antimicrobial susceptibility testing methodology created by the Dutch Commissie Richtlijnen Gevoeligheidsbepalingen in 1981.
Commissie Richtlijnen Gevoeligheidsbepalingen (CRG)
Committee Guidelines Susceptibility Testing
Working Group Guidelines Susceptibility Testing
Werkgroep Richtlijnen Gevoeligheidsbepalingen (WRG)
Specific automated system of analysis for determining antimicrobial susceptibility developed by Giles Scientific.
A Nilotic Eastern population with a population size of 0.9 millions
A Nilotic Eastern population with a population size of 0.1 millions
A Bantu Western population with a population size of 3.8 millions
A Khoisan South population with a population size of 0.13 millions
A Mande Western population with a population size of 2.2 millions
A Bantu Eastern population with a population size of 0.026 millions
A Bantu Western population with a population size of 0.8 million
A Nguni population with a population size of 12 millions
A Nilotic Eastern population with a population size of 5 millions
A Mande Western population with a population size of 14 millions
A Kalenjin population with a population size of 0.3 million
A Bantu Eastern population with a population size of 0.34 millions
A Western African population with a population size of >34 millions
A Bantu Eastern population with a population size of 5.3 millions
A Kalenjin population with a population size of 937,884
A Bantu Southern population with a population size of 6 millions
A Northern African, Central African, Western African, Eastern African population with a population size of 25 millions
A Western African population with a population size of 45 millions
A Nilotic Central, Nilotic Eastern, Northern African population with a population size of 0.4 million
A Kalenjin population with a population size of 197556
A Bantu Eastern population with a population size of 2.7 Millions
A Cushitic Eastern population with a population size of 40 millions
A Nilotic Eastern population with a population size of 1 million
A Nguni population with a population size of 7.9 millions
A Senufo population with a population size of 0.74 million
A Western African, Eastern African population with a population size of 90 millions
The Nuer are a Nilotic Eastern population with a population size of 3 million.
A Bantu Eastern population with a population size of 2.488 Millions
A Bantu Central population with a population size of 1 million
A Gurma population with a population size of 7.6 millions
A Bantu Southern population with a population size of 5 millions
A Bantu Eastern population with a population size of 4.663 millions
The Ga-Adangbe are a Western African population with a population size of 2 million.
A Bantu Eastern population with a population size of 9 millions
The Soninke are a Mande Western population with a population size of 2 million.
A Bantu Southern population with a population size of 15 millions
A Berber Northern, Berber Western population with a population size of 2.5 millions
A Western African population with a population size of 0.93 millions
A Gurunsi population with a population size of 0.3 millions
A Gurma population with a population size of 0.8 millions
A Western African population with a population size of 3.3 millions
The Dagaaba are a Western African population with a population size of 1 million.
A Mande Western population with a population size of 6.8 millions
A Eastern African population with a population size of 1.2 millions
A Eastern African population with a population size of 0.055 millions
A Eastern African population with a population size of 0.4 million
People living in: Burundi OR Comoros OR Djibouti OR Eritrea OR Ethiopia OR Kenya OR Madagascar OR Malawi OR Mauritius OR Mayotte OR Mozambique OR Rwanda OR Réunion OR Seychelles OR Somalia OR South Sudan OR Sudan OR Uganda OR United Republic of Tanzania OR Zimbabwe
'The Nubians are known as people of the Nile and are located between Egypt and northern Sudan.' taken from: Culture and Customs of Sudan. Written by De Kwame Essien, Toyin Falola Ph.D.
A Nubian Northern population with a population size of 0.050 million
A Ubangi Central population with a population size of 1.5 millions
A Nilotic Eastern population with a population size of Nilo-Saharan, Luo, River-Lake
The Kalenjin are a Nilotic Eastern population with a population size of 3 million.
The Senufo are a Western African population with a population size of 2 million.
A Western African population with a population size of 20 millions
A Toubou population with a population size of Nilo-Saharan
A Western African population with a population size of 0.5 millions
A Nilotic Western population with a population size of 5 millions
A Bantu Eastern population with a population size of 15.109 millions
A Eastern African population with a population size of 0.462 million
A Eastern African population with a population size of 4 millions
'The Nuba trace their geographical roots to the area around the Nuba mountains, the uppermost regions around the Ingessana hills and communities close to the Red Sea.' taken from: Culture and Customs of Sudan. Written by De Kwame Essien, Toyin Falola Ph.D.
A Berber Northern population with a population size of 0.57 million
A Bantu Western population with a population size of 0.250 million
A Eastern African population with a population size of 1300 persons
A Western African population with a population size of 1.9 millions
A Western African population with a population size of 0.285 million
A Western African population with a population size of 0.324 million
A Berber Northern population with a population size of 0.150 million
A Bantu Eastern, Bantu Southern population with a population size of 0.758 million
A Bantu Eastern population with a population size of > 2 millions
A Chewa population with a population size of 2.486 millions, known as the people of the lake
The Sena are a Bantu Eastern population with a population size of 2 million.
A Sudanic population with a population size of Nilo-Saharan|Satellite-Core|Satellites|Central Sudanic|West|Bongo-Bagirmi|Bongo-Baka|Bongo|Kacipo-Balesi|Tennet|Luo|Lango-Acholi
A Bantu Eastern population with a population size of 1.050 millions
A Cushitic Eastern population with a population size of 0.030 million
A Malagasy population with a population size of 0.05 million
The Tsimihety are a Malagasy population with a population size of 1.2 million.
The Sakalava are a Malagasy population with a population size of 1.2 million.
A Malagasy population with a population size of 1.5 millions
A Malagasy population with a population size of 0.5 million
A Malagasy population with a population size of 4.359 millions
A Betsileo population with a population size of 0.015 million
A Malagasy population with a population size of > 5 millions
A Malagasy population with a population size of 0.52 million
A Malagasy population with a population size of 0.0012 million
A Malagasy population with a population size of 0.6 million
A Malagasy population with a population size of 0.15 million
A Eastern African population with a population size of 0.18 million
French people who were born in Metropolitan France.
A Eastern African population with a population size of 0.025 million
A Ubangi Central population with a population size of 0.011 million
People living in: Angola OR Cameroon OR Central African Republic OR Chad OR Congo OR Democratic Republic of the Congo OR Gabon OR Zambia
People living in: Algeria OR Egypt OR Libya OR Mauritania OR Morocco OR Tunisia OR Western Sahara
People living in: Botswana OR Eswatini OR Lesotho OR Namibia OR South Africa
People living in: Benin OR Burkina Faso OR Cabo Verde OR Cote d'Ivoire OR Equatorial Guinea OR Gambia OR Ghana OR Guinea OR Guinea-Bissau OR Liberia OR Mali OR Niger OR Nigeria OR Saint Helena OR Sao Tome and Principe OR Senegal OR Sierra Leone OR Togo
A Nilotic Central, Nilotic Western population with a population size of >10 millions
A Central African population with a population size of < 1 million
A Central African population with a population size of 0.45 millions
A Pygmy Central population with a population size of 0.03 milion
A Pygmy Central population with a population size of 0.01 milion
A Pygmy Central population with a population size of 0.07 million
A Pygmy Eastern, Pygmy Southern, Banyarwanda, Pygmy Central population with a population size of 0.04 million
A Kanuri population with a population size of 0.655 millions
A Bantu Western, Bantu Central population with a population size of 3.3 millions with a group of 20 sub-ethnicities
A Bantu Central population with a population size of 1.1 million
A Bantu Central population with a population size of 17 millions
The Luba are a Bantu Central population with a population size of >15 million.
A Bantu Central population with a population size of 6.4 millions
A Bantu Central population with a population size of 0.018 million
The Mongo are a Bantu Central population with a population size of >15 million.
A Bantu Central population with a population size of 25 millions
A Bantu Central population with a population size of 0.08 million
A Bantu Central population with a population size of 0.025 million
A Bantu Central population with a population size of 4.6 milions
A Kongo population with a population size of 0.5 million
A Ubangi Central population with a population size of 1.5 million
A Ubangi Central population with a population size of 0.122 million
A Ubangi Central, Eastern African population with a population size of 1-4 millions
A Semite Central, Semitic Eastern population with a population size of 6 million
A Western African, Nilotic Central population with a population size of 3.5 millions
A Nilotic Eastern, Nilotic Western, Northern African, Nilotic Central population with a population size of 2.25 millions
A Southern African population with a population size of 2.8–3.5 million
A Southern African, Eastern African population with a population size of 2.5 millions
A Southern African population with a population size of 4.7 millions
A Southern African population with a population size of 0.03 millions. People of mixed race claiming both European and African descent.
A Southern African population with a population size of 0.1 million
A Khoekhoe, San population with a population size of 0.4 millions
The Himba are a Bantu Southern population with a population size of 0.05 million.
The Lemba are a Bantu Southern population with a population size of 0.05 million
A Bantu Southern population with a population size of 4.037 Millions
A Bantu Southern population with a population size of > 28 millions
A Bantu Southern population with a population size of 1.6 million
A Bantu Southern, Bantu Eastern population with a population size of 10.6 millions
A Bantu Southern population with a population size of 7.130 millions
A Bantu Southern, Bantu Eastern population with a population size of 2 millions
A Bantu Southern population with a population size of 1 million
A Bantu Southern population with a population size of 0.3 million
A Sotho population with a population size of 4.7 millions
A Shona population with a population size of 0.75 million
A Shona population with a population size of 0.1 million
A Nguni population with a population size of 2.3 millions
A Ndebele population with a population size of 1.5 million
A Ndebele population with a population size of 0.7 million
A Northern African population with a population size of 38 millions
A Eastern African, Northern African population with a population size of 20 millions
A Northern African population with a population size of 1.7 million
A Berber Northern population with a population size of Afro-Asiatic|Berber|Northern|Atlas
A Semite Northern population with a population size of 85 millions
A Semite Northern population with a population size of 2 millions
A Semite Northern population with a population size of >72 millions
A Nilotic Eastern population with a population size of 0.2 million
A Semite Northern, Semitic Eastern population with a population size of 2 millions
A Eastern African population with a population size of 25 millions
A Eastern African population with a population size of >22 millions
A Eastern African population with a population size of 2 millions
A Nilotic Eastern population with a population size of 0.475 millon
A Luo population with a population size of 2 Millions
A Nilotic Eastern population with a population size of 1,016 millions
A Luo population with a population size of 1.7 million
A Luo population with a population size of 2.2 millions
A Luo population with a population size of 1.5 million
'The Birked live north and east of Dago and Bayko, between Gebel Harayz and Rizaykat and are much larger tribe then either.' from a: A History of the Arabs in the Sudan. Written by De H. A. MacMichael.
A Nubian Eastern population with a population size of 0.063 million
A Cushitic Eastern population with a population size of 6.3 million
A Cushitic Eastern population with a population size of 1 million
A Cushitic Eastern population with a population size of 2.8 millions
The Bilen are a Cushitic Eastern population with a population size of 0.2 million.
The Saho are a Cushitic Eastern population with a population size of 0.2 million.
A Cushitic Eastern population with a population size of >3 millions
A Cushitic Eastern population with a population size of >20 millions
A Sudanic population with a population size of 11 millions
A Semitic Eastern population with a population size of 24 millions
A Semitic Eastern population with a population size of 1.9 millions. Subdivided into three groups: East, North, West.
A Semitic Eastern population with a population size of 0.2 millions
A Semitic Eastern population with a population size of 28 millions
A Semitic Eastern population with a population size of 10.3 millions
A Semitic Eastern population with a population size of 1.5 millions
A Pygmy Eastern population with a population size of 0.25 million
A Khoisan Eastern population with a population size of 0.06 million
A Bantu Eastern population with a population size of 2.9
The Chaga are a Bantu Eastern population with a population size of 2 million.
A Bantu Eastern population with a population size of >0.4 million
A Bantu Eastern population with a population size of 6.7 millions
A Bantu Eastern population with a population size of 2.2 millions
A Bantu Eastern population with a population size of 5.4 millions
A Bantu Eastern population with a population size of 1.3 millions
A Bantu Eastern population with a population size of 1.4 million
A Bantu Eastern population with a population size of >0.1 millons
A Bantu Eastern population with a population size of 1.546 millions
A Western African population with a population size of 0.05 million
A Western African population with a population size of 0.01 million
A Western African population with a population size of 0.04
A Western African population with a population size of 0.1 million
The Bubi are an amalgamation of first nation clans with various ancient mainland origins that later integrated with Krio, Efik, Igbo, Emancipado and Fernandino settlers.
A Western African population with a population size of 0.128 millions
A Western African population with a population size of 1.591 millions
A Western African population with a population size of 1.6 millions
A Western African population with a population size of 0.9 millions
A Western African population with a population size of 0.3 millions
A Western African population with a population size of 1.5 millions
A Western African population with a population size of 6 millions
The Fon are a Western African population with a population size of 4 million.
A Western African population with a population size of 9.6 millions
A Western African population with a population size of >14 millions
A Western African population with a population size of >30 millions
A Gurma population with a population size of 8.6 millions
The Urhobo are a Western African population with a population size of 2 million.
The Wolof are a Western African population with a population size of 4 million.
A Mande Western population with a population size of 1.7 millions
A Mande Western population with a population size of 13 millions
A Mande Western population with a population size of 0.4 millions
The Mende are a Mande Western population with a population size of 2 million.
A Gurunsi population with a population size of 0.161 millions
A Songhai population with a population size of >5 millions
A Songhai population with a population size of 0.2 million
A Banyarwanda population with a population size of 16 millions
A Banyarwanda, Southern African population with a population size of 3 millions
A Pygmy Central, Western African population with a population size of 6.8 millions
A Bantu Central population with a population size of 260000
Duala
A Bantu Central population with a population size of 74000
Eshira
A Bantu Central population with a population size of 215000
Hema
A Bantu Central population with a population size of 81500
Kota
A Bantu Central population with a population size of 89500
Makaa
A Bantu Central population with a population size of 117030
Myene
A Bantu Central population with a population size of 2.355 millions
Nande
Ngumba
Obamba
A Bantu Central population with a population size of 250000
Pende
A Bantu Central population with a population size of 317000
Punu
Teke
A Bantu Central population with a population size of 100000
Vili
A Central African population with a population size of 90500
Mandar
A Central African population with a population size of 1.8 millions
Mangbetu
A Central African population with a population size of 346000
Manja
A Central African population with a population size of 228000
Marba
A Central African population with a population size of 165000
Mbum
A Central African population with a population size of 347614
Nzebi
A Central African population with a population size of 65000
Podoko
A Pygmy Central population with a population size of 5500
Gyele
Yaka
Tupuri
Wuzlam
A Central African population with a population size of 177000
Yakoma
A Bantu Eastern population with a population size of 760000
Chopi
A Embu population with a population size of 195250
Mbeere
A Bantu Eastern population with a population size of 3,420 Millions
Kiga
A Bantu Eastern population with a population size of 89900
Lambya
A Bantu Eastern population with a population size of 2.233 millions
Masaba
A Mijikenda population with a population size of <25,000
Segeju
A Bantu Eastern population with a population size of 4,436 Millions
Nkole
A Bantu Eastern population with a population size of 4 Millions
Nyamwezi
A Bantu Eastern population with a population size of 112075
Pokomo
Ndau
A Bantu Eastern population with a population size of 10 Millions
Sukuma
A Bantu Eastern population with a population size of 175905
Tharaka
A Cushitic Eastern population with a population size of 20103
Aweer
A Cushitic Eastern population with a population size of 1104
Elmolo
A Cushitic Eastern population with a population size of 2 million
Hadiya
A Oromo population with a population size of 1025000
Borana
A Oromo population with a population size of 700000
Gabra
A Malagasy population with a population size of 50000
Antambahoaka
A Malagasy population with a population size of 772000
Antanosy
A Malagasy population with a population size of 100000
Bezanozano
A Malagasy population with a population size of 1500
Mikea
A Malagasy population with a population size of 200000
Sihanaka
A Malagasy population with a population size of 400000
Tanala
A Kalenjin population with a population size of 180000
Marakwet
A Kalenjin population with a population size of 969000
Pokot
A Nilotic Eastern population with a population size of 260000
Kunama
A Nilotic Eastern population with a population size of 108000
Nara
A Nilotic Eastern population with a population size of 2,873 Millions
Teso
Jeberti
A Bemba population with a population size of 433000
Aushi
Okavango
A Sotho population with a population size of 3,575 Millions
Lozi
A Khoisan South population with a population size of 146000
Damara
A Western African population with a population size of 61500
Aghem
A Western African population with a population size of 810000
Aja
A Akan population with a population size of 2 millions
Fante
A Western African population with a population size of 2.6 million
Anaang
A Akan population with a population size of 5 millions
Baule
A Western African population with a population size of 659000
Bamum
Kombe
Luvale
A Western African population with a population size of 2500
Bedik
A Western African population with a population size of 40800
Bassari
A Western African population with a population size of 150000
Diffa Arabs
Ditammari
Ekoi
A Western African population with a population size of 304000
Gola
The Guan are a Western African population with a population size of 1 million.
Guan
A Gurma population with a population size of 1.4 million
Bariba
A Gurma population with a population size of 950000
Konkomba
Lilse
Lobi
A Gurma population with a population size of 19700
Pana
A Gurma population with a population size of 30900
Samoya
A Western African population with a population size of 2.7 Million
Itsekiri
A Jola population with a population size of 10125
Bandial
A Mande Western population with a population size of 700000
Dan
A Gurma population with a population size of 1.22 millions
Kabye
A Western African population with a population size of 104311
Krio
A Kru population with a population size of 214000
Krahn
A Kru population with a population size of 387000
Grebo
A Western African population with a population size of 311500
Kulango
A Western African population with a population size of 792190
Limba
A Mande Western population with a population size of 115200
Jakhanke
A Mande Western population with a population size of 363000
Kono
The Kpelle are a Mande Western population with a population size of 2 million.
Kpelle
A Mande Western population with a population size of > 2 millions
Kuranko
A Mande Western population with a population size of 165692
Loko
A Mande Western population with a population size of 498000
Mano
A Mande Western population with a population size of 240000
Vai
A Mande Western population with a population size of 206000
Yalunka
A Western African population with a population size of 106900
Mankanya
A Western African population with a population size of 1.407 million
Oron
A Western African population with a population size of 140000
Papel
A Western African population with a population size of 134606
Sherbro
A Western African population with a population size of 2,225 Millions
Temne
A Wolof population with a population size of 210000
Lebu
Nuna
A Pygmy Central population with a population size of 12500
A Beti-Pahuin population with a population size of 2500000
A Southern African population with a population size of 35500
A Western African population with a population size of 1,224,545
A Swahili population with a population size of 416,200
A Swahili population with a population size of 217,400
A Swahili population with a population size of 45,000
A Swahili population with a population size of 365,900
A Bantu Eastern population with a population size of 1 million
A Jola population with a population size of 117000
An entity is anything that exists or has existed or will exist.
entity
An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts.
continuant
An entity that has temporal parts and that happens, unfolds or develops through time.
occurrent
A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything.
b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])
independent continuant
A process is an entity that exists in time by occurring or happening, has temporal parts and always involves and depends on some entity during the time it occurs.
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
A disposition is an entity that causes a specific process or transformation in an entity in which it inheres, under specific circumstances and in conjunction with the laws of nature. For example, the disposition of vegetables to decay when not refrigerated, the disposition of blood to coagulate, the disposition of a patient with a weakened immune system to contract disease.
disposition
realizable entity
A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities.
A quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized.
A quality is an attribute that is intrinsically associated with its bearer (or its parts), but whose presence/absence and observed/measured value may vary.
The etymology of "quality" is fairly well elucidated coming from Middle English, from Old French qualité, from Latin qualitatem, accusative of qualitas, from qualis (“of what kind”), from Proto-Indo-European *kʷo- (“who, how”). Cicero coined qualitas as a calque to translate the Ancient Greek word ποιότης (poiótēs, “quality”), coined by Plato from ποῖος (poîos, “of what nature, of what kind”).
quality
A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same.
An experimental factor which is a property or characteristic of some other entity. For example, the mouse has the colour white.
b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n > 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i < j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004])
b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence.
b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])
characteristic
specifically dependent continuant
A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts.
A role is an entity which is borne in a material entity in some kinds of natural, social or institutional contexts, but which is not essential to the fundamental definition of that material entity (i.e. the material entity exists with or without the role). For example, the role of a person as a surgeon, the role of an artificial heart in pumping blood, the role of a chemical compound in an experiment, the role of a drug in the treatment of a disease.
role
fiat object
fiat object part
ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158.
object aggregate
object
A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time.
b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001])
generically dependent continuant
material entity
A material entity is an entity that exists in full during the length of time of its existence, persists through this time while maintaining its identity and has no temporal parts. For example a heart, a human, a fly, a microarray.
An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time.
immaterial entity
Human colon adenocarcinoma cell line, established from the primary colon tumor (adenocarcinoma) of a 72-year-old Caucasian man in 1974.
Hepatoma is a cancer originating in the liver, in liver cells. More often called hepatocarcinoma or hepatocellular carcinoma.
A glioma is a type of tumor that starts in the glial cells of the brain or the spine. Gliomas comprise about 30 per cent of all brain tumors and central nervous system tumors, and 80 per cent of all malignant brain tumors.
The MDBK cell line was derived from a kidney of an apparently normal adult steer, February 18, 1957, by S.H. Madin and N.B. Darby.
The Vero cell line was initiated from the kidney of a normal adult African green monkey on March 27, 1962, by Y. Yasumura and Y. Kawakita at the Chiba University in Chiba, Japan.
Pig kidney cell line. Original line: PK-2a; contains type C viruses. Morphology: epithelial-like.
Human glioma cell line. Morphology: glial; Species: human; Tumor: glioma.
A highly transformed human renal epithelial line expressing two viral oncogenes, adenovirus E1a and SV40 large T antigen.
Human lung adenocarcinoma cell line; established from a 25-year-old caucasian male.
Normal human bronchial epithelial cell line.
A monocarboxylic acid comprising 1,8-naphthyridin-4-one substituted by carboxylic acid, ethyl and methyl groups at positions 3, 1, and 7, respectively. An orally administered antibacterial, it is used in the treatment of lower urinary-tract infections due to Gram-negative bacteria, including the majority of E. coli, Enterobacter, Klebsiella, and Proteus species.
A quinolone that is quinolin-4(1H)-one bearing cyclopropyl, carboxylic acid, fluoro and piperazin-1-yl substituents at positions 1, 3, 6 and 7, respectively.
A quinolinemonocarboxylic acid with broad-spectrum antibacterial activity against most gram-negative and gram-positive bacteria. Norfloxacin is bactericidal and its mode of action depends on blocking of bacterial DNA replication by binding itself to an enzyme called DNA gyrase.
A sulfonamide consisting of pyrimidine with methyl substituents at the 4- and 6-positions and a 4-aminobenzenesulfonamido group at the 2-position.
A sulfonamide antibacterial with an oxazole substituent. It has antibiotic activity against a wide range of gram-negative and gram-positive organisms.
A fluoroquinolone antibiotic, used (generally as the hydrochloride salt) to treat bacterial infections including bronchitis and urinary tract infections. It is also used to prevent urinary tract infections prior to surgery.
A semisynthetic, first-generation cephalosporin antibiotic with acetoxymethyl and (2-thienylacetyl)nitrilo moieties at positions 3 and 7, respectively, of the core structure. Administered parenterally during surgery and to treat a wide spectrum of blood infections.
A class of carbonyl compound encompassing dicarboxylic acids and any derivatives obtained by substitution of either one or both of the carboxy hydrogens.
dicarboxylic acids and O-substituted derivatives
Any aromatic amide obtained by acylation of aniline.
Any main group molecular entity that is gaseous at standard temperature and pressure (STP; 0degreeC and 100 kPa).
An alpha-oxyketone that has a hydroxy group as the alpha-oxy moiety.
An alpha-hydroxy ketone in which the carbonyl group and the hydroxy group are linked by a carbon bearing two organyl groups.
A carboxamide resulting from the formal condensation of a carboxylic acid with a primary amine; formula RC(=O)NHR(1).
A carboxamide resulting from the formal condensation of a carboxylic acid with a secondary amine; formula RC(=O)NHR(1)R(2).
A compound having bonds between one or more metalloid atoms and one or more carbon atoms of an organyl group.
Any organic heterotricyclic compound whose core skeleton consists of a benzodioxin ring that is ortho-fused to a pyran ring.
A large group of antibiotics isolated from various species of Streptomyces and characterised by having a substituted phenoxazine ring linked to two cyclic heterodetic peptides.
A 1,8-naphthyridine derivative that is 1,4-dihydro-1,8-naphthyridine with an ethyl group at the 1 position, a carboxy group at the 3-position, an oxo sustituent at the 4-position, a fluoro substituent at the 5-position and a piperazin-1-yl group at the 7 position. An antibacterial, it is used in the treatment of urinary-tract infections and gonorrhoea.
A primary alcohol is a compound in which a hydroxy group, -OH, is attached to a saturated carbon atom which has either three hydrogen atoms attached to it or only one other carbon atom and two hydrogen atoms attached to it.
A cyclic peptide antibiotic produced by the actinomycete Streptomyces puniceus, used in the treatment of tuberculosis.
A peptide containing ten or more amino acid residues.
A nucleobase-containing molecular entity with a polymeric structure comprised of a linear sequence of 13 or more nucleotide residues.
A synthetic monocyclic beta-lactam antibiotic (monobactam), used primarily to treat infections caused by Gram-negative bacteria. It inhibits mucopeptide synthesis in the bacterial cell wall, thereby blocking peptidoglycan crosslinking.
A lipid containing phosphoric acid as a mono- or di-ester. The term encompasses phosphatidic acids and phosphoglycerides.
The nitrogen oxoanion formed by loss of a proton from nitrous acid.
Compounds having the structure RSR (R =/= H). Such compounds were once called thioethers.
An aromatic ether that is phenol which is substituted at C-5 by a chloro group and at C-2 by a 2,4-dichlorophenoxy group. It is widely used as a preservative and antimicrobial agent in personal care products such as soaps, skin creams, toothpaste and deodorants as well as in household items such as plastic chopping boards, sports equipment and shoes.
An alpha-amino acid that consists of propionic acid bearing an amino substituent at position 2.
A naturally occurring polypeptide synthesized at the ribosome.
Amide derived from two or more amino carboxylic acid molecules (the same or different) by formation of a covalent bond from the carbonyl carbon of one to the nitrogen atom of another with formal loss of water. The term is usually applied to structures formed from alpha-amino acids, but it includes those derived from any amino carboxylic acid. X = OH, OR, NH2, NHR, etc.
Any oligosaccharide, polysaccharide or their derivatives consisting of monosaccharides or monosaccharide derivatives linked by glycosidic bonds. See also http://www.ontobee.org/ontology/GNO?iri=http://purl.obolibrary.org/obo/GNO_00000001.
High molecular weight, linear polymers, composed of nucleotides containing deoxyribose and linked by phosphodiester bonds; DNA contain the genetic information of organisms.
deoxyribonucleic acid
A amino cyclitol glycoside that consists of streptidine having a disaccharyl moiety attached at the 4-position. The parent of the streptomycin class
A compound in which a carbonyl group is bonded to two carbon atoms: R2C=O (neither R may be H).
A pyridinecarboxamide that is pyridine in which the hydrogen at position 3 is replaced by a carboxamide group.
Any member of the group of substituted penams containing two methyl substituents at position 2, a carboxylate substituent at position 3 and a carboxamido group at position 6.
A compound RC(=O)H, in which a carbonyl group is bonded to one hydrogen atom and to one R group.
A nitrogen oxoanion formed by loss of a proton from nitric acid. Principal species present at pH 7.3.
A macrolide antibiotic that is tylonolide having mono- and diglycosyl moieties attached to two of its hydroxy groups. It is found naturally as a fermentation product of Streptomyces fradiae.
Any member of a group of vitamers that belong to the chemical structural class called pyridines that exhibit biological activity against vitamin B3 deficiency. Vitamin B3 deficiency causes a condition known as pellagra whose symptoms include depression, dermatitis and diarrhea. The vitamers include nicotinic acid and nicotinamide (and their ionized and salt forms).
An organochlorine compound that is dichloro-substituted acetamide containing a nitrobenzene ring, an amide bond and two alcohol functions.
A compound containing at least one carbon-halogen bond (where X is a halogen atom).
An aminonucleoside antibiotic, derived from the Streptomyces alboniger bacterium, that causes premature chain termination during translation taking place in the ribosome.
'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.
RNA molecules which are essential structural and functional components of ribosomes, the subcellular units responsible for protein synthesis.
A penicillin in which the substituent at position 6 of the penam ring is a phenylacetamido group.
Any nucleoside where the sugar component is D-ribose.
An oxazinoquinoline that is 2,3-dihydro-7H-[1,4]oxazino[2,3,4-ij]quinolin-7-one substituted by methyl, carboxy, fluoro, and 4-methylpiperazin-1-yl groups at positions 3, 6, 9, and 10, respectively.
9-fluoro-3-methyl-10-(4-methylpiperazin-1-yl)-7-oxo-2,3-dihydro-7H-[1,4]oxazino[2,3,4-ij]quinoline-6-carboxylic acid
A cephalosporin compound having acetoxymethyl and [2-(2-amino-1,3-thiazol-4-yl)-2-(methoxyimino)acetyl]amino side groups.
A semisynthetic cephamycin antibiotic which, in addition to the methoxy group at the 7alpha position, has 2-thienylacetamido and carbamoyloxymethyl side-groups. It is resistant to beta-lactamase.
A glycosyl compound arising formally from the elimination of water from a glycosidic hydroxy group and an H atom bound to a nitrogen atom, thus creating a C-N bond.
Compounds with the general formula RNHC(=O)CH3.
Any purine ribonucleoside that is a derivative of adenosine.
Any of the naturally occurring, basic nitrogen compounds (mostly heterocyclic) occurring mostly in the plant kingdom, but also found in bacteria, fungi, and animals. By extension, certain neutral compounds biogenetically related to basic alkaloids are also classed as alkaloids. Amino acids, peptides, proteins, nucleotides, nucleic acids, amino sugars and antibiotics are not normally regarded as alkaloids. Compounds in which the nitrogen is exocyclic (dopamine, mescaline, serotonin, etc.) are usually classed as amines rather than alkaloids.
An alcohol containing an amino functional group in addition to the alcohol-defining hydroxy group.
Any aromatic amine that is benzene carrying at least one amino substituent and its substituted derivatives.
A monoatomic or polyatomic species having one or more elementary charges of the electron.
A class of macrocyclic lactams that consist of an aromatic (phenyl or naphthyl) or quinonoid (benzoquinone or naphthoquinone) moiety that is bridged by an aliphatic chain.
obsolete: antibiotic
Any benzenoid aromatic compound consisting of the benzene skeleton and its substituted derivatives.
Any aromatic carboxylic acid that consists of benzene in which at least a single hydrogen has been substituted by a carboxy group.
A glycopeptide produced by the bacterium Streptomyces verticillus. The term, 'bleomycin' refers to a family of structurally related compounds. When used as an anti-cancer agent, the chemotherapeutical forms are primarily bleomycin A2 and B2.
Any ester of carbamic acid or its N-substituted derivatives.
Any carbohydrate derivative that exhibits antibiotic activity.
A class of beta-lactam antibiotics differing from the penicillins in having a 6-membered, rather than a 5-membered, side ring. Although cephalosporins are among the most commonly used antibiotics in the treatment of routine infections, and their use is increasing over time, they can cause a range of hypersensitivity reactions, from mild, delayed-onset cutaneous reactions to life-threatening anaphylaxis in patients with immunoglobulin E (IgE)-mediated allergy.
A halogen molecular entity containing one or more atoms of chlorine.
Any organochlorine compound containing a benzene ring which is substituted by one or more chlorines.
Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity.
A polyol consisting of a cycloalkane containing at least three hydroxy groups, each attached to a different ring carbon atom.
A member of the class of oxazolidines that is isoxazoldin-3-one which is substituted at position 4 by an amino group.
A natural or synthetic compound having a sequence of amino and hydroxy carboxylic acid residues (usually alpha-amino and alpha-hydroxy acids), commonly but not necessarily regularly alternating.
An azole that is either one of a pair of heterocyclic organic compounds comprising three carbon atoms and two nitrogen atoms arranged in a ring.
Any member of the class of chlorobenzenes carrying two chloro groups at unspecified positions.
Any organic heteromonocyclic compound with a structure based on a dihydropyrrole.
A compound that contains two hydroxy groups, generally assumed to be, but not necessarily, alcoholic. Aliphatic diols are also called glycols.
Compounds containing at least one furan ring.
Any carbohydrate derivative that consists of glycan moieties covalently attached to the side chains of the amino acid residues that constitute the peptide.
Any phospholipid that contain both phosphate and carbohydrate as integral structural components.
A glycosyl compound resulting from the attachment of a glycosyl group to a non-acyl group RO-, RS-, RSe-, etc. The bond between the glycosyl group and the non-acyl group is called a glycosidic bond. By extension, the terms N-glycosides and C-glycosides are used as class names for glycosylamines and for compounds having a glycosyl group attached to a hydrocarbyl group respectively. These terms are misnomers and should not be used. The preferred terms are glycosylamines and C-glycosyl compounds, respectively.
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.
A heterodetic cyclic peptide is a peptide consisting only of amino-acid residues, but in which the linkages forming the ring are not solely peptide bonds; one or more is an isopeptide, disulfide, ester, or other bond.
A homodetic cyclic peptide is a cyclic peptide in which the ring consists solely of amino-acid residues in peptide linkages.
An imidazolidinone with oxo groups at position 2 and 4.
A compound, RkE(=O)lNHOH, derived from an oxoacid RkE(=O)l(OH) (l =/= 0) by replacing -OH with -NHOH, and derivatives thereof. Specific examples of hydroxamic acids are preferably named as N-hydroxy amides.
Hydroxides are chemical compounds containing a hydroxy group or salts containing hydroxide (OH(-)).
Any benzoic acid carrying one or more phenolic hydroxy groups on the benzene ring.
A five-membered organic heterocycle containing two nitrogen atoms at positions 1 and 3, or any of its derivatives; compounds containing an imidazole skeleton.
A compound which contains oxygen, at least one other element, and at least one hydrogen bound to oxygen, and which produces a conjugate base by loss of positive hydrogen ion(s) (hydrons).
A molecular entity that contains no carbon.
A salt is an assembly of cations and anions.
A molecular entity having a net electric charge.
Oximes of ketones R2C=NOH (where R =/= H).
Cyclic amides of amino carboxylic acids, having a 1-azacycloalkan-2-one structure, or analogues having unsaturation or heteroatoms replacing one or more carbon atoms of the ring.
Any cyclic carboxylic ester containing a 1-oxacycloalkan-2-one structure, or an analogue having unsaturation or heteroatoms replacing one or more carbon atoms of the ring.
A macrocyclic lactone with a ring of twelve or more members which exhibits antibiotic activity.
A macrocyclic lactone with a ring of twelve or more members derived from a polyketide.
A molecule all atoms of which have the same atomic number.
Any polyatomic entity that is an electrically neutral entity consisting of more than one atom.
An oxoacid containing a single carboxy group.
Any hydroxybenzoic acid having a single phenolic hydroxy substituent on the benzene ring.
Any benzenoid aromatic compound having a skeleton composed of two ortho-fused benzene rings.
A member of the class of pyridines that is a substituted pyridine in which at least one of the substituents is a carboxamide or N-substituted caraboxamide group.
Any organic ion with a net negative charge.
An organooxygen compound with formula ROR, where R is not hydrogen.
An organophosphorus compound is formally a compound containing at least one carbon-phosphorus bond, but the term is often extended to include esters and thioesters.
An oxide is a chemical compound of oxygen with other chemical elements.
Compounds of structure R2C=NOH derived from condensation of aldehydes or ketones with hydroxylamine. Oximes from aldehydes may be called aldoximes; those from ketones may be called ketoximes.
Any compound that has an aldehydic or ketonic group as well as a carboxylic acid group in the same molecule.
A chemically diverse class of peptides that exhibit antimicrobial properties.
Any organic aromatic compound with a structure based on a phenylpropane skeleton. The class includes naturally occurring phenylpropanoid esters, flavonoids, anthocyanins, coumarins and many small phenolic molecules as well as their semi-synthetic and synthetic analogues. Phenylpropanoids are also precursors of lignin.
Salts and esters of phosphoric and oligophosphoric acids and their chalcogen analogues. In inorganic chemistry, the term is also used to describe anionic coordination entities with phosphorus as central atom.
HP(=O)(OH)2 (phosphonic acid) and its P-substituted derivatives.
Natural and synthetic compounds containing alternating carbonyl and methylene groups ('beta-polyketones'), biogenetically derived from repeated condensation of acetyl coenzyme A (via malonyl coenzyme A), and usually the compounds derived from them by further condensations, etc. Considered by many to be synonymous with the less frequently used terms acetogenins and ketides.
A compound that contains two or more hydroxy groups.
Members of the class of phenols that contain 2 or more benzene rings each of which is substituted by at least one hydroxy group.
An amino acid derivative resulting from reaction of proline at the amino group or the carboxy group, or from the replacement of any hydrogen of proline by a heteroatom. The definition normally excludes peptides containing proline residues.
An amino cyclitol glycoside that is kanamycin A acylated at the N-1 position by a 4-amino-2-hydroxybutyryl group.
A ribonucleoside that has a purine moiety as the nucleobase (the R group in the illustration).
A class of imidazopyrimidines that consists of purine and its substituted derivatives.
Any organonitrogen heterocyclic compound based on a pyridine skeleton and its substituted derivatives.
An azole that includes only one N atom and no other heteroatom as a part of the aromatic skeleton.
A nitrogen molecular entity that is electronically neutral but which contains a quaternary nitrogen.
Any aromatic carboxylic acid that contains a quinoline moiety that is substituted by one carboxy substituent.
A class of aromatic heterocyclic compounds each of which contains a benzene ring ortho fused to carbons 2 and 3 of a pyridine ring.
An amino acid derivative resulting from reaction of serine at the amino group or the carboxy group, or from the replacement of any hydrogen of serine by a heteroatom. The definition normally excludes peptides containing serine residues.
A monohydroxybenzoic acid consisting of 5-aminosalicylic acid (mesalazine) linked to 4-aminobenzoyl-beta-alanine via an azo bond.
A penicillin in which the substituent at position 6 of the penam ring is a 2-amino-2-(4-hydroxyphenyl)acetamido group.
Any sulfur molecular entity that involves either covalently bonded or anionic sulfur.
A tertiary alcohol is a compound in which a hydroxy group, -OH, is attached to a saturated carbon atom which has three other carbon atoms attached to it.
A subclass of polyketides having an octahydrotetracene-2-carboxamide skeleton, substituted with many hydroxy and other groups.
Any oxacycle having an oxolane (tetrahydrofuran) skeleton.
Compounds containing at least one thiophene ring.
An organic tricyclic compound in which at least one of the rings of the tricyclic skeleton contains one or more heteroatoms.
A chemical compound containing three hydroxy groups.
A neutral compound having formal unit electrical charges of opposite sign on non-adjacent atoms. Sometimes referred to as inner salts, dipolar ions (a misnomer).
An aminobenzoic acid that is salicylic acid substituted by an amino group at position 4.
A member of the class of tetracyclines with formula C22H23ClN2O8 isolated from Streptomyces aureofaciens.
An aminoglycoside that is 2-deoxystreptamine that is substituted on the oxygen at position 4 by an (8R)-2-amino-8-O-(4-amino-4-deoxy-alpha-D-glucopyranosyl)-2,3,7-trideoxy-7-(methylamino)-D-glycero-alpha-D-allo-octodialdo-1,5:8,4-dipyranos-1-yl) group.
An organonitrogen heterocyclic antibiotic that contains a beta-lactam ring.
A complex glycopeptide from Streptomyces orientalis. It inhibits a specific step in the synthesis of the peptidoglycan layer in the Gram-positive bacteria Staphylococcus aureus and Clostridium difficile.
A member of the class of rifamycins that is a a semisynthetic antibiotic derived from Amycolatopsis rifamycinica (previously known as Amycolatopsis mediterranei and Streptomyces mediterranei).
A coumarin-derived antibiotic obtained from Streptomyces niveus.
A amino cyclitol glycoside that is kanamycin B lacking the 3-hydroxy substituent from the 2,6-diaminoglucose ring.
A glycophospholipid antibiotic compound with the lipid portion conjugated to a pentasaccharide fraction via a phosphate linkage.
A phosphonic acid having an (R,S)-1,2-epoxypropyl group attached to phosphorus.
Any sugar having one or more alcoholic hydroxy groups replaced by substituted or unsubstituted amino groups.
A penicillin in which the substituent at position 6 of the penam ring is a 2-amino-2-phenylacetamido group.
A third-generation cephalosporin compound having 2-(2-amino-1,3-thiazol-4-yl)-2-(methoxyimino)acetylamino and [(2-methyl-5,6-dioxo-1,2,5,6-tetrahydro-1,2,4-triazin-3-yl)sulfanyl]methyl side-groups.
A steroid antibiotic that is isolated from the fermentation broth of Fusidium coccineum.
The conjugate base formed when the carboxy group of a carboxylic acid is deprotonated.
A carboxamide derived from a monocarboxylic acid.
A macrolide antibiotic useful for the treatment of bacterial infections.
A complex glycopeptide antibiotic that is isolated from Amycolatopsis orientalis.
A semisynthetic penicillin having a 6beta-{(2R)-2-[(2-oxoimidazolidine-1-carbonyl)amino]-2-phenylacetyl}amino side-group. It is an antibiotic used in treating infections caused by Pseudomonas aeruginosa, Escherichia coli and Haemophilus influenzae.
A twelve-membered macrolide antibiotic that is biosynthesised by Streptomyces venezuelae.
A macrolide antibiotic that is narbonolide having a 3,4,6-trideoxy-3-(dimethylamino)-beta-D-xylo-hexopyranosyl residue attached at position 6. It is biosynthesised by Streptomyces venezuelae.
A macrolide antibiotic that is biosynthesised by Streptomyces venezuelae.
A member of the class of rifamycins that exhibits antibiotic and antitubercular properties.
A heterodetic cyclic peptide, in which the cyclisation step involves a formal lactonisation between the carboxy group of a quinaldic acid-based residue and a secondary alcohol. An antibiotic that inhibits bacterial protein synthesis. Also acts as an antitumor agent.
A compound in which a hydroxy group, -OH, is attached to a saturated carbon atom.
Any organic amino compound that is a derivative of ethylenediamine.
A macrolide antibiotic produced by certain strains of Streptomyces narbonensis var. josamyceticus.
A macrolide antibiotic produced by Streptomyces kitasatoensis, showing activity against a wide spectrum of pathogens.
A fluoroquinolone antibiotic that is 4-oxo-1,4-dihydroquinoline which is substituted at positions 1, 3, 6, 7 and 8 by 2-fluoroethyl, carboxy, fluoro, 4-methylpiperazin-1-yl and fluoro groups, respectively. It is active against many Gram-positive and Gram-negative bacteria.
Any cyclic ether in which the oxygen atom forms part of a 3-membered ring.
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.
An organic fundamental parent is a structure used as a basis for substitutive names in organic nomenclature, containing, in addition to one or more hydrogen atoms, a single atom of an element, a number of atoms (alike or different) linked together to form an unbranched chain, a monocyclic or polycyclic ring system, or a ring assembly or ring/chain system.
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 derivative of two oxoacids RkE(=O)l(OH)m (l =/= 0) in which two acyl groups are attached to the amino or substituted amino group.
A molecular entity all atoms of which have the same atomic number.
An organosulfur compound is a compound containing at least one carbon-sulfur bond.
An anion consisting of more than one atom.
A substance that kills or slows the growth of microorganisms, including bacteria, viruses, fungi and protozoans.
A heteroorganic entity is an organic molecular entity in which carbon atoms or organic groups are bonded directly to one or more heteroatoms.
food role
A physiological role played by any substance of either plant, animal or artificial origin which contains essential body nutrients that can be ingested by an organism to provide energy, promote growth, and maintain the processes of life.
An alkaline earth molecular entity is a molecular entity containing one or more atoms of an alkaline earth metal.
Any p-block element atom that is in group 15 of the periodic table: nitrogen, phosphorus, arsenic, antimony and bismuth.
A p-block molecular entity containing any pnictogen.
Any p-block molecular entity containing a chalcogen.
An ester of a carboxylic acid, R(1)C(=O)OR(2), where R(1) = H or organyl and R(2) = organyl.
An atom belonging to one of the main groups (found in the s- and p- blocks) of the periodic table.
Any main group element atom belonging to the p-block of the periodic table.
Any member of class of 1,2-di-O-acylglycerols joined at oxygen 3 by a glycosidic linkage to a carbohydrate part (usually a mono-, di- or tri-saccharide). Some substances classified as bacterial glycolipids have the sugar part acylated by one or more fatty acids and the glycerol part may be absent.
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 cyclic compound having as ring members atoms of the same element only.
A homocyclic compound in which all of the ring members are carbon atoms.
A molecule that features two fused rings.
A cyclically conjugated molecular entity with a stability (due to delocalization) significantly greater than that of a hypothetical localized structure (e.g. Kekule structure) is said to possess aromatic character.
A polycyclic compound in which at least one of the rings contains at least one non-carbon atom.
A bicyclic compound in which at least one of the rings contains at least one skeletal heteroatom.
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.
Hydrides are chemical compounds of hydrogen with other chemical elements.
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.
An amino acid in which the amino group is located on the carbon atom at the position alpha to the carboxy group.
A carboxylic acid containing one or more amino groups.
An organic compound having at least one hydroxy group attached to a carbon atom.
Any organic molecule that consists of atoms connected in the form of a ring.
A heterocyclic compound formally derived from an arene by replacement of one or more methine (-C=) and/or vinylene (-CH=CH-) groups by trivalent or divalent heteroatoms, respectively, in such a way as to maintain the continuous pi-electron system characteristic of aromatic systems and a number of out-of-plane pi-electrons corresponding to the Hueckel rule (4n+2).
An N-glycosyl compound that has both a nucleobase, normally adenine, guanine, xanthine, thymine, cytosine or uracil, and either a ribose or deoxyribose as functional parents.
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.
Organic aromatic compounds having one or more hydroxy groups attached to a benzene or other arene ring.
An amino acid whose structure includes an aromatic ring.
Any carboxylic acid in which the carboxy group is directly bonded to an aromatic ring.
An amino compound in which the amino group is linked directly to an aromatic system.
A penicillin antibiotic having a 6beta-2-carboxy-2-phenylacetamido side-chain.
A cephalosporin bearing chloro and (R)-2-amino-2-phenylacetamido groups at positions 3 and 7, respectively, of the cephem skeleton.
A cephalosporin bearing methyl and (2R)-2-amino-2-(4-hydroxyphenyl)acetamido groups at positions 3 and 7, respectively, of the cephem skeleton.
A cephalosporin compound having (R)-mandelamido and N-methylthiotetrazole side-groups.
A cephalosporin compound having 7beta-2-(2-amino-thiazol-4-yl)-2-[(Z)-hydroxyimino]-acetylamino- and 3-vinyl side groups.
A second-generation cephalosporin antibiotic having N(1)-methyltetrazol-5-ylthiomethyl, {[(cyanomethyl)sulfanyl]acetyl}amino and methoxy side-groups at positions 3, 7beta and 7alpha respectively of the parent cephem bicyclic structure.
A cephalosporin bearing {[1-(sulfomethyl)-1H-tetrazol-5-yl]sulfanyl}methyl and (R)-2-hydroxy-2-phenylacetamido groups at positions 3 and 7, respectively, of the cephem skeleton.
A semi-synthetic parenteral cephalosporin with a tetrazolyl moiety that confers beta-lactamase resistance.
Any of the glycopeptides whose structure consists of teicoplanin A3-1 in which the hydroxy group of the di(aryloxy)-substituted phenol moiety has been converted to the corresponding 2-acylamino-2-deoxy-beta-D-glucoside. Members of the class differ only in the nature of the acyl group.
A teicoplanin A2 that has decanoyl as the variable N-acyl group.
A third-generation cephalosporin antibiotic with methoxymethyl and (2Z)-2-(2-amino-1,3-thiazol-4-yl)-2-(methoxyimino)acetamino substituents at positions 3 and 7, respectively, of the cephem skeleton. Given by mouth as its proxetil ester prodrug, it is used to treat acute otitis media, pharyngitis, and sinusitis.
A semisynthetic, second-generation cephalosporin, with prop-1-enyl and (R)-2-amino-2-(4-hydroxyphenyl)acetamido groups at positions 3 and 7, respectively, of the cephem skeleton. It is used to treat bronchitis as well as ear, skin and other bacterial infections.
A third-generation cephalosporin antibiotic bearing pyridinium-1-ylmethyl and {[(2Z)-2-(2-amino-1,3-thiazol-4-yl)-2-{[(2-carboxypropan-2-yl)oxy]imino}acetamido groups at positions 3 and 7, respectively, of the cephem skeleton.
A third-generation cephalosporin antibiotic with a [(2Z)-2-(2-amino-1,3-thiazol-4-yl)-4-carboxybut-2-enoyl]amino substituent at the 7 position of the cephem skeleton. An orally-administered agent, ceftibuten is used as the dihydrate to treat urinary-tract and respiratory-tract infections.
A depsipeptide in which the amino and hydroxy carboxylic acid residues are connected in a ring.
A glycosyl compound arising formally from the elimination of water from a glycosidic hydroxy group and a S atom bound to a carbon atom, thus creating a C-S bond.
Neutral molecules having charge-separated forms with an onium atom which bears no hydrogen atoms and that is not adjacent to the anionic atom.
A polyclic compound in which all of the ring members are carbon atoms.
A semisynthetic first-generation cephalosporin antibiotic having methyl and beta-(2R)-2-amino-2-phenylacetamido groups at the 3- and 7- of the cephem skeleton, respectively. It is effective against both Gram-negative and Gram-positive organisms, and is used for treatment of infections of the skin, respiratory tract and urinary tract.
Any of naturally occurring compounds and synthetic analogues, based on the cyclopenta[a]phenanthrene carbon skeleton, partially or completely hydrogenated; there are usually methyl groups at C-10 and C-13, and often an alkyl group at C-17. By extension, one or more bond scissions, ring expansions and/or ring contractions of the skeleton may have occurred. Natural steroids are derived biogenetically from squalene which is a triterpene.
Any heteroorganic entity containing at least one carbon-nitrogen bond.
An amide of a sulfonic acid RS(=O)2NR'2.
Compounds derived from oxoacids RkE(=O)l(OH)m (l =/= 0) by replacing -OH by -NRNR2 (R groups are commonly H). (IUPAC).
A hydrazide consisting of hydrazine carrying one or more carboacyl groups.
An oxoanion is an anion derived from an oxoacid by loss of hydron(s) bound to oxygen.
Any glucoside in which the glycoside group is derived from D-glucose.
A first-generation cephalosporin antibiotic with a methyl substituent at position 3, and a (2R)-2-amino-2-cyclohexa-1,4-dien-1-ylacetamido substituent at position 7, of the cephem skeleton.
Any fluoroarene that is a benzene or a substituted benzene carrying at least one fluoro group.
An addition compound contains two or more simpler compounds that can be packed in a definite ratio into a crystal. The term covers donor-acceptor complexes (adducts) and a variety of lattice compounds.
An addition compound that contains water in weak chemical combination with another compound.
A cephalosporin with ({1-[2-(dimethylamino)ethyl]-1H-tetrazol-5-yl}sulfanyl)methyl and (2-amino-1,3-thiazol-4-yl)acetamido substituents at positions 3 and 7, respectively, of the cephem skeleton. A third generation beta-lactam cephalosporin antibiotic, it is active against a broad spectrum of both Gram positive and Gram negative bacteria.
Any molecular entity that consists of a ring having (formally) the maximum number of noncumulative double bonds.
Any ether in which the oxygen is attached to at least one aryl substituent.
A lactam in which the amide bond is contained within a four-membered ring, which includes the amide nitrogen and the carbonyl carbon.
A secondary alcohol is a compound in which a hydroxy group, -OH, is attached to a saturated carbon atom which has two other carbon atoms attached to it.
An azole in which the five-membered heterocyclic aromatic skeleton contains four N atoms and one C atom.
Any carboxylic acid containing two carboxy groups.
A compound formally derived from an oxoacid RkE(=O)l(OH)m (l > 0) and an alcohol, phenol, heteroarenol, or enol by linking with formal loss of water from an acidic hydroxy group of the former and a hydroxy group of the latter.
A compound having a nitro group, -NO2 (free valence on nitrogen), which may be attached to carbon, nitrogen (as in nitramines), or oxygen (as in nitrates), among other elements (in the absence of specification, C-nitro compounds are usually implied).
A nitro compound having the nitro group (-NO2) attached to a carbon atom.
An azole in which the five-membered heterocyclic aromatic skeleton contains three N atoms and two C atoms.
A carboxylic acid anion formed when the carboxy group of a monocarboxylic acid is deprotonated.
An azole based on a five-membered heterocyclic aromatic skeleton containing one N and one O atom.
An organosulfur compound having the structure RS(=O)2R (R =/= H).
Any monocarboxylic acid having at least one additional oxo functional group.
A steroid ester obtained by formal condensation of the carboxy group of any carboxylic acid with the 3-hydroxy group of a sterol.
A polycyclic compound in which two rings have two or more atoms in common.
Compound comprising a beta-lactam ring fused to a saturated 5-membered ring containing one sulfur atom.
Natural and synthetic antibiotics containing the 4-thia-1-azabicyclo[3.2.0]heptan-7-one structure, generally assumed to have the 5R configuration unless otherwise specified.
A biological macromolecule minimally consisting of one polypeptide chain synthesized at the ribosome.
Any molecular entity consisting of more than one atom.
An ion consisting of more than one atom.
A polycyclic heteroarene that is anthracene in which one of the central CH groups is replaced by a nitrogen 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 organochlorine compound is a compound containing at least one carbon-chlorine bond.
Any member of the class of quinolines in which the quinoline skeleton is substituted by one or more amino or substituted-amino groups.
A bicyclic compound in which all the ring atoms are carbon.
A salt formally resulting from the reaction of hydrochloric acid with an organic base.
Any hydroxy steroid carrying a hydroxy group at position 3.
A 3-hydroxy steroid in which the 3-hydroxy substituent is in the alpha-position.
An organochalcogen compound is a compound containing at least one carbon-chalcogen bond.
An organochalcogen compound containing at least one carbon-oxygen bond.
A compound containing at least one carbon-bromine bond.
An organofluorine compound is a compound containing at least one carbon-fluorine bond.
A member of the class of cinnolines that is 6,7-methylenedioxycinnolin-4(1H)-one bearing an ethyl group at position 1 and a carboxylic acid group at position 3. An analogue of oxolinic acid, it has similar antibacterial actions. It was formerly used for the treatment of urinary tract infections.
The 6-O-methyl ether of erythromycin A, clarithromycin is a macrolide antibiotic used in the treatment of respiratory-tract, skin and soft-tissue infections. It is also used to eradicate Helicobacter pylori in the treatment of peptic ulcer disease. It prevents bacteria from growing by interfering with their protein synthesis.
Any ether in which the oxygen atom forms part of a ring.
A carbohydrate-containing antibiotic that is the semisynthetic derivative of lincomycin, a natural antibiotic.
3-Isopropylimino-3,5-dihydro-phenazine in which the hydrogen at position 5 is substituted substituted by a 4-chlorophenyl group, and that at position 2 is substituted by a (4-chlorophenyl)amino group. A dark red crystalline solid, clofazimine is an antimycobacterial and is one of the main drugs used for the treatment of multi-bacillary leprosy. However, it can cause red/brown discolouration of the skin, so other treatments are often preferred in light-skinned patients.
A molecular entity consisting of two or more chemical elements.
Any heteroatomic molecular entity that is a chemical compound of halogen with other chemical elements.
An amide of a carboxylic acid, having the structure RC(=O)NR2. The term is used as a suffix in systematic name formation to denote the -C(=O)NH2 group including its carbon atom.
Any imide in which the acyl substituents are any two from carboacyl, sulfonyl and phosphoryl
Any coumarin carrying at least one hydroxy substituent.
A kanamycin that is kanamycin B bearing an N-(2S)-4-amino-2-hydroxybutyryl group on the aminocyclitol ring.
An amino cyclitol glycoside that is L-chiro-inositol in which the hydroxy groups at positions 1, 4, and 6 are replaced by aminoacetyl)methylamino, amino, and methoxy groups, respectively, and in which the hydroxy group at position 3 is converted to the corresponding 2,6-diamino-2,3,4,6,7-pentadeoxy-beta-L-lyxo-heptopyranoside. The major component of fortimicin, obtained from Micromonospora olivasterospora. It is administered (as the sulfate salt) by intramuscular injection or intravenous infusion for the treatment of severe systemic infections due to sensitive Gram-negative organisms.
A kanamycin that is kanamycin B lacking the 3- and 4-hydroxy groups on the 2,6-diaminosugar ring.
A carbopolyclic compound comprising of three carbocyclic rings.
Any organonitrogen compound containing a cyclic component with nitrogen and at least one other element as ring member atoms.
Any organic heterocyclic compound containing at least one ring oxygen atom.
Cyclic hemiacetals formed by intramolecular addition of a hydroxy group to an aldehydic or ketonic carbonyl group. They are thus 1-oxacycloalkan-2-ols or unsaturated analogues.
Any of a class of heterocyclic amines having a saturated five-membered ring.
Any organic heterocyclic compound containing a benzene ring in which two of the C-H fragments have been replaced by isolobal nitrogens (the diazine parent structure).
The 10-methochloride salt of 3,6-diaminoacridine. Note that a mixture of this compound with 3,6-diaminoacridine (proflavine) is known as acriflavine or neutral acriflavine.
3,6-diamino-10-methylacridinium chloride
Compounds having the structure R2C=NNR2, formally derived from aldehydes or ketones by replacing =O by =NNH2 (or substituted analogues).
Any member of the class of fluorobenzenes containing a mono- or poly-substituted benzene ring carrying two fluorine atoms.
Any organic heteropolycyclic compound based on the 1,2-diaza analogue of naphthalene and its substituted derivatives.
Any compound containing morpholine as part of its structure.
A hydroxycoumarin antibiotic that is obtained from Streptomyces rishiriensis and exhibits potent antibacterial and anticancer activity.
Any organonitrogen heterocyclic compound based on a phenazine skeleton and derivatives.
Any compound with a 1,2,4-triazine skeleton, in which nitrogen atoms replace carbon at positions 1, 2 and 4 of the core benzene ring structure.
Any compound having a pyrimidine as part of its structure.
A 4-amino-1,2-oxazolidin-3-one that has R configuration. It is an antibiotic produced by Streptomyces garyphalus or S. orchidaceus and is used as part of a multi-drug regimen for the treatment of tuberculosis when resistance to, or toxicity from, primary drugs has developed. An analogue of D-alanine, it interferes with bacterial cell wall synthesis in the cytoplasm by competitive inhibition of L-alanine racemase (which forms D-alanine from L-alanine) and D-alanine--D-alanine ligase (which incorporates D-alanine into the pentapeptide required for peptidoglycan formation and bacterial cell wall synthesis).
Meropenem in which the one of the two methyl groups attached to the amide nitrogen is replaced by hydrogen while the other is replaced by a 3-carboxyphenyl group. The sodium salt is used for the treatment of moderate to severe susceptible infections including intra-abdominal and acute gynaecological infections, pneumonia, and infections of the skin and of the urinary tract.
A macrolide that is pristinamycin IIA in which the double bond between positions 26 and 26a of the pyrroline ring has been reduced and position 26R carries a [2-(diethylamino)ethyl]sulfonyl group. It is a semi-synthetic streptogramin antibiotic and often used as a mixture with quinupristin for the treatment of vancomycin-resistant Enterococcus faecium.
A carbapenemcarboxylic acid in which the azetidine and pyrroline rings carry 1-hydroxymethyl and in which the azetidine and pyrroline rings carry 1-hydroxymethyl and 5-(dimethylcarbamoyl)pyrrolidin-3-ylthio substituents respectively.
Propylphosphonic acid in which one of the hydrogens at position 3 is substituted by a formyl(hydroxy)amino group. An antibiotic obtained from Streptomyces lavendulae, it specifically inhibits DXP reductoisomerase (EC 1.1.1.267), a key enzyme in the non-mevalonate pathway of isoprenoid biosynthesis.
A penicillin that is 6-aminopenicillanic acid in which one of the amino hydrogens is replaced by a 3-(2,6-dichlorophenyl)-5-methyl-1,2-oxazol-4-yl]formyl group.
An amino cyclitol glycoside that is 4,6-diaminocyclohexane-1,2,3-triol having a 2,6-diamino-2,6-dideoxy-alpha-D-glucosyl residue attached at position 1 and a beta-D-ribosyl residue attached at position 2. It is an antibiotic produced by Streptomyces ribosidificus (formerly S. thermoflavus).
pyrazinamide
A monocarboxylic acid amide resulting from the formal condensation of the carboxy group of pyrazinoic acid (pyrazine-2-carboxylic acid) with ammonia. A prodrug for pyrazinoic acid, pyrazinecarboxamide is used as part of multidrug regimens for the treatment of tuberculosis.
The class of beta-lactam antibiotics that whose members have a carbapenem skeleton which is variously substituted at positions 3, 4, and 6.
A compound consisting of a peptide with attached lipid.
Any organic heteromonocyclic compoundthat is oxane or its substituted derivatives.
A broad-spectrum, intravenous beta-lactam antibiotic of the carbapenem subgroup.
A third-generation cephalosporin antibiotic bearing vinyl and (2Z)-2-(2-amino-1,3-thiazol-4-yl)-2-[(carboxymethoxy)imino]acetamido groups at positions 3 and 7, respectively, of the cephem skeleton. It is used in the treatment of gonorrhoea, tonsilitis, pharyngitis, bronchitis, and urinary tract infections.
The hemi-aminal resulting from the condensation of the erythromycin derivative (9S)-erythromycyclamine with 2-(2-methoxyethoxy)acetaldehyde. As the oxazine ring containing the hemi-aminal group is unstable under both acidic and alkaline conditions, dirithromycin functions as a more lipid-soluble prodrug for (9S)-erythromycyclamine. Administered as enteric coated tablets to protect it from acid catalysed hydrolysis in the stomach, it is used to treat respiratory tract, skin, and soft tissue infections caused by susceptible organisms.
A first-generation cephalosporin compound having [(5-methyl-1,3,4-thiadiazol-2-yl)sulfanyl]methyl and (1H-tetrazol-1-ylacetyl)amino side-groups at positions 3 and 7 respectively.
Any carboxylic ester where the carboxylic acid component is acetic acid.
A cephalosporin bearing (1-methylpyrrolidinium-1-yl)methyl and (2Z)-2-(2-amino-1,3-thiazol-4-yl)-2-(methoxyimino)acetamido groups at positions 3 and 7, respectively, of the cephem skeleton.
Any steroid substituted by at least one carboxy group.
Any primary amide having its amide oxygen replaced by sulfur.
An ethylenediamine derivative that is ethane-1,2-diamine in which one hydrogen attached to each of the nitrogens is sutstituted by a 1-hydroxybutan-2-yl group (S,S-configuration). It is a bacteriostatic antimycobacterial drug, effective against Mycobacterium tuberculosis and some other mycobacteria. It is used (as the dihydrochloride salt) in combination with other antituberculous drugs in the treatment of pulmonary and extrapulmonary tuberculosis; resistant strains of M. tuberculosis are readily produced if ethambutol is used alone.
Semisynthetic derivative of erythromycin A.
A thiocarboxamide that is pyridine-4-carbothioamide substituted by an ethyl group at position 2. A prodrug that undergoes metabolic activation by conversion to the corresponding S-oxide.
An azole in which the five-membered heterocyclic aromatic skeleton contains a N atom and one S atom.
Antibiotic isolated from Streptomyces clavuligerus. It acts as a suicide inhibitor of bacterial beta-lactamase enzymes.
A semisynthetic penicillin antibiotic carrying a 3-(2-chlorophenyl)-5-methylisoxazole-4-carboxamido group at position 6.
A compound formally derived from ammonia by replacing one, two or three hydrogen atoms by organyl groups.
A quinolone that is 4-oxo-1,4-dihydroquinoline which is substituted at positions 1, 3, 6 and 7 by ethyl, carboxy, fluorine, and 4-methylpiperazin-1-yl groups, respectively.
Monocyclic, bacterially produced or semisynthetic beta-lactam antibiotic. It lacks the double ring construction of the traditional beta-lactam antibiotics and can be easily synthesized.
Any molecular entity that contains carbon.
A penicillin compound having a 6beta-[3-(2-chloro-6-fluorophenyl)-5-methyl-1,2-oxazole-4-carboxamido] side-chain.
A compound formally derived from ammonia by replacing one hydrogen atom by an organyl group.
A compound formally derived from ammonia by replacing two hydrogen atoms by organyl groups.
A compound formally derived from ammonia by replacing three hydrogen atoms by organyl groups.
A cyclic compound containing nine or more atoms as part of the cyclic system.
An organic molecule that is electrically neutral carrying a positive and a negative charge in one of its major canonical descriptions. In most dipolar compounds the charges are delocalized; however the term is also applied to species where this is not the case.
Cyclopropane and its derivatives formed by substitution.
An alpha,beta-unsaturated ketone of general formula R(1)R(2)C=CR(3)-C(=O)R(4) (R(4) =/= H) in which the C=O function is conjugated to a C=C double bond at the alpha,beta position.
A ketone of general formula R(1)R(2)C=CR(3)-C(=O)R(4) (R(4) =/= H) or R(1)C#C-C(=O)R(2) (R(2) =/= H) in which the ketonic C=O function is conjugated to an unsaturated C-C bond at the alpha,beta position.
A carboxylic ester of general formula R(1)R(2)C=CR(3)-C(=O)OR(4) (R(4) =/= H) or R(1)C#C-C(=O)OR(2) (R(2) =/= H) in which the ester C=O function is conjugated to an unsaturated C-C bond at the alpha,beta position.
A monocarboxylic amide of general formula R(1)R(2)C=CR(3)-C(=O)NR(4)R(5) or R(1)C#C-C(=O)NR(2)R(3) in which the amide C=O function is conjugated to an unsaturated C-C bond at the alpha,beta position.
alpha,beta-unsaturated carboxylic acid amide
An alpha,beta-unsaturated carboxylic acid amide of general formula R(1)R(2)C=CR(3)-C(=O)NR(4)R(5) in which the amide C=O function is conjugated to a C=C double bond at the alpha,beta position.
A member of the class of oxazolidines that is 1,3-oxazolidin-2-one in which the hydrogen attached to the nitrogen is replaced by an N-{[(5-nitro-2-furyl)methylene]amino} group. It has antibacterial and antiprotozoal properties, and is used in the treatment of giardiasis and cholera.
A compound with the general formula R2C=O (R=/=H) where one or more of the R groups contains an oxy (-O-) group.
An oxyketone with the general formula R2C(=O) (R=/=H) where one or more of the R groups contains an oxy (-O-) group and the oxy and carbonyl groups are bonded to the same carbon atom.
A monocarboxylic acid that is 4-oxo-1,4-dihydroquinoline-3-carboxylic acid which is substituted on the nitrogen by a cyclopropyl group and at positions 6, 7, and 8 by fluoro, 3-methylpiperazin-1-yl, and methoxy groups, respectively. Gatifloxacin is an antibiotic of the fourth-generation fluoroquinolone family, that like other members of that family, inhibits the bacterial topoisomerase type-II enzymes.
A cyclic macromolecule containing one or more nitrogen atoms in place of carbon either as the divalent group NH for the group CH2 or a single trivalent nitrogen atom for the group CH.
Any organic heterotricyclic compound based on a skeleton comprised of an oxazine ring fused onto a quinoline system.
A parenteral third-generation cephalosporin, bearing a 2-(2-amino-1,3-thiazol-4-yl)-2-(methoxyimino)acetyl]amino group at the 7beta-position.
An imidazolidine containing one or more oxo groups.
Oxazoles in which the N and O atoms are adjacent.
An oxazolidine containing one or more oxo groups.
Any member of the cephamycin sub-group of cephem antibiotics, differing from cephalosporins in possessing a methoxy group at the 7alpha-position of the cephem nucleus, and in being resistant to beta-lactamase.
A cephalosporin with acetoxymethyl and 2(pyridin-4-ylsulfanyl)acetamido substituents at positions 3 and 7, respectively, of the cephem skeleton. It is used (as its sodium salt) as an antibiotic, being effective against gram-negative and gram-positive organisms.
Any member of a group of synthetic antibiotics, similar to cephems but with carbon substituted for the sulfur; all possessing an acylated amine functionality at C-6 and (S,R) stereochemistry at C-6 and C-7.
Any member of the oxacephem sub-group of cephem antibiotics, in which the thiaazabicyclo moiety of the cephalosporins is replaced by an oxaazabicyclo moiety, and where R3 is -H or -OCH3.
A compound having the general formula RR'C(OH)OR'' (R'' =/= H).
A cyclic compound having as ring members atoms of at least two different elements.
Polymyxins are antibiotics with a general structure consisting of a cyclic peptide with a long hydrophobic tail. They disrupt the structure of the bacterial cell membrane by interacting with its phospholipids. Polymyxins are produced by the Gram-positive bacterium Bacillus polymyxa and are selectively toxic for Gram-negative bacteria.
A polymyxin having a 6-methylheptanoyl group at the amino terminus.
A polymyxin having a (6R)-6-methyloctanoyl group at the amino terminus.
Any substance that stimulates an immune response in the body, such as through antibody production or by presentation to a T-cell receptor after binding to a major histocompability complex (MHC).
Currently "K antigen" is a CHEBI_73772 chemical entity rather than a role.
K antigen
A broad spectrum, third-generation cephalosporin antibiotic with (Z)-2-(4-methyl-1,3-thiazol-5-yl)ethenyl and (2Z)-2-(2-amino-1,3-thiazol-4-yl)-2-(methoxyimino)acetamido groups at positions 3 and 7, respectively, of the cephem skeleton. Generally administered as its orally absorbed pivaloyloxymethyl ester prodrug, it is used for the treatment of mild to moderate infections caused by susceptible strains of microorganisms in acute bacterial exacerbation of chronic bronchitis, community-acquired pneumonia, pharyngitis/tonsillitis, and uncomplicated skin and skin-structure infections.
An organooxygen compound having the structure RR'C(OR'')(OR''') (R'', R''' =/= H). Mixed acetals have R'' and R''' groups which differ.
An acetal in the molecule of which the acetal carbon and one or both oxygen atoms thereon are members of a ring.
A hemiacetal having the structure RR(1)C(OH)OR(2) (R, R(1), R(2) =/= H), derived from a ketone by formal addition of an alcohol to the carbonyl group.
An acetal of formula R2C(OR)2 (R =/= H) derived from a ketone by replacement of the oxo group by two hydrocarbyloxy groups. The class name 'ketals', once abandoned by IUPAC, has been reinstated as a subclass of acetals.
A ketal in the molecule of which the ketal carbon and one or both oxygen atoms thereon are members of a ring.
A hemiacetal having the structure R2C(OH)OR (R =/= H), derived from a ketone by formal addition of an alcohol to the carbonyl group. The term 'cyclic hemiketals', once abandoned by IUPAC, has been reinstated as a subclass of hemiacetals.
The sulfur analogue of 'acetal'. The term includes monothioacetals having the structure R2C(OR')(SR') (subclass monothioketals, R =/= H); and dithioacetals having the structure R2C(SR')2 (subclass dithioketals, R =/= H, R' =/= H).
A thioacetal having the structure R2C(OR')(SR'). The term includes monothioketals, R =/= H, as a subclass.
A broad-spectrum oxacephem antibiotic in which the oxazine ring is substituted with a tetrazolylthiomethyl group and the azetidinone ring carries methoxy and 2-carboxy-2-(4-hydroxyphenyl)acetamido substituents.
A chemical substance is a portion of matter of constant composition, composed of molecular entities of the same type or of different types.
A mixture is a chemical substance composed of multiple molecules, at least two of which are of a different kind.
A polypeptide comprising N-decanoyltryptophan, asparagine, aspartic acid, threonine, glycine, ornithine, aspartic acid, D-alanine, aspartic acid, glycine, D-serine, threo-3-methylglutamic acid and 3-anthraniloylalanine (also known as kynurinine) coupled in sequence and lactonised by condensation of the carboxylic acid group of the 3-anthraniloylalanine with the alcohol group of the threonine residue.
A carbohydrazide obtained by formal condensation between pyridine-4-carboxylic acid and hydrazine.
isoniazid
A commercially important azabicyclic antibiotic obtained from Streptomyces sapporonensis. It inhibits the Rho protein of E. coli.
A racemate is an equimolar mixture of a pair of enantiomers.
A glucoside in which the anomeric carbon of the glycosidic bond is in an alpha configuration
Kanamycin is a naturally occurring antibiotic complex from Streptomyces kanamyceticus that consists of several components: kanamycin A, the major component (also usually designated as kanamycin), and kanamycins B, C, D and X the minor components.
Any compound that has a nucleobase as a part.
Any cyclitol having one or more alcoholic hydroxy groups replaced by substituted or unsubstituted amino groups.
An ester where the ester linkage is bonded directly to an aromatic system.
An amide in which the amide linkage is bonded directly to an aromatic system.
A family of nitrogen molecular entities which are highly reactive and derived from nitric oxide (.NO) and superoxide (O2.(-)) produced via the enzymatic activity of inducible nitric oxide synthase 2 (NOS2) and NADPH oxidase respectively.
A carbohydrate derivative arising formally from the elimination of water from a glycosidic hydroxy group and an H atom bound to an oxygen, carbon, nitrogen or sulfur atom of a separate entity.
Name for a family of macrolide antibiotics with more than twenty members produced by the rare actinomycete Micromonospora griseorubida.
A mycinamicin composed of a 16-membered ring macrolactone core, an N,N-dimethylated deoxysugar desosamine and a 2,3-di-O-methylated 6-deoxysugar mycinose.
Any organooxygen compound derived from a carbohydrate by replacement of one or more hydroxy group(s) by an amino group, a thiol group or similar heteroatomic groups. The term also includes derivatives of these compounds.
A carbohydrate derivative that is formally obtained from a disaccharide.
A carbohydrate derivative that is formally obtained from a monosaccharide.
A carbohydrate derivative that is formally obtained from an oligosaccharide.
An oligosaccharide derivative that is formally obtained from a tetrasaccharide.
An optically active form of ofloxacin having (S)-configuration; an inhibitor of bacterial topoisomerase IV and DNA gyrase.
An organofluorine compound that consists of 1,3-oxazolidin-2-one bearing an N-3-fluoro-4-(morpholin-4-yl)phenyl group as well as an acetamidomethyl group at position 5. A synthetic antibacterial agent that inhibits bacterial protein synthesis by binding to a site on 23S ribosomal RNA of the 50S subunit and prevents further formation of a functional 70S initiation complex.
A quinolone that consists of 4-oxo-1,4-dihydroquinoline-3-carboxylic acid bearing a cyclopropyl substituent at position 1, a fluoro substitiuent at position 6, a (4aS,7aS)-octahydro-6H-pyrrolo[3,4-b]pyridin-6-yl group at position 7 and a methoxy substituent at position 8. A member of the fluoroquinolone class of antibacterial agents.
1H-imidazole substituted at C-1 by a (2-ethylsulfonyl)ethyl group, at C-2 by a methyl group and at C-5 by a nitro group. It is used as an antiprotozoal, antibacterial agent.
Any organic heterobicyclic compound containing ortho-fused pyrrolidine and piperidine rings.
A sulfonamide that is sulfanilamide acylated on the sulfonamide nitrogen.
Any lactone in which the cyclic carboxylic ester group forms a part of a cyclic macromolecule.
A fused-ring beta-lactam system where the beta-lactam ring is fused to a 1,3-oxazolidine ring.
Any organic molecular entity that is acidic and contains carbon in covalent linkage.
A carbohydrate-containing antibiotic produced by the actinomyces Streptomyces lincolnensis.
A carbohydrate derivative that is any derivative of a polysaccharide.
A penicillin that is 6-aminopenicillanic acid in which one of the amino hydrogens is replaced by a 2,6-dimethoxybenzoyl group.
Any monocyclic heteroarene consisting of a five-membered ring containing nitrogen. Azoles can also contain one or more other non-carbon atoms, such as nitrogen, sulfur or oxygen.
An 18-membered macrolide that is a fermentation product obtained from the Actinomycete Dactylosporangium aurantiacum. A narrow spectrum antibiotic used for treatment of Clostridium difficile-related infections.
A member of the class of imidazoles substituted at C-1, -2 and -5 with 2-hydroxyethyl, nitro and methyl groups respectively. It has activity against anaerobic bacteria and protozoa, and has a radiosensitising effect on hypoxic tumour cells. It may be given by mouth in tablets, or as the benzoate in an oral suspension. The hydrochloride salt can be used in intravenous infusions. Metronidazole is a prodrug and is selective for anaerobic bacteria due to their ability to intracellularly reduce the nitro group of metronidazole to give nitroso-containing intermediates. These can covalently bind to DNA, disrupting its helical structure, inducing DNA strand breaks and inhibiting bacterial nucleic acid synthesis, ultimately resulting in bacterial cell death.
A penicillin in which the substituent at position 6 of the penam ring is a (2R)-2-[3-(methanesulfonyl)-2-oxoimidazolidine-1-carboxamido]-2-phenylacetamido group.
An alpha,beta-unsaturated ester resulting from the formal condensation of the alcoholic hydroxy group of 9-hydroxynonanoic acid with the carboxy group of (2E)-4-[(2S)-tetrahydro-2H-pyran-2-yl]-3-methylbut-2-enoic acid in which the tetrahydropyranyl ring is substituted at positions 3 and 4 by hydroxy groups and at position 5 by a {(2S,3S)-3-[(2S,3S)-3-hydroxybutan-2-yl]oxiran-2-yl}methyl group. Originally isolated from the Gram-negative bacterium Pseudomonas fluorescens, it is used as a topical antibiotic for the treatment of Gram-positive bacterial infections.
A cephalosporin having [4-(1-methylpyridinium-4-yl)-1,3-thiazol-2-yl]sulfanyl and {(2Z)-2-(ethoxyimino)-2-[5-(phosphonoamino)-1,2,4-thiadiazol-3-yl]acetyl}amino side groups located at positions 3 and 7 respectively. The N-phospho prodrug of ceftaroline, a broad-spectrum antibiotic active against methicillin-resistant Staphylococcus aureus (MRSA). It is used for the treatment of adults with acute bacterial skin and skin structure infections.
A glycopeptide that is vancomycin substituted at position N-3'' by a 2-(decylamino)ethyl group and at position C-29 by a (phosphonomethyl)aminomethyl group. Used as its hydrochloride salt for treatment of adults with complicated skin and skin structure infections caused by bacteria.
An imidazolidine-2,4-dione that is hydantoin substituted at position 1 by a [(5-nitro-2-furyl)methylene]amino group. An antibiotic that damages bacterial DNA.
Any member of a family of aminoglycosidic antibiotics produced by the bacterium Streptomyces lividus. Note that one member of this class, lividomycin A, is also known as lividomycin.
A member of the class of lividomycins that is lividomycin B in which position 4 of the diamino-L-idopyranosyl moiety has been converted into its alpha-D-mannopyranoside.
A member of the class of lividomycins that is paromomycin in which the 2-amino-2-deoxyglucopyranosyl moiety is lacking the hydroxy group at position 3.
A quinoline-based antimycobacterial drug used (as its fumarate salt) for the treatment of pulmonary multi-drug resistant tuberculosis by inhibition of ATP synthase, an enzyme essential for the replication of the mycobacteria.
Any organic molecular entity derived from a natural product by partial chemical synthesis.
Any molecule that consists of at least one carbon atom as part of the electrically neutral entity.
Any naphthyridine derivative that is a derivative of 1,8-naphthyridine.
Any organonitrogen heterocyclic compound that is a derivative of a naphthyridine.
A carbohydrate derivative in which one or more of the oxygens or hydroxy groups of the parent carbohydrate is replaced by sulfur or -SR, where R can be hydrogen or any group.
Any capsular polysaccharide derivative which is carried on the surface of a bacterial capsule or formed on the outer portion of a cell wall and masks somatic O antigens.
Damion Dooley's note: 'K antigen' can't be a subclass of antigen as chemical entity is disjoint from role.
A zwitterion resulting from the transfer of a proton from the ring nitrogen to the primary amino group of D-cycloserine. The major species at pH 7.3.
A penicillin in which the substituent at position 6 of the penam ring is a (2-ethoxy-1-naphthoyl)amino group.
A tetracyclic antibacterial agent derived from neomycin, being a glycoside ester of neamine and neobiosamine B.
A semisynthetic member of the class of rifamycins and non-systemic gastrointestinal site-specific broad spectrum antibiotic. Used in the treatment of traveller's diarrhoea, hepatic encephalopathy and irritable bowel syndrome.
A carboxamide that is a hydroxamic acid in which the hydrogen of the hydroxy group is replaced by an organyl group.
Any member of the group of eight water-soluble vitamins originally thought to be a single compound (vitamin B) that play important roles in cell metabolism. The group comprises of vitamin B1, B2, B3, B5, B6, B7, B9, and B12 (Around 20 other compounds were once thought to be B vitamins but are no longer classified as such).
An organic anion obtained by deprotonation of the carboxy, sulfo and one of the hydroxy groups as well as protonation of the amino group of A47934; major species at pH 7.3.
A racemate comprising equimolar amounts of levofloxacin and dextrofloxacin. It is a synthetic fluoroquinolone antibacterial agent which inhibits the supercoiling activity of bacterial DNA gyrase, halting DNA replication.
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
Any organic molecular entity that contains at least one C=C bond.
A monocarboxylic acid in which the carbon of the carboxy group is directly attached to a C=C or C#C bond.
alpha,beta-unsaturated monocarboxylic acid
An amino cyclitol glycoside that is the 1-O-(2-amino-2-deoxy-alpha-D-glucopyranoside) and the 3-O-(2,6-diamino-2,6-dideoxy-beta-L-idopyranosyl)-beta-D-ribofuranoside of 4,6-diamino-2,3-dihydroxycyclohexane (the 1R,2R,3S,4R,6S diastereoisomer). It is obtained from various Streptomyces species. A broad-spectrum antibiotic, it is used (generally as the sulfate salt) for the treatment of acute and chronic intestinal protozoal infections, but is not effective for extraintestinal protozoal infections. It is also used as a therapeutic against visceral leishmaniasis.
Any inorganic anion with a valency of one.
A penicillin in which the substituent at position 6 of the penam ring is a 2-[(4-ethyl-2,3-dioxopiperazin-1-yl)carboxamido]-2-phenylacetamido group.
A semisynthetic glycopeptide used (as its bisphosphate salt) for the treatment of acute bacterial skin and skin structure infections caused or suspected to be caused by susceptible isolates of designated Gram-positive microorganisms including MRSA.
Any member of the class of chlorobenzenes containing a mono- or poly-substituted benzene ring in which only one substituent is chlorine.
A carboxamide obtained by the formal condensation of the carboxy group of any carboxylic acid with ammonia.
Any derivative of a proteinogenic amino acid resulting from reaction at an amino group, carboxy group, or a side-chain functional group, or from the replacement of any hydrogen by a heteroatom.
Any derivative of an amino acid resulting from reaction at an amino group, carboxy group, side-chain functional group, or from the replacement of any hydrogen by a heteroatom. The definition normally excludes peptides containing amino acid residues.
A proteinogenic amino acid derivative resulting from reaction of L-proline at the amino group or the carboxy group, or from the replacement of any hydrogen of L-proline by a heteroatom.
A heterodetic cyclic peptide that is produced by species of Amycolatopsis and Nocardia.
A macrolide antibiotic produced by various Streptomyces species that is used to treat toxoplasmosis and various other infections of soft tissues.
An organonitrogen heterocyclic antibiotic whose structure contains a quinolone or quinolone-related skeleton.
Heteroorganic entities that are microbial metabolites (or compounds derived from them) which have significant antifungal properties.
Any antibiotic antifungal agent used to treat fungal infections in humans or animals.
Any antibiotic antifungal agent that has been used as a fungicide.
An organonitrogen heterocyclic antibiotic containing a quinolone (or quinolone-like) moiety and which have a fluorine atom attached to the central ring system.
A class of sulfonamides whose members generally have bacteriostatic antibiotic properties.
A member of the class of furans in which the furan ring is substituted by a nitro group and which also has significant antibiotic properties.
Any penicillin which causes the onset of an allergic reaction.
Any beta-lactam antibiotic which causes the onset of an allergic reaction.
A mixed diacylamine resulting from the formal condensation of the nitrogen of a carboxamide with a sulphonic acid.
A pyranobenzodioxin and antibiotic that is active against gram-negative bacteria and used (as its dihydrochloride pentahydrate) to treat gonorrhea. It is produced by the bacterium Streptomyces spectabilis.
A sulfonamide consisting of pyrimidine with a 4-aminobenzenesulfonamido group at the 2-position.
A sulfonamide consisting of pyrimidine having methoxy substituents at the 5- and 6-positions and a 4-aminobenzenesulfonamido group at the 4-position. In combination with the antiprotozoal pyrimethamine (CHEBI:8673) it is used as an antimalarial.
A sulfonamide consisting of a 1,3,4-thiadiazole nucleus with a methyl substituent at C-5 and a 4-aminobenzenesulfonamido group at C-2.
An isoxazole (1,2-oxazole) compound having a methyl substituent at the 5-position and a 4-aminobenzenesulfonamido group at the 3-position.
A member of the class of penicillanic acids that is sulbactam in which one of the exocyclic methyl hydrogens is replaced by a 1,2,3-triazol-1-yl group; used (in the form of its sodium salt) in combination with ceftolozane sulfate for treatment of complicated intra-abdominal infections and complicated urinary tract infections.
A penicillin compound having a 6beta-[(2R)-2-carboxy-2-thiophen-3-ylacetyl]amino side-group.
A macrolide that is (together with pristinamycin IA) a component of pristinamycin, an oral streptogramin antibiotic produced by Streptomyces pristinaespiralis. Pristinamycin exhibits bactericidal activity against Gram positive organisms including methicillin-resistant Staphylococcus aureus.
An independent material continuant that is self-connected and retains its identity over time.
A method that results in the separation of two or more components according to some property.
A separation method where colloidal particles move at different speeds according to their electrophoretic mobilities in a separation medium, across which an electric field is applied.
A separation method where colloidal particles move at different speeds according to their electrophoretic mobilities in a separation medium consisting of gel, across which an electric field is applied.
An electrophoresis method where the separation medium contains a reticulated system, for example an entangled polymer network, that further separates the analytes according to their size and shape.
A separation method where colloidal particles move at different speeds according to their electrophoretic mobilities in a separation medium, across which a pulsed electric field is applied (a field in which the voltage changes direction).
A separation method where colloidal particles move at different speeds according to their electrophoretic mobilities in a separation medium consisting of gel, across which a pulsed electric field is applied (one in which the voltage direction is periodically switched among three directions; one that runs through the central axis of the gel and two that run at an angle of 120° either side).
specimen extraction matrix
Those components of a sample that are not measured by an experiment.
"This observable is important where process of capturing sample can affect dna extraction."
A COVID-19 nucleic acid diagnostic assay that uses RT-PCR
COVID-19 RT-PCR assay
A COVID-19 diagnostic process by viral genome sequencing and identification of the SARS-CoV-2 based on the genome sequence.
COVID-19 diagnostic process by viral genome sequencing
A cultured cell that is part of a cell line - a stable and homogeneous population of cells with a common biological origin and propagation history in culture
Yongqun He, Matthew Brush, Sirarat Sarntivijai, Alexander Diehl, Jie Zheng, Yu Lin, Bjoern Peters
A 'cell line cell' is a part of a cell line established through the passaging/selection of a primary cultured cells or the experimental modification of an existing cell line. New types of cell line cells are established after sufficient passaging of a primary culture to establish a stable and homogenous population that qualifies as a line (typically 1-20 passages), or following some spontaneous or experimental modification that confers novel characteristics to an existing line. A cell line cell typically has mutations of five or more genes compared to the original cell that derives the cell line cell. Some gene mutations may turn on some oncogenes. Cell line cells can be in active culture, stored in a quiescent state for future use (e.g. frozen in liquid nitrogen), or applied in experimental procedures.
A cell line cell that is expected to be capable of an unlimited number of divisions, and is thus able to support indefinite propagation in vitro as part of an immortal cell line.
Yongqun He, Matthew Brush, Allen Xiang, Asiyah Yu Lin, Sirarat Sarntivijai, James Malone, Jie Zheng, Tomasz Adamusiak
cell line
A cultured cell population that represents a genetically stable and homogenous population of cultured cells that shares a common propagation history (i.e. has been successively passaged together in culture).
The term 'line' is used when a culture has undergone an intentional experimental process to establish a more uniform and stable population of cells (see 'establishing cell line'). This will require one or more passages, but may involve additional selection processes. Through such passaging and/or selection processes, the resulting 'line' attains some level of genetic stability and compositional homogeneity which is typically absent in primary cultures. Because of their relative homogeneity, ‘lines’ are capable of being characterized and stably propagated over a period of time. A new *type* of cell line can be established not only through the passaging/selection of a primary culture, but also through experimental modifications of existing lines (e.g. immortalization, stable genetic modifications, drug selection for a resistant subset, etc.). The definition provided here establishes the 'scale' of cell populations that qualify as cell lines - specifically those with a shared propagation history in culture. In this way, the 'cell line' class demarcates populations that represent what researchers actually use in the practice of science - e.g. as inputs to culturing, experimentation, and sharing. The definition is such that cell lines will exhibit important attributes. For example, they will have a relatively homogenous cell type composition as they have experienced similar selective pressures due to their continuous co-propagation. In addition, these populations can also be characterized by a passage number, again owing to their common passaging history. As defined here, 'cell line' can refer to a population of cells in active culture, applied experimentally, or stored in a quiescent state for future use.
An immortal cell line cell that derives from kidney.
An immortal kidney-derived cell line cell that derives from rhesus macaque.
immortal rhesus macaque kidney-derived cell line cell
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.
The definition of cell is intended to represent all cells, and thus a cell is defined as a material entity and not an anatomical structure, which implies that it is part of an organism (or the entirety of one).
A cell in vitro that is or has been maintained or propagated as part of a cell culture.
Note that this class was re-labeled to 'cultured cell' instead of 'cell line cell', as it intent was clarified to cover any cultured cells of multicellular and unicellular organisms. This includes cells actively being cultured, or cells that have been cultured but are stored in a quiescent state for future use. In having been cultured, cells must establish homeostasis and often replicate in a foreign environment. Accomodation of this stress initiates a selection of cells fit for such challenges, wherein necessary adaptive biochemical and.or genetic changes can occur. These changes can set them apart from the in vivo cells from which they derive, and such changes will typically accumulate and change over increasing time in culture.
A cell in vitro that has undergone physical changes as a consequence of a deliberate and specific experimental procedure.
This class has been re-labeled to imply reference only to in vitro experimentally modified cells, similarly, the definition has been slightly updated to reflect this. 'experimentally modified cell' refers only to cells in vitro, and not modified in vivo/in environment cells. There is currently no class representing unmodified in vitro cells (other than the parent 'cell in vitro'), or a class representing modified native cells. More granular subclassing of experimentally modified cell can be found in ReO. MHB 1.12.12
A cell that is maintained or propagated in a controlled artificial environment for use in an investigation.
'In vitro', translating literally to 'in glass', typically refers to a controlled, often sterile, laboratory setting where cells or other specimens are placed by some agent for the purpose of studying or manipulating them as part of some research investigation. 'In vitro' is intended to contrast with 'native',which refers to cells or other biological entities that are found in a natural setting. It describes unicellular organisms removed from a natural environement and multicellular organism cells removed from an organism, or cells derived in culture from such displaced cells.
A disease existing at birth, or developping during the first month after birth.
congenital disease
A crustacean allergy that has_allergic_trigger shrimp.
shrimp allergy
A bacterial pneumonia has_material_basis_in Chlamydia pneumoniae.
Chlamydia pneumonia
A bacterial pneumonia has_material_basis_in Streptococcus pneumoniae.
Streptococcus pneumonia
A bacterial infectious disease has_material_basis_in Bacteria.
bacterial sepsis
A gonococcal seminal vesiculitis that is characterized by back pain, perineal pain, pain with ejaculation, hematospermia and voiding symptoms resulting from inflammation located_in the seminal vesicles caused by Neisseria gonorrhoeae infection.
seminal vesicle acute gonorrhea
An ehrlichiosis that results in infection located in granular leukocyte, has_material_basis_in Anaplasma phagocytophilum, which is transmitted by lone star tick (Amblyomma americanum). The infection has symptom headache, has symptom muscle aches, has symptom fatigue, has symptom fever and has symptom rash.
human granulocytic anaplasmosis
An ehrlichiosis that results in infection located in monocyte or located in macrophage, has_material_basis_in Ehrlichia chaffeensis, which is transmitted by black-legged tick (Ixodes scapularis), transmitted by western black-legged tick (Ixodes pacificus) or transmitted by castor bean tick (Ixodes ricinus). The infection has symptom headache, has symptom muscle aches, has symptom fatigue, has symptom fever and has symptom rash.
human monocytic ehrlichiosis
A spotted fever that has_material_basis_in Rickettsia africae, which is transmitted_by ticks (Amblyomma hebraeum and Amblyomma variegatum). The infection has_symptom fever, has_symptom eschar and has_symptom maculopapular rash.
African tick-bite fever
A spotted fever that has_material_basis_in Rickettsia conorii subsp caspia, which is transmitted_by ticks (Rhipicephalus pumilio and Rhipicephalus sanguineus). The infection has_symptom fever, has_symptom eschar (usually single), has_symptom regional adenopathy, has_symptom maculopapular rash on extremities.
Astrakhan spotted fever
A spotted fever that has_material_basis_in Rickettsia conorii subsp indica, which is transmitted_by ticks (Rhipicephalus sanguineus). The infection has_symptom fever, has_symptom eschar, has_symptom regional adenopathy, and has_symptom maculopapular rash on extremities.
Indian tick typhus
A spotted fever that has_material_basis_in Rickettsia conorii subsp israelensis, which is transmitted_by ticks (Rhipicephalus sanguineus). The infection has_symptom fever, has_symptom eschar, has_symptom regional adenopathy, and has_symptom maculopapular rash on extremities.
Israeli tick typhus
A spotted fever that has_material_basis_in Rickettsia heilongjiangensis, which is transmitted_by ticks (Haemaphysalis concinna). The infection has_symptom fever, has_symptom eschar, has_symptom maculopapular rash, and has_symptom regional adenopathy.
Far Eastern spotted fever
A spotted fever that has_material_basis_in Rickettsia honei, which is transmitted_by cayenne ticks (Amblyomma cajennense). The infection has_symptom mild spotted fever, has_symptom eschar and has_symptom adenopathy.
Flinders Island spotted fever
A spotted fever that has_material_basis_in Rickettsia japonica, which is transmitted_by ticks (Dermacentor taiwanensis and Haemaphysalis flava). The infection has_symptom fever, has_symptom eschars, has_symptom regional adenopathy, and has_symptom rash on extremities.
Japanese spotted fever
A spotted fever that has_material_basis_in Rickettsia parkeri, which is transmitted_by Gulf Coast tick (Amblyomma maculatum). The infection has_symptom fever, has_symptom headache, has_symptom eschar, and has_symptom rash.
Rickettsia parkeri spotted fever
A spotted fever that has_material_basis_in Rickettsia rickettsii, which is transmitted_by ticks (Dermacentor variabilis and Dermacentor andersoni). The infection has_symptom fever, has_symptom headache, has_symptom abdominal pain, and has_symptom maculopapular rash progressing into papular or petechial rash.
Rocky Mountain spotted fever
A gastrointestinal anthrax that results in infection located in mucosa of oropharynx, has_material_basis_in Bacillus anthracis, which is transmitted by ingestion of anthrax-infected meat. The infection has symptom lesions, has symptom vomiting of blood, has symptom severe diarrhea, has symptom loss of appetite.
oropharyngeal anthrax
A primary bacterial infectious disease that results_in infection located_in skin, has_material_basis_in Erysipelothrix rhusiopathiae, which is transmitted_by contact with infected animals. The infection has_symptom redness of skin, has_symptom tenderness of skin and has_symptom warmth of skin.
erysipeloid
A disease that is the consequence of the presence of pathogenic microbial agents, including pathogenic viruses, pathogenic bacteria, fungi, protozoa, multicellular parasites, and aberrant proteins known as prions.
disease by infectious agent
A botulism that involves intoxication caused by botulinum neurotoxins (BoNTA, B, E and F) in adults, has_material_basis_in Clostridium botulinum A, has_material_basis_in Clostridium botulinum B, has_material_basis_in Clostridium botulinum E and has_material_basis_in Clostridium botulinum F, which are transmitted by ingestion of bacterial spores, which then grow in the intestine and release toxins.
intestinal botulism
A legionellosis that involves a milder respiratory illness without pneumonia. Symptoms include fever, headache and muscle aches which last for 2 to 5 days.
Pontiac fever
A bacterial pneumonia which is an acute pulmonary inflammatory response that develops after the inhalation of colonized oropharyngeal material containing bacteria. It is seen in individuals with dysphagia and gastric dysmotility. The disease has_symptom tachypnea and has_symptom cough.
aspiration pneumonia
A nervous system disease which is located in a part of the nervous system responsible for processing sensory information that consists of sensory receptors, neural pathways, and parts of the brain involved in sensory perception. Commonly recognized sensory systems are those for vision, hearing, somatic sensation (touch), taste and olfaction (smell).
sensory system disease
An anthrax disease that results in infection located in lung lymph nodes brought on by breathing in the spores of the bacteria Bacillus anthracis. The first symptoms of inhalation anthrax are like cold or flu symptoms and can include a sore throat, mild fever and muscle aches. Later symptoms include cough, chest discomfort, shortness of breath, tiredness and muscle aches.
inhalation anthrax
A respiratory system disease which involves the lower respiratory tract.
lower respiratory tract disease
An urogenital tuberculosis that results_in formation of granulomas located_in fallopian tube.
tuberculous salpingitis
A bacterial infectious disease that results_in infection by bacteria as a result of their presence or activity within the normal, healthy host, and their intrinsic virulence is, in part, a necessary consequence of their need to reproduce and spread.
primary bacterial infectious disease
A bacterial infectious disease that results_in infection by bacteria which are part of the normal human flora when one or more of the defense mechanisms designed to restrict them from the usually sterile internal tissues are breached by accident, by intent (surgery), or by an underlying metabolic or an infectious disorder.
commensal bacterial infectious disease
A bacterial infectious disease that results_in infection by bacteria in individuals whose host defense mechanisms have been compromised.
opportunistic bacterial infectious disease
A botulism that involves intoxication caused by botulinum neurotoxins (BoNTA, B, E and F), which are transmitted by ingestion of food contaminated with preformed toxins, has_material_basis_in Clostridium botulinum A, has_material_basis_in Clostridium botulinum B, has_material_basis_in Clostridium botulinum E and has_material_basis_in Clostridium botulinum F. The infection has symptom blurred vision, has symptom diplopia, has symptom dysarthria, has symptom dysphonia, has symptom dysphagia and has symptom descending muscle paralysis.
foodborne botulism
A botulism that involves intoxication caused by botulinum neurotoxins (BoNTA, B, E and F), has_material_basis_in Clostridium botulinum A, has_material_basis_in Clostridium botulinum B, has_material_basis_in Clostridium botulinum E and has_material_basis_in Clostridium botulinum F, which are transmitted by contact of spores with the open wounds, which then reproduce in an anaerobic environment to produce toxins.
wound botulism
A botulism that involves intoxication caused by botulinum neurotoxins (BoNTA or B) in infants, has_material_basis_in Clostridium botulinum A or has_material_basis_in Clostridium botulinum B, which are transmitted_by ingestion of bacterial spores, which then grow in the intestine and release toxins. The infection has_symptom constipation, has_symptom lethargy, has_symptom difficulty feeding, has_symptom swallowing, has_symptom ptosis, has_symptom loss of head control, and has_symptom muscle weakness.
infant botulism
A tularemia that results_in swelling of regional lymph glands.
glandular tularemia
A tularemia that results_in bacteremia and has_symptom fever, has_symptom chills, has_symptom myalgia, has_symptom malaise, and has_symptom weight loss.
typhoidal tularemia
A bartonellosis that results_in infection located_in endothelial cells or located_in red blood cells, has_material_basis_in Bartonella bacilliformis, which is transmitted_by sandflies of genus Lutzomyia. The infection has acute and chronic phases. The acute phase is characterized by severe hemolytic anemia and transient immunosuppression. The chronic phase is characterized by verruga peruana lesions which may ulcerate and bleed.
Carrion's disease
A primary bacterial infectious disease that results_in infection located_in skin or located_in subcutaneous tissue, has_material_basis_in Mycobacterium ulcerans, which could be transmitted_by insects. The bacterium produces a toxin, named mycolactone, which causes subcutaneous fat necrosis and inhibits an immune response. The infection has_symptom nodule, which is a painless, mobile swelling in the skin.
Buruli ulcer disease
A typhus that has_material_basis_in Rickettsia prowazekii, which is transmitted by human body louse (Pediculus humanus corporis). The infection has_symptom high fever, has_symptom cough, has_symptom rash, has_symptom severe muscle pain, has_symptom chills, has_symptom falling blood pressure, has_symptom stupor, has_symptom sensitivity to light, and has_symptom delirium.
epidemic typhus
A typhus that has_material_basis_in Rickettsia typhi or has_material_basis_in Rickettsia felis, which are transmitted by fleas (Xenopsylla cheopis). The infection has symptom headache, has symptom fever, has symptom chills, has symptom myalgia, has symptom nausea, has symptom vomiting, has symptom cough and has symptom rash.
endemic typhus
A spotted fever that has_material_basis_in Rickettsia helvetica, which is transmitted_by ticks (Ixodes sp). The infection has_symptom fever, has_symptom headache, has_symptom myalgia.
aneruptive fever
A primary bacterial infectious disease that results_in infection, has_material_basis_in Neorickettsia sennetsu, which is transmitted_by ingestion of raw or under-cooked gray mullet fish infected with the trematodes. The infection has_symptom fever, has_symptom malaise, has_symptom anorexia, has_symptom lymphadenopathy, has_symptom hepatosplenomegaly, has_symptom fatigue, has_symptom chills, has_symptom headache, has_symptom backache and has_symptom myalgia.
sennetsu fever
A skin disease that is characterized by a rash that results from a variety of causes including bacteria, viruses, toxins, drugs and autoimmune disorders.
exanthem
An exanthem that is characterized by a diffuse, reddened, blanchable, finely papular, sandpaper like rash due to infection by group A streptococcus and the production of an erythrogenic toxin.
bacterial exanthem
A congenital syphilis that is manifested during the first 3 months of life. The infection has_symptom skin lesions, has_symptom lymphadenopathy, has_symptom hepatosplenomegaly, has_symptom failure to thrive, has_symptom blood-stained nasal discharge, has_symptom perioral fissures, has_symptom meningitis, has_symptom choroiditis, has_symptom hydrocephalus, has_symptom seizures, has_symptom intellectual disability, has_symptom osteochondritis, and has_symptom pseudoparalysis.
early congenital syphilis
A tertiary neurosyphilis that results when chronic meningoencephalitis causes destruction of cortical parenchyma. The infection has_symptom irritability, has_symptom difficulty concentrating, has_symptom deterioration of memory, has_symptom defective judgment, has_symptom headaches, has_symptom insomnia, has_symptom fatigue, and has_symptom lethargy.
parenchymatous neurosyphilis
A tertiary neurosyphilis that results in inflammation located_in arteries of the brain or located_in arteries of spinal cord. The infection has_symptom headache, has_symptom neck stiffness, has_symptom dizziness, has_symptom behavioral abnormalities, has _symptom poor concentration, has_symptom memory loss, has _symptom lassitude, has_symptom insomnia, has_symptom blurred vision, has_symptom weakness and wasting of shoulder-girdle and arm muscles, has_symptom slowly progressive leg weakness with urinary or fecal incontinence or both, and has_symptom paralysis of the legs due to thrombosis of spinal arteries.
meningovascular neurosyphilis
A tertiary syphilis that is characterized by granulomatous lesions, called gummas, which are characterized by a center of necrotic tissue with a rubbery texture. They form in the liver, bones, and testes but may affect any organ.
gummatous syphilis
An intestinal disease characterized by inflammation located in all parts of digestive tract.
inflammatory bowel disease
A tuberculosis that occurs at body sites other than the lung.
extrapulmonary tuberculosis
An extrapulmonary tuberculosis that is located_in gastrointestinal tract, located_in peritoneum, located_in omentum, located_in mesentery, located_in liver, located_in spleen or located_in pancreas.
abdominal tuberculosis
A cancer that is classified based on the organ it starts in.
organ system cancer
A heart disease and a myopathy that is characterized by deterioration of the function of the heart muscle.
cardiomyopathy
A heart disease that is located_in the innermost layer of tissue that lines the chambers of the heart.
endocardium disease
A cardiovascular system disease that is located_in the fibrous sac surrounding the heart.
pericardium disease
An endocarditis that is characterized by inflammation of the endocardium caused by infectious agents.
infective endocarditis
An autoimmune disease that is the abnormal functioning of the immune system that causes your immune system to produce antibodies or T cells against cells and/or tissues in the gastrointestinal tract.
autoimmune disease of gastrointestinal tract
A food allergy that develops from an immune reaction to eating gluten, a protein found in wheat, barley, rye and triticale and that is characterized by stomach cramping, diarrhea and gastrointestinal upset and is unrelated to the gluten intolerance.
gluten allergy
A disease of anatomical entity that is located_in the thoracic cavity.
thoracic disease
An inflammatory bowel disease that involves inflammation located_in colon.
colitis
A bartonellosis that has_material_basis_in Bartonella henselae or has_material_basis_in Bartonella quintana. The disease is characterized by the proliferation of blood vessels, resulting in them forming tumour-like masses in the skin and other organs.
bacillary angiomatosis
An egg allergy triggered by Gallus gallus eggs.
chicken egg allergy
A food allergy triggered by Crustacea or Mollusca.
shellfish allergy
An allergic disease that is located_in the gastrointestinal tract.
gastrointestinal allergy
A food allergy triggered by a plant fruit product.
fruit allergy
A fruit allergy triggered by Malus domestica plant fruit food product.
apple allergy
A fruit allergy triggered by Prunus armeniaca plant fruit food product.
apricot allergy
A fruit allergy triggered by Prunus avium plant fruit food product.
cherry allergy
A fruit allergy triggered by Ziziphus mauritiana plant fruit food product.
Indian plum allergy
A fruit allergy triggered by Citrus sinensis plant fruit food product.
orange allergy
A fruit allergy triggered by Cucumis melo plant fruit food product.
melon allergy
A fruit allergy triggered by Prunus persica plant fruit food product.
peach allergy
A fruit allergy triggered by Prunus domestica plant fruit food product.
plum allergy
A fruit allergy triggered by Solanum lycopersicum plant fruit food product.
tomato allergy
A food allergy triggered by fish.
fish allergy
A fish allergy triggered by Gadus morhua.
Atlantic cod allergy
A fish allergy triggered by Salmo salar.
Atlantic salmon allergy
A fish allergy triggered by Cyprinus carpio.
carp allergy
A fish allergy triggered by Danio rerio.
zebrafish allergy
A fish allergy triggered by Oncorhynchus mykiss.
rainbow trout allergy
A milk allergy triggered by Bos taurus milk.
cow milk allergy
A milk allergy triggered by Capra hircus milk.
goat milk allergy
A shellfish allergy triggered by Mollusca.
mollusc allergy
A shellfish allergy triggered by Crustacea.
crustacean allergy
A crustacean allergy triggered by Farfantepenaeus aztecus.
brown shrimp allergy
A crustacean allergy triggered by Scylla paramamosain.
crab allergy
A crustacean allergy triggered by Fenneropenaeus indicus.
Indian prawn allergy
A crustacean allergy triggered by Penaeus monodon.
tiger prawn allergy
A crustacean allergy triggered by Litopenaeus vannamei.
white shrimp allergy
A mollusc allergy triggered by snails.
snail allergy
A snail allergy triggered by the horned turban snail.
horned turban snail allergy
A bone disease that is located_in the spine.
spinal disease
A tuberculosis located in the heart.
cardiac tuberculosis
An osteomyelitis characterized by multiple foci of painful swelling of bones, mainly in the metaphyses of the long bones, in addition to the pelvis, the shoulder girdle and the spine.
chronic recurrent multifocal osteomyelitis
A primary bacterial infectious disease caused by the bacteria of the genus Salmonella. It has symptoms diarrhea, fever, vomiting, and abdominal cramps 12 to 72 hours after infection. In most cases, the illness lasts four to seven days, and most people recover without treatment.
salmonellosis
A fruit allergy triggered by Fabaceae (legume) plant fruit or seed food product.
legume allergy
A food allergy triggered by a vegetable food product.
vegetable allergy
A vegetable allergy triggered by celery (Apium graveolens).
celery allergy
A tuberculosis that is located_in some eye, has_material_basis_in Mycobacterium tuberculosis, and has_symptom inflamed eyes.
ocular tuberculosis
A primary bacterial infectious disease that has_material_basis_in Borrelia miyamotoi, which is transmitted_by the blacklegged tick (Ixodes scapularis), the western blacklegged tick (Ixodes pacificus), the taiga tick (Ixodes persulcatus), or the castor bean tick (Ixodes ricinus). The infection has_symptom fever, headache, chills, muscle pain, joint pain, asthenia, fatigue and nausea, and rarely relapses.
Borrelia miyamotoi disease
An opportunistic bacterial infectious disease characterized by necrotizing pneumonia, acute respiratory distress syndrome, and bacteremia that has_material_basis_in Burkholderia cepacia complex, which is transmitted_by contact transmission, droplet spread transmission, vehicle-borne fomite transmission, and vehicle-borne ingestion transmission.
cepacia syndrome
A musculoskeletal system disease that affects the muscles.
muscular disease
A connective tissue disease that affects the structure or development of bone or causes an impairment of normal bone function.
bone disease
A disease that has_material_basis_in a genetic abnormality, error with embryonic development, infection or compromised intrauterine environment.
physical disorder
A bacterial meningitis that has_material_basis_in Neisseria meningitidis infection.
meningococcal meningitis
A bacterial meningitis that has_material_basis_in Haemophilus influenzae infection.
haemophilus meningitis
A male reproductive system disease that is located_in the epididymis.
epididymis disease
A viral infectious disease that has_material_basis_in Coronavirus.
Coronavirus infectious disease
An urinary system disease that is characterized by an infection in any part of the urinary system, including the kidneys, ureters, bladder or urethra.
urinary tract infection
A tuberculosis that is characterized by cerebral edema sometimes with features similar to acute disseminated encephalomyelitis (ADEM) and may manifest with a variety of symptoms ranging from focal neurological deficits to convulsions and decreased conscious state.
tuberculous encephalopathy
A vegetable allergy triggered by parsley (Petroselinum).
parsley allergy
A food allergy triggered by dill (Anethum graveolens).
dill allergy
An anthrax disease that is characterized by infection at the injection site or deep under the skin or in the muscle where the drug was injected and is caused by heroin contaminated with anthrax spores.
injection anthrax
A tertiary neurosyphilis that results in slow degeneration of the nerve cells and nerve fibers that carry sensory information to the brain. The infection has symptom intense, stabbing pain in the back and legs that recurs irregularly, has symptom gait ataxia, has symptom hyperesthesia, has symptom paresthesia, has symptom loss of bladder sensation leading to urine retention, has symptom erectile dysfunction.
tabes dorsalis
A female reproductive system disease that is characterized by an infection of the female reproductive organs.
pelvic inflammatory disease
A tertiary neurosyphilis that results_in mild meningitis.
asymptomatic neurosyphilis
A congenital syphilis that occurs in children at or greater than two years of age who acquired the infection trans-placentally. The infection has_symptom gummatous ulcers, has_symptom periosteal lesions, has_symptom paresis, has_symptom tabes, has_symptom optic atrophy, has_symptom interstitial keratitis, has_symptom sensorineural deafness, and has_symptom dental deformities.
late congenital syphilis
A bacterial meningitis that is characterized by inflammation of the tissues covering the brain and spinal cord.
syphilitic meningitis
A bone inflammation disease that has_material_basis_in infection located_in bone or located_in bone marrow.
osteomyelitis
A primary bacterial infectious disease that results_in infection located_in skin, has_material_basis_in Treponema carateum, which is transmitted_by contact with skin and mucous membrane of an infected person. The infection has_symptom pruritic plaque, which slowly enlarges and becomes pigmented and hyperkeratotic.
pinta disease
A leprosy that results in small numerous red irregularly shaped plaques.
borderline leprosy
A primary bacterial infectious disease that results_in infection located_in superficial peripheral nerves, located_in skin, located_in mucous membranes of the upper respiratory tract, located_in anterior chamber of the eyes, or located_in testes, has_material_basis_in Mycobacterium leprae, which is transmitted_by aerosol spread from infected nasal secretions to exposed nasal and oral mucosa. The infection has_symptom skin lesions, has_symptom sensory loss, has_symptom motor loss and has_symptom eye damage.
leprosy
A primary bacterial infectious disease that results in infection located_in leukocyte, has_material_basis_in Ehrlichia chaffeensis or Anaplasma phagocytophilum, which are transmitted_by lone star tick and transmitted_by black-legged tick respectively. The infection has_symptom headache, has_symptom muscle aches, has_symptom fatigue and has_symptom rash.
ehrlichiosis
A leprosy that results in one erythematous large plaque with well-defined borders that are elevated and that slope down into an atrophic center.
tuberculoid leprosy
A endocardium disease characterized by inflammation of the endocardium of the heart chambers and valves.
endocarditis
A primary bacterial infectious disease that results in infection located in skin, located in joint or located in bone, has_material_basis_in Treponema pallidum subsp pertenue, which is transmitted by direct skin contact with an infected person. The infection has symptom skin lesions.
yaws
A plague that results_in infection located_in lung, which results from direct inhalation of the bacillus and has_symptom fever, has_symptom chills, has_symptom cough and has_symptom difficulty breathing.
pneumonic plague
seminal vesicle chronic gonorrhea
A disease by infectious agent that results_in infection, has_material_basis_in Bacteria.
bacterial infectious disease
gonococcal seminal vesiculitis
A legionellosis that is characterized by severe form of infection producing pneumonia. Symptoms include fever, chills, and cough.
Legionnaires' disease
A primary bacterial infectious disease that results_in infection located_in respiratory tract, has_material_basis_in Legionella pneumophila, which is transmitted_by inhalation of droplets containing bacteria. The symptoms include dry cough, fever, headache and diarrhea.
legionellosis
A yaws that appears after five years of the initial infection and is characterized by disabling consequences of the nose, bones and palmar/plantar hyperkeratosis.
late yaws
A yaws that results in initial papule at the site of entry of bacteria. Without treatment, this is followed by disseminated skin lesions over the body. Bone pain and bone lesions may also occur.
early yaws
An extrapulmonary tuberculosis that results_in lymphocyte-predominant exudative pleural effusion, located_in pleura. This results from an allergic response to tuberculoprotein causing the permeabiltity of the pleural vasculature to alter leading to a sub-pleural caseous focus rupture into the pleural sac.
pleural tuberculosis
A breast disease characterized by painful infection of the breast tissue.
mastitis
An osteomyelitis that has_material_basis_in infection located_in petrous part of temporal bone.
petrositis
A plague that results_in infection located_in lymph node producing a bubo, which is an inflamed, necrotic, and hemorrhagic lymphoid tissue. The infection has_symptom enlarged, tender lymph nodes, has_symptom fever, has_symptom chills and has_symptom prostration.
bubonic plague
A spotted fever that has_material_basis_in Rickettsia australis, which is transmitted_by ticks (Ixodes holocyclus). The infection has_symptom fever, has_symptom headache, has_symptom myalgia, has_symptom maculopapular rash, and has_symptom lymphadenopathy.
Queensland tick typhus
A leprosy that results in early cutaneous lesions which consist of pale macules that are small, diffuse, and symmetric. This form of leprosy is characterized by hypoesthesia over extensor surfaces of the distal extremities, alopecia affecting lateral aspects of the eyebrows, saddle-nose deformity and oral lepromas.
lepromatous leprosy
A spotted fever that has_material_basis_in Rickettsia sibirica, which is transmitted_by ticks (Dermacentor nuttalli, Dermacentor marginatus and Haemaphysalis concinna). The infection has_symptom fever, has_symptom eschar, has_symptom regional adenopathy, and has_symptom maculopapular rash.
Siberian tick typhus
A female reproductive system disease that is located_in the ovary.
ovarian disease
A primary bacterial infectious disease that results_in systemic infection, has_material_basis_in Pasteurella multocida, which is transmitted_by animal bite, scratch, or lick. The infection has_symptom joint pain has_symptom fever, has_symptom rigors, has_symptom pneumonia, has_symptom meningeal irritation, and has_symptom tachycardia.
pasteurellosis
A brucellosis that involves an infection caused by Brucella suis [NCBITaxon:29461] in swine and humans. The disease has_symptom fever, has_symptom chills, has_symptom malaise, has_symptom diaphoresis, has_symptom arthralgia, has_symptom myalgia, has_symptom headache, has_symptom anorexia, and has_symptom fatigue.
Brucella suis brucellosis
A primary bacterial infectious disease that is caused by the bacteria of the genus Brucella, when humans come in contact with contaminated animals or animal products or ingestion of infected food products. The disease has_symptom fever, has_symptom sweat, has_symptom headache, has_symptom back pain, has_symptom physical weakness, has_symptom joint pain and has_symptom fatigue.
brucellosis
A primary bacterial infectious disease that is a zoonotic infectious disease affecting multiple organs, has_material_basis_in Coxiella burnetii, which is transmitted_by inhalation of air contaminated by barnyard dust containing dried placental material, birth fluids, or excreta of infected herd animals, transmitted_by ingestion of contaminated milk, transmitted_by tick bites and transmitted_by contact with infected person. The infection has_symptom fever, has_symptom headache, has_symptom cough, has_symptom pleuritic chest pain, has_symptom myalgia and has_symptom arthralgia.
Q fever
A primary bacterial infectious disease that results in systemic infection, has_material_basis_in Bartonella quintana, which is transmitted by body lice (Pediculus humanus corporis). The infection has symptom relapsing fever, has symptom headache, has symptom shin pain, and has symptom soreness of the muscles of the legs and back.
trench fever
A primary bacterial infectious disease that is caused by the bacteria of the genus Bartonella.
bartonellosis
A spotted fever that has_material_basis_in Rickettsia akari, which is transmitted_by house mouse mite (Liponyssoides sanguineus) found on mice and other rodents. The infection has_symptom fever, has_symptom chills, has_symptom headache, has_symptom myalgia, and has_symptom papulovesicular rash.
rickettsialpox
A primary bacterial infectious disease that results in infection, located in endothelial cell of artery or located in endothelial cell of vein, has_material_basis_in Rickettsia, which is transmitted by ticks and mites. The infection has symptom fever, has symptom headache, has symptom fatigue, has symptom muscle aches, and has symptom maculopapular or petechial rash. A distinctive eschar (blackened or crusted skin) may develop at the site of a tick bite.
spotted fever
A commensal bacterial infectious disease that results_in inflammation located_in respiratory tract, has_material_basis_in Bordetella pertussis, or has_material_basis_in Bordetella parapertussis, which produce toxins that paralyze the cilia of the respiratory epithelial cells. The infection is characterized by a prolonged, high-pitched, deeply indrawn breath (whoop).
pertussis
A lung disease characterized by inadequate gas exchange by the respiratory system.
respiratory failure
disseminated intravascular coagulation
An epidemic typhus that is a mild form of the disease, which recurs in someone after a long period of latency due to immunosuppression, malnutrition or other illnesses.
Brill-Zinsser disease
A primary bacterial infectious disease that refers to a group of diseases, located in endothelial cells of the small venous, arterial, and capillary vessels, has_material_basis_in Rickettsia bacteria, which are transmitted by lice, transmitted by fleas, and transmitted by mites.
typhus
A bartonellosis that results_in infection located_in lymph node, has_material_basis_in Bartonella henselae or has_material_basis_in Bartonella clarridgeiae, which are transmitted_by scratch or bite of a kitten, or transmitted_by contact of animal's saliva with an eye or through broken skin. The infection has_symptom regional lymphadenopathy, has_symptom headache, has_symptom chills, has_symptom backache, and has_symptom abdominal pain.
cat-scratch disease
A primary bacterial infectious disease that results_in systemic infection, has_material_basis_in Chlamydia psittaci, which is transmitted_by inhaling aerosolized dried droppings or transmitted_by contact with infected birds. The infection has_symptom fever, has_symptom headache, has_symptom rash, has_symptom chills, and has_symptom pneumonia.
ornithosis
A commensal bacterial infectious disease that is caused by Chlamydia trachomatis.
chlamydia
A commensal bacterial infectious disease that results_in infection located_in eye, has_material_basis_in Chlamydia trachomatis (A, B, Ba and C serovars), which is transmitted_by contact with eye discharge from the infected person and transmitted_by congenital method. The infection causes eyelid to turn inward which makes eyelashes to scratch the cornea.
trachoma
A primary bacterial infectious disease that involves the inflammation of mucosa lining the nasal cavity, pharynx, larynx, trachea and bronchi that is characterized by the formation of granulomas, dense induration of the tissues and nodular deformity caused by Klebsiella rhinoscleromatis.
rhinoscleroma
A commensal bacterial infectious disease that is characterized by systemic sepsis, ulcerative or necrotic lesions and multisystem abscesses caused by Fusobacterium necrophorum. The disease often first presents as a severe tonsillitis or pharyngitis with high-grade fever and chills together with leukocytosis, cervical pain and neck swelling.
Lemierre's syndrome
A primary bacterial infectious disease that results in prolonged contraction of skeletal muscle fibers, has_material_basis_in Clostridium tetani, which produces tetanospasmin, a neurotoxin, which is carried to the brain and spinal cord, where it binds irreversibly to receptors inhibiting neurotransmission. Damaged upper motor neurons cannot control reflex responses to afferent sensory stimuli.
tetanus
A respiratory failure that results from diffuse injury to the endothelium of the lung (as in sepsis, chest trauma, massive blood transfusion, aspiration of the gastric contents, or pneumonia) and is characterized by pulmonary edema with an abnormally high amount of protein in the edematous fluid and by difficult rapid breathing and hypoxemia.
adult respiratory distress syndrome
A cardiovascular system disease that involves the heart.
heart disease
A primary bacterial infectious disease that is characterized by sore throat, low fever, and an adherent membrane (a pseudomembrane) on the tonsils, pharynx, and/or nasal cavity. A milder form of diphtheria can be restricted to the skin. It is caused by Corynebacterium diphtheriae, an aerobic Gram-positive bacterium. Diphtheria toxin spreads through the bloodstream and can lead to potentially life-threatening complications that affect other organs of the body, such as the heart and kidneys.
diphtheria
A bacterial meningitis that has_material_basis_in Listeria monocytogenes infection.
Listeria meningitis
A primary bacterial infectious disease that results_in infection, has_material_basis_in Listeria monocytogenes, which is transmitted_by ingestion of contaminated food or raw milk or transmitted_by congenital method. Ingestion of Listeria by pregnant women has_symptom nausea, has_symptom vomiting, has_symptom diarrhea, has_symptom fever, has_symptom malaise, has_symptom back pain, and has_symptom headache. Maternal infection with Listeria can result in chorioamnionitis, premature labor, spontaneous abortion, or stillbirth.
listeriosis
A bacterial meningitis that has_material_basis_in streptococcal bacteria.
streptococcal meningitis
A primary bacterial infectious disease that results_in infection, has_material_basis_in Borrelia burgdorferi, which is transmitted_by blacklegged tick (Ixodes scapularis) or transmitted_by western blacklegged tick (Ixodes pacificus). The infection has_symptom fever, has_symptom headache, has_symptom fatigue, and has_symptom skin rash called erythema migrans. If left untreated, infection can spread to joints, the heart, and the nervous system.
Lyme disease
A pertussis that is a milder disease caused by the bacterium Bordetella parapertussis. The disease has_symptom coughing, has_symptom sneezing, or has_symptom runny nose.
Bordetella parapertussis whooping cough
A leprosy that is an early form of the disease which causes one to a few hypopigmented or erythematous macules.
indeterminate leprosy
esophagitis
A primary bacterial infectious disease that involves intoxication caused by botulinum neurotoxins (BoNTA, B, E and F) located in neuromuscular junction resulting in descending muscle paralysis, has_material_basis_in Clostridium botulinum A, has_material_basis_in Clostridium botulinum B, has_material_basis_in Clostridium botulinum E and has_material_basis_in Clostridium botulinum F.
botulism
A tularemia that results_in painful regional lymphadenopathy and an ulcerated skin lesion.
ulceroglandular tularemia
An immune system disease that is an exaggerated immune response to allergens, such as insect venom, dust mites, pollen, pet dander, drugs or some foods.
allergic disease
A primary bacterial infectious disease that results_in infection, has_material_basis_in Spirillum minus, which is transmitted_by contact with urine or secretions from the mouth, eye, or nose of an infected animal or transmitted_by bite of an infected animal, especially rat. The infection has_symptom chills, has_symptom relapsing fever, has_symptom rash and has_symptom joint pain.
sodoku disease
A female reproductive system disease that is located_in the vagina.
vaginal disease
A primary bacterial infectious disease that results_in infection located_in epithelium of colon, has_material_basis_in Shigella boydii, has_material_basis_in Shigella dysenteriae, has_material_basis_in Shigella flexneri, or has_material_basis_in Shigella sonnei, which produce toxins that can attack the lining of the large intestine, causing swelling, ulcers on the intestinal wall, and bloody diarrhea. The bacteria are transmitted_by ingestion of food and water contaminated with feces.
shigellosis
A hematopoietic system disease that is characterized by abnormal blood clotting or bleeding.
blood coagulation disease
An urogenital tuberculosis that is located_in epididymis, has_symptom pain and has_symptom scrotal swelling.
tuberculous epididymitis
A kidney disease that is characterized by hemolytic anemia, thrombocytopenia, and renal failure caused by platelet thrombi in the microcirculation of the kidney and other organs.
hemolytic-uremic syndrome
parametritis
A respiratory failure that is characterized by deficiency of the surfactant coating the inner surface of the lungs, by failure of the lungs to expand and contract properly during breathing with resulting collapse, and by the accumulation of a protein-containing film lining the alveoli and their ducts.
newborn respiratory distress syndrome
A disease of anatomical entity which occurs in the blood, heart, blood vessels or the lymphatic system that passes nutrients (such as amino acids and electrolytes), gases, hormones, blood cells or lymph to and from cells in the body to help fight diseases and help stabilize body temperature and pH to maintain homeostasis.
cardiovascular system disease
A primary bacterial infectious disease that results_in infection, has_material_basis_in Borrelia, which is transmitted_by tick or transmitted_by body louse.
relapsing fever
A relapsing fever that is characterized by relapsing or recurring episodes of fever, has_material_basis_in Borrelia recurrentis, which is transmitted_by body louse (Pediculus humanus). The infection has_symptom tachypnea, has_symptom tachycardia, has_symptom hepatosplenomegaly and has_symptom lymphadenopathy.
louse-borne relapsing fever
A relapsing fever that is characterized by relapsing or recurring episodes of fever, has_material_basis_in Borrelia hermsii, has_material_basis_in Borrelia parkeri or has_material_basis_in Borrelia duttoni, which are transmitted_by soft ticks (Ornithodoros parkeri and Ornithodoros hermsii). The infection has_symptom tachypnea, has_symptom tachycardia, has_symptom hepatosplenomegaly and has_symptom lymphadenopathy.
tick-borne relapsing fever
A cystitis characterized by a sudden onset or severe symptoms.
acute cystitis
A tularemia that results_in inflammation of eye and swelling of lymph glands in front of the ear.
oculoglandular tularemia
A primary bacterial infectious disease that results_in infection, has_material_basis_in Streptobacillus moniliformis, which is transmitted_by contact with urine or secretions from the mouth, eye, or nose of an infected animal or transmitted_by bite of an infected animal, especially rat. The infection has_symptom chills, has_symptom fever, has_symptom rash and has_symptom joint pain.
Haverhill fever
A primary bacterial infectious disease that is a communicable systemic illness, has_material_basis_in Salmonella enterica subsp enterica serovar Typhi, which is transmitted_by ingestion of food or water contaminated with the feces of an infected person. The infection has_symptom fever, has_symptom diarrhea, has_symptom prostration, has_symptom headache, has_symptom splenomegaly, has_symptom liver enlargement, has_symptom eruption of rose-colored spots, and has_symptom leukopenia.
typhoid fever
A bacterial pneumonia involving Klebsiella pneumoniae infection. Patients with Klebsiella pneumonia tend to cough up a characteristic sputum that is said to resemble red-currant jelly. Klebsiella pneumonia tends to affect people with underlying diseases, such as alcoholism, diabetes and chronic lung disease. The symptoms include high fever, rigors and pleuritic pain, and hemoptysis.
Klebsiella pneumonia
A bacterial pneumonia that is caused by the bacterial species Mycoplasma pneumoniae. The symptoms include chest pain, chills, dry cough which is not bloody, excessive sweating, fever, headache and sore throat.
Mycoplasma pneumoniae pneumonia
A gastrointestinal tuberculosis that involves diffuse mucosal fold thickening, formation of ulcers and fistulae located_in intestine. The infection has_symptom abdominal pain, has_symptom gastrointestinal bleeding, has_symptom nausea and has_symptom vomiting.
intestinal tuberculosis
A typhus that has_material_basis_in Orientia tsutsugamushi, which is transmitted by trombiculid mites (Leptotrombidium deliense). The infection has symptom fever, has symptom headache, has symptom muscle pain, has symptom cough, has symptom maculopapular rash, has symptom eschar, has symptom splenomegaly and has symptom lymphadenopathy.
scrub typhus
An anthrax disease that results in infection located in mucosa of gastrointestinal tract, has_material_basis_in Bacillus anthracis, which is transmitted by ingestion of anthrax-infected meat. The infection has symptom lesions, has symptom vomiting of blood, has symptom severe diarrhea, has symptom loss of appetite.
gastrointestinal anthrax
A primary bacterial infectious disease that results in infection located in mucosa of mouth, located in skin or located in bone, has_material_basis_in Treponema pallidum subsp endemicum, which is transmitted by contact or transmitted by sharing of domestic utensils. The infection has symptom moist patches in the mouth, has symptom lumps in long bones, tissues around the mouth, nose, and roof of the mouth. These lumps destroy tissue, causing bones to be deformed and disfiguring the face.
bejel
A primary bacterial infectious disease that results in septicemic infection, has_material_basis_in Burkholderia mallei, which is transmitted by contact with tissues or body fluids of infected animals, or through mucosal surfaces such as the eyes and nose. The infection has symptom fever, has symptom chills, has symptom sweating, has symptom muscle aches, has symptom chest pain, has symptom muscle tightness, has symptom headache, has symptom mucopurulent nasal discharge, and has symptom nodular lesions in the lungs.
glanders
A tetanus that occurs in newborn babies when the birth cord stump gets dirty through cutting it with an unclean blade or applying substances containing bacteria to it. The infection has symptom stiff body, has symptom muscle spasms, has symptom difficulty in breathing, and has symptom exhaustion.
tetanus neonatorum
A primary bacterial infectious disease that results_in infection located_in intestine, has_material_basis_in Campylobacter jejuni, which is transmitted_by ingestion of contaminated food or water or transmitted_by contact with infected people or animals. The infection has_symptom diarrhea or has_symptom dysentery, has_symptom abdominal cramps and pain, and has_symptom fever.
campylobacteriosis
A primary bacterial infectious disease that is a sexually transmitted infection located in skin of the genitals, has_material_basis_in Haemophilus ducreyi, which is transmitted by sexual contact. The infection has symptom painful and soft ulcers.
chancroid
A commensal bacterial infectious disease that results_in inflammation, located_in conjunctiva of the eye, has_material_basis_in Chlamydia trachomatis, which is transmitted_by sexual contact. The infection has_symptom swollen conjunctiva and eyelids and has_symptom discharge of pus and mucus.
inclusion conjunctivitis
A commensal bacterial infectious disease that results_in infection located_in lymph nodes, has_material_basis_in Chlamydia trachomatis, which is transmitted_by sexual contact, and transmitted_by fomites. The infection has_symptom inguinal lymphadenitis, has_symptom abscesses in the groin area, and has_symptom lymphangitis.
lymphogranuloma venereum
bacterial esophagitis
A brucellosis involving an infection caused by Brucella canis [NCBITaxon:36855] in dogs and humans. The disease has_symptom fever, has_symptom sweats, has_symptom weakness, has_symptom weight loss, has_symptom headache, has_symptom lymphadenopathy and has_symptom splenomegaly.
Brucella canis brucellosis
A spotted fever that has_material_basis_in Rickettsia conorii subsp conorii, which is transmitted_by dog tick (Rhipicephalus sanguineus). The infection has_symptom fever, has_symptom eschar (usually single), has_symptom regional adenopathy, has_symptom maculopapular rash on extremities.
boutonneuse fever
A commensal bacterial infectious disease that results_in infection, has_material_basis_in Streptococcus pyogenes or has_material_basis_in Staphylococcus aureus, which produce toxins that are absorbed systemically and produce the systemic manifestations. The infection has_symptom fever, has_symptom rash, has_symptom hypotension, has_symptom multiorgan failure, has_symptom desquamation, has_symptom vomiting, has_symptom diarrhea, has_symptom headache, and has_symptom nonfocal neurologic abnormalities.
toxic shock syndrome
A tularemia that results in formation of ulcerative lesions located in gastrointestinal tract. The infection has symptom fever, has symptom chills, has symptom malaise, has symptom muscle aches, and has symptom vomiting.
gastrointestinal tularemia
A urinary system disease that is located_in the ureter.
ureteral disease
A brucellosis that involves an infection caused by Brucella melitensis [NCBITaxon:29459] in cattle, goats, sheep and humans. The disease has_symptom fever, has_symptom malaise, has_symptom anorexia, has_symptom limb pain and has_symptom back pain.
Brucella melitensis brucellosis
A brucellosis that involves an infection caused by Brucella abortus [NCBITaxon:235] in cattle and humans. The disease has_symptom fever, has_symptom chills, has_symptom sweats, has_symptom weight loss, has_symptom malaise, has_symptom headaches, has_symptom myalgia, and has_symptom arthralgia.
Brucella abortus brucellosis
anaerobic meningitis
A disease that is characterized by abnormally rapid cell division.
disease of cellular proliferation
A primary bacterial infectious disease that is described as an acute, diarrheal illness caused by infection of the intestine with the bacterium Vibrio cholerae, which is characterized by profuse watery diarrhea, vomiting, leg cramps, circulatory collapse and shock.
cholera
A disease of anatomical entity that is located_in reproductive system organs.
reproductive system disease
A thoracic disease which may involve inflammation of pleura, collection of air within the pleural cavity, abnormal collection of pleural fluid, abnormal growths on the pleura (pleural tumor) and pleural plaques. The main causes of pleural diseases including pleural effusions are congestive heart failure, malignancy, parapneumonic infections and pulmonary embolism.
pleural disease
A disease by infectious agent that results_in infection, has_material_basis_in Fungi, which pass the resistance barriers of the human or animal body.
fungal infectious disease
A disease of anatomical entity that located_in the respiratory system which extends from the nasal sinuses to the diaphragm.
respiratory system disease
A connective tissue disease that develops from an antecedent Group A Streptococcal pharyngeal infection and has_symptom carditis, has_symptom polyarthritis, has_symptom chorea, has_symptom erythema marginatum, has_symptom subcutaneous nodules, has_symptom arthralgia, has_symptom prolonged PR interval, and/or has_symptom fever.
rheumatic fever
A disease of anatomical entity that is located_in the integumentary system comprising the skin and its appendages.
integumentary system disease
A disease of cellular proliferation that is malignant and primary, characterized by uncontrolled cellular proliferation, local cell invasion and metastasis.
cancer
An extrapulmonary tuberculosis that results in formation of tuberculomas located_in brain or located_in spinal cord.
central nervous system tuberculosis
An extrapulmonary tuberculosis that results in formation of lesions located in bone.
skeletal tuberculosis
A bladder disease that is characterized by inflammation of the bladder.
cystitis
A disease of anatomical entity that occurs in the muscular and/or skeletal system.
musculoskeletal system disease
A disease of anatomical entity that is located_in kidney, ureter, bladder and urethra.
urinary system disease
A female reproductive system disease that is located_in the fallopian tube.
fallopian tube disease
A tularemia that is located_in lungs. The bacteria are transmitted_by breathing dusts or aerosols containing the organisms. The infection has_symptom cough, has_symptom chest has_symptom pain, and has_symptom difficulty breathing.
pneumonic tularemia
A primary bacterial infectious disease that has_material_basis_in Francisella tularensis, which is transmitted by dog tick bite (Dermacentor variabilis), transmitted by deer flies (Chrysops sp) or transmitted by contact with infected animal tissues.
tularemia
An urogenital tuberculosis that results_in inflammtion located_in ovary.
tuberculous oophoritis
An extrapulmonary tuberculosis that is located_in urogenital system.
urogenital tuberculosis
A vaginal disease that is characterized by inflammation of the vagina.
vaginitis
An endocrine system disease that is located_in the gonads.
gonadal disease
A reproductive system disease that impairs the ability to reproduce and is located in the uterus, vagina, cervix, ovaries or fallopian tubes.
female reproductive system disease
A primary bacterial infectious disease that involves systemic infection, has_material_basis_in Leptospira, which is transmitted by contact with water, food, or soil containing urine from the infected animals. The infection has symptom jaundice, has symptom chills, has symptom fever, has symptom muscle pain, and has symptom hepatomegaly.
leptospirosis
An opportunistic bacterial infectious disease that results_in disseminated infection in immunocompromised hosts, has_material_basis_in Nocardia asteroides. The infection has_symptom pneumonia, has_symptom cellulitis, has_symptom lesions in the brain or meninges, and has_symptom ascending regional lymphadenopathy.
nocardiosis
A gastrointestinal system infectious disease that involves inflammation of the lining of the stomach and small and large intestines, which is caused by viruses, bacteria, or parasites. Chemicals and drugs also cause gastroenteritis. The symptoms include diarrhea, loss of appetite, nausea, vomiting, cramps, and discomfort in the abdomen.
gastroenteritis
A blood coagulation disease that is characterized by an increased tendency to form clots.
thrombophilia
splenic disease
An organ system cancer located in the hematological system that is characterized by uncontrolled cellular proliferation in blood, bone marrow and lymph nodes.
hematologic cancer
A primary bacterial infectious disease that results_in infection, has_material_basis_in Mycobacterium avium complex (MAC), which is transmitted_by inhalation or transmitted_by ingestion of via the respiratory or gastrointestinal tract respectively. The bacteria cause disseminated infection in HIV infected people, while pulmonary disease in immunocompetent persons.
Mycobacterium avium complex disease
A disease of anatomical entity that is located_in endocrine glands which secretes a type of hormone directly into the bloodstream to regulate the body.
endocrine system disease
A disease of anatomical entity that is located_in the immune system.
immune system disease
A Coronavirus infectious disease that results_in infection located_in respiratory tract, has_material_basis_in SARS coronavirus (SARS-CoV), which is transmitted_by droplet spread of respiratory secretions, transmitted_by ingestion of contaminated food, or transmitted_by fomites. The infection has_symptom fever, has_symptom headache, has_symptom body aches, has_symptom dry cough, and has_symptom hypoxia.
severe acute respiratory syndrome
A tuberculosis that is a contagious disease located_in lungs. The infection has_symptom fever, has_symptom cough, has_symptom difficulty in breathing, has_symptom inflammatory infiltrations, has_symptom formation of tubercles, has_symptom caseation, has_symptom pleural effusion, and has_symptom fibrosis.
pulmonary tuberculosis
A hypersensitivity reaction type I disease that is an abnormal response to a food, triggered by the body's immune system.
food allergy
A primary bacterial infectious disease that results_in infection located_in intestine, has_material_basis_in Salmonella enterica subsp enterica serovar Paratyphi A, B or C, which are transmitted_by ingestion of contaminated food. The infection has_symptom fever, has_symptom headache, has_symptom abdominal pain, has_symptom malaise, has_symptom anorexia, has_symptom constipation, has_symptom rosy spots on the central body, has_symptom non productive cough (in early stage of illness), has_symptom bradycardia, and has_symptom hepatosplenomegaly.
paratyphoid fever
An opportunistic bacterial infectious disease that has_material_basis_in Acinetobacter.
Acinetobacter infectious disease
A gastrointestinal system disease that is located_in the liver and/or biliary tract.
hepatobiliary disease
spinal cord disease
A nervous system disease that affects either the spinal cord (myelopathy) or brain (encephalopathy) of the central nervous system.
central nervous system disease
A bone disease that results_in inflammation of the located_in bone.
bone inflammation disease
A vaginitis that is characterized by a grayish vaginal discharge usually of foul odor and the presence of Gardnerella vaginalis.
bacterial vaginosis
A disease of anatomical entity that is located_in the breast.
breast disease
A plague that results_in infection located_in vasculature where bacterial endotoxins cause coagulation, which leads to formation of tiny clots throughout the body. The infection has_symptom fever, has_symptom chills, has_symptom prostration, has_symptom abdominal pain, has_symptom shock and has_symptom bleeding into skin and other organs.
septicemic plague
A primary bacterial infectious disease that results_in infection, located_in lymph node, located_in vasculature or located_in lungs, has_material_basis_in Yersinia pestis, which is transmitted_by oriental rat flea (Xenopsylla cheopis) infected by feeding on rodents and other mammals, transmitted_by air, transmitted_by direct contact or transmitted_by ingestion of contaminated undercooked food.
plague
A urinary system disease that is located_in the bladder.
bladder disease
A food allergy that develops_from exposure to and particularly consumption of wheat, and has_symptom that are both gastrointestinal and nongastrointestinal in nature, such as diarrhea, mouth and throat irritation, headache, hives, skin rashes, and anaphylaxis.
wheat allergy
An integumentary system disease that is located_in skin.
skin disease
A cardiomyopathy that is characterized by the pathology occurring outside of the myocardium.
extrinsic cardiomyopathy
A primary bacterial infectious disease that is located_in lungs, located_in lymph nodes, located_in pericardium, located_in brain, located_in pleura or located_in gastrointestinal tract, has_material_basis_in Mycobacterium tuberculosis, which is transmitted_by droplets released into the air when an infected person coughs or sneezes.
tuberculosis
A disease is a disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism.
disease
A tuberculosis that is resistant to isoniazid and rifampicin, the two most powerful first-line anti-TB drugs.
multidrug-resistant tuberculosis
A gastrointestinal tuberculosis that involves formation of painful ulcerative mucosal lesions located in tongue, located in palate, located in maxilla or located in mandible.
oral tuberculosis
A stomach disease that is an inflammation of the lining of the stomach.
gastritis
A gastrointestinal system disease that is located_in the mouth.
mouth disease
A gastritis that involves inflammation of the stomach lining caused by bacteria. The disease has_symptom abdominal pain, has_symptom indigestion, has_symptom ulcer formation, has_symptom abdominal bloating, has_symptom nausea and has_symptom vomiting.
bacterial gastritis
An abdominal tuberculosis that results_in infection located_in gastrointestinal tract. The infection has_symptom abdominal pain, has_symptom weight loss, has_symptom fever, has_symptom anorexia, has_symptom constipation, has_symptom nausea, and has_symptom vomiting.
gastrointestinal tuberculosis
A gastrointestinal tuberculosis that involves infection located_in liver, which results in the formation of tuberculous granulomas. The infection has_symptom fever, has_symptom anorexia, has_symptom weight loss, has_symptom abdominal pain and has_symptom jaundice.
hepatic tuberculosis
liver disease
A syphilis that is the first stage of syphilis, marked by the development of a chancre, which is characterized by mononuclear leukocytic infiltration, macrophages, and lymphocytes.
primary syphilis
A syphilis that is characterized as the second stage of syphilis which appears from 2 to 6 months after primary infection, and is marked by lesions especially in the skin but also in organs and tissues, and that lasts from 3 to 12 weeks.
secondary syphilis
A primary bacterial infectious disease that is a sexually transmitted systemic disease, has_material_basis_in Treponema pallidum subsp pallidum, which is transmitted_by sexual contact, transmitted_by blood product transfusion, transmitted_by congenital method from mother to fetus or transmitted_by contact with infectious lesions. If left untreated, produces chancres, rashes, and systemic lesions in a clinical course with three stages continued over many years.
syphilis
An immune system disease that is an overactive immune response of the body against substances and tissues normally present in the body resulting from an abnormal functioning of the immune system that results in the production of antibodies or T cell directed against the host tissues.
autoimmune disease
An eye disease affecting the conjunctiva, which is the mucous membrane surrounding the eye and interior of the eyelids.
conjunctival disease
A food allergy that results in adverse immune reaction to one or more of the proteins in cow's milk and/or the milk of other animals, which are normally harmless to the non-allergic individual.
milk allergy
A food allergy that is an allergy or hypersensitivity to dietary substances from the yolk or whites of eggs, causing an overreaction of the immune system which may lead to severe physical symptoms.
egg allergy
A legume allergy that is an allergy or hypersensitivity to dietary substances from peanuts causing an overreaction of the immune system which in a small percentage of people may lead to severe physical symptoms.
peanut allergy
A food allergy that develops_from exposure to and particularly consumption of nuts, and has_symptom asthma, skin rashes, throat and eye irritation, and anaphylaxis.
nut allergy
subacute bacterial endocarditis
A reproductive system disease that affects male reproductive organs.
male reproductive system disease
An extrapulmonary tuberculosis that is located_in lymph node, and has_symptom lymphadenopathy, has_symptom fever, has_symptom weight loss, has_symptom fatigue, has_symptom night sweats and has_symptom cough.
lymph node tuberculosis
An extrapulmonary tuberculosis that is located_in pericardium resulting in acute pericarditis, chronic pericardial effusion, cardiac tamponade or pericardial constriction.
pericardial tuberculosis
A commensal bacterial infectious disease that results_in infection, has_material_basis_in Actinobacillus ureae, which is a commensal of the human respiratory tract. The pathogen causes meningitis, endocarditis, bacteremia, atrophic rhinitis, bronchitis, pneumonia, conjunctivitis, peritonitis, and otitis media.
actinobacillosis
A primary bacterial infectious disease that results_in infection, has_material_basis_in Burkholderia pseudomallei, which is transmitted_by contact with the contaminated water or soil. The infection has_symptom fever, has_symptom respiratory distress, has_symptom chest pain, and has_symptom stomach pain.
melioidosis
A gastrointestinal system disease that is located_in the intestine.
intestinal disease
An adnexa disease that is located_in the eyelid.
eyelid disease
A intestinal disease located in the colon.
colonic disease
A lung disease that involves lung parenchyma or alveolar inflammation and abnormal alveolar filling with fluid (consolidation and exudation). It results from a variety of causes including infection with bacteria, viruses, fungi or parasites, and chemical or physical injury to the lungs. It is accompanied by fever, chills, cough, and difficulty in breathing.
pneumonia
A urinary system disease that is located_in the kidney.
kidney disease
An eye and adnexa disease that is located_in the eye.
eye disease
A gastrointestinal system disease that is located_in the esophagus.
esophageal disease
An immune system disease that results when one or more essential parts of the immune system is missing or not working properly at birth due to a genetic mutation.
primary immunodeficiency disease
A conjunctival disease characterized by an inflammation of the conjunctiva, the outermost layer of the eye and the inner surface of the eyelids.
conjunctivitis
A musculoskeletal system disease that affects tissues such as skin, tendons, and cartilage.
connective tissue disease
A disease that manifests in a defined anatomical structure.
disease of anatomical entity
A gastrointestinal tuberculosis that involves formation of tuberculous ulcers located_in esophagus. The infection has_symptom dysphagia, has_symptom cough, has_symptom chest pain, has_symptom fever and has_symptom weight loss.
esophageal tuberculosis
A disease of anatomical entity that has_material_basis_in hematopoietic cells.
hematopoietic system disease
An anthrax disease that results_in infection located_in skin, has_material_basis_in Bacillus anthracis, which is transmitted_by contact with infected animals or animal products. The infection has_symptom skin lesion that eventually forms an ulcer with a black center.
cutaneous anthrax
A primary bacterial infectious disease that results_in infection located_in skin, located_in lung lymph nodes or located_in gastrointestinal tract, has_material_basis_in Bacillus anthracis, transmitted_by contact with infected animals or animal products, transmitted_by airborne spores or transmitted_by ingestion of undercooked meat from infected animals and has_symptom skin ulcer, has_symptom nausea, has_symptom poor appetite, has_symptom bloody diarrhea, has_symptom fever or has_symptom shortness of breath.
anthrax disease
An immune system disease that is located_in the lymphatic system.
lymphatic system disease
An urogenital tuberculosis that is located_in urinary bladder, which results in fibrosis of bladder wall muscles.
bladder tuberculosis
A primary bacterial infectious disease that is a sexually transmitted infection, located_in uterus, located_in fallopian tube, located_in urethra, located_in mouth, located_in throat, located_in eye or located_in anus, has_material_basis_in Neisseria gonorrhoeae, which is transmitted_by contact with the penis, vagina, mouth, or anus or transmitted_by congenitally from mother to baby during delivery. The infection has_symptom burning sensation during urination, has_symptom discharge from the penis, has_symptom increased vaginal discharge, or has_symptom vaginal bleeding between periods.
gonorrhea
A gastrointestinal system disease that is located_in the stomach.
stomach disease
A disease of anatomical entity that is located_in the gastrointestinal tract.
gastrointestinal system disease
An extrinsic cardiomyopathy that is characterized as an inflammation of the heart muscle.
myocarditis
A syphilis that is characterized as the third stage of syphilis that develops after the disappearance of the secondary symptoms and is marked by ulcers and gummas under the skin and commonly by involvement of the skeletal, cardiovascular, and nervous systems.
tertiary syphilis
An urogenital tuberculosis that is located_in ureter resulting in ureteral strictures.
ureter tuberculosis
A gastrointestinal system disease that involves inflammation of the peritoneum resulting from perforation of the gastrointestinal tract, which produces immediate chemical inflammation followed shortly by infection from intestinal organisms. Peritonitis can also result from appendicitis, diverticulitis, strangulating intestinal obstruction, pancreatitis, pelvic inflammatory disease, mesenteric ischemia, intraperitoneal blood, barium, or peritoneo-systemic shunts, drains, and dialysis catheters in the peritoneal cavity. The symptoms include abdominal pain and tenderness, fever, fluid in the abdomen, nausea, vomiting and low urine output.
peritonitis
A commensal bacterial infectious disease that results in infection, which is characterized by contiguous spread, suppurative and granulomatous inflammation, and formation of multiple abscesses and sinus tracts that may discharge sulfur granules, has_material_basis_in Actinomyces israelii, has_material_basis_in Actinomyces gerencseriae, has_material_basis_in Actinomyces naeslundii, has_material_basis_in Actinomyces odontolyticus, has_material_basis_in Actinomyces viscosus, has_material_basis_in Actinomyces meyeri, has_material_basis_in Propionibacterium propionicum, which require a break in the integrity of the mucous membranes and the presence of devitalized tissue to invade deeper body structures.
actinomycosis
rheumatic myocarditis
A lower respiratory tract disease in which the function of the lungs is adversely affected by narrowing or blockage of the airways resulting in poor air flow, a loss of elasticity in the lungs that produces a decrease in the total volume of air that the lungs are able to hold, and clotting, scarring, or inflammation of the blood vessels that affect the ability of the lungs to take up oxygen and to release carbon dioxide.
lung disease
A colitis that is predominantly confined to the mucosa located_in colon and includes characteristic ulcers, or open sores.
ulcerative colitis
An upper respiratory tract disease described as an acute contagious disease caused by Group A bacteria of the genus Streptococcus (especially various strains of S. pyogenes) and characterized by inflammation of the nose, throat, and mouth, generalized toxemia, and a red rash.
scarlet fever
A disease of anatomical entity that is located_in the central nervous system or located_in the peripheral nervous system.
nervous system disease
An aspiration pneumonia caused by anaerobic bacteria like Bacteroides fragilis, Peptostreptococcus, anaerobic streptococci, Fusobacterium species (Fusobacterium nucleatum and Fusobacterium necrophoram). Lung abscess and empyema are diagnosed in this disease.
anaerobic pneumonia
A pneumonia involving inflammation of the lungs caused by bacteria.
bacterial pneumonia
A commensal bacterial infectious disease that is characterized by widespread erythema, peeling, and necrosis of the skin, that is caused by a toxin produced by a bacterium of the genus Staphylococcus (S. aureus). The infection has_symptom redness of skin, has_symptom fluid-filled blister formation, has_symptom fever and has_symptom irritability.
Ritter's disease
A primary bacterial infectious disease that results_in infection located_in skin or located_in mucosa of genital tract, has_material_basis_in Klebsiella granulomatis, transmitted by sexual contact or transmitted_by contact with the open sores. The infection has_symptom painless genital ulcers.
granuloma inguinale
A commensal bacterial infectious disease that results in infection, located in muscle tissue, has_material_basis_in Clostridium perfringens, which produce gas that becomes trapped in the infected tissue. Gas gangrene usually develops after injuries or surgery. The infection has symptom large blisters, has symptom pain in the infected area, has symptom myonecrosis, has symptom gas production, and has symptom sepsis.
gas gangrene
An abdominal tuberculosis that results_in formation of granulomas or abscesses located_in spleen.
splenic tuberculosis
A disease by infectious agent that results in infection, has_material_basis_in Viruses.
viral infectious disease
A central nervous system disease that is located_in the brain.
brain disease
vesiculitis
A meningitis that has_material_basis_in a bacterial infection.
bacterial meningitis
A central nervous system disease that is characterized by an inflammation of the pia-arachnoid meninges. It can be caused by growth of bacteria, fungi, or parasites within the subarachnoid space or by the growth of bacteria or viruses within the meningeal or ependymal cells.
meningitis
A syphilis that is characterized as having serologic proof of infection without signs or symptoms of disease.
latent syphilis
A brain disease that is characterized as an acute inflammation of the brain with flu-like symptoms.
encephalitis
A primary bacterial infectious disease that results_in infection located_in intestine caused by eating food contaminated with enterotoxins produced by bacteria, has_material_basis_in Staphylococcus aureus. The infection has_symptom diarrhea, has_symptom vomiting, has_symptom nausea, has_symptom cramps, and has_symptom weakness.
staphyloenterotoxemia
A bacterial conjuctivitis that is characterized by pain and tenderness in the eyeball and conjuctival discharge.
ophthalmia neonatorum
bacterial conjunctivitis
An urogenital tuberculosis that results_in formation of granulomas located_in kidney.
renal tuberculosis
A respiratory system disease which involves the upper respiratory tract.
upper respiratory tract disease
A gastrointestinal tuberculosis that results_in inflammation located_in peritoneum, which results in formation of tubercles. The infection has_symptom abdominal discomfort, has_symptom pain, has_symptom distention from gas or fluid, has_symptom digestive disturbances and has_symptom emaciation.
tuberculous peritonitis
A syphilis that results_in a multisystem infection in the fetus via the placenta.
congenital syphilis
An extrapulmonary tuberculosis that results in formation of tiny lesions in all the organs.
miliary tuberculosis
A tertiary syphilis that is manifested as aneurysm formation in the ascending aorta, caused by chronic inflammatory destruction of the vasa vasorum, insufficiency of the aortic valve, or narrowing of the coronary arteries.
cardiovascular syphilis
internal hordeolum
An eyelid disease that is characterized by an infection of the sebaceous glands at the base of the eyelashes. Styes are generally caused by a Staphylococcus aureus bacterial infection.
hordeolum
lymph node disease
acute female pelvic peritonitis
A tertiary syphilis that results in infection located in brain or located in spinal cord.
tertiary neurosyphilis
A exposure event involving the interaction of an exposure receptor to environmental system.
A exposure event involving the interaction of an exposure receptor to construction.
A exposure event involving the interaction of an exposure receptor to abattoir.
A exposure event involving the interaction of an exposure receptor to farm.
A exposure event involving the interaction of an exposure receptor to hospital.
A exposure event involving the interaction of an exposure receptor to laboratory facility.
A exposure event involving the interaction of an exposure receptor to office.
A exposure event involving the interaction of an exposure receptor to restaurant.
A exposure event involving the interaction of an exposure receptor to shop.
A exposure event involving the interaction of an exposure receptor to geographic feature.
A exposure event involving the interaction of an exposure receptor to petting zoo.
A exposure event involving the interaction of an exposure receptor to campground.
An exposure event involving hunting behavior
An astrononmical body part which delimited by physical discontinuities with its surroundings.
This class is being depopulated and will be filled only with inferred subclasses. Please do not use this for direct annotation, favouring instead a more descriptive subclass.
constructed feature
An anthropogenic geographic feature is a geographic feature resulting from the influence of human beings on nature.
state / province / territory / region
A primary administrative division of a country, such as a state in the United States.
A political association with effective dominion over a geographic area.
A construction which enables the movement of humans, their animals or their vehicles.
An enclosure for displaying selected plant or animal life.
A geographical feature associated with water.
Artificial watercourse with no flow or a controlled flow used for navigation, drainage or irrigation.
This class refers to the water contained in a canal channel, and not the channel itself.
A marine water body which is constitutes the majority of an astronomical body's hydrosphere.
A large expanse of saline water usually connected with an ocean.
A body of water or other liquid of considerable size contained in a depression on a landmass.
A stream which, through permanent or seasonal flow processes, moves from elevated land towards lower elevations through a definite channel and empties either into a sea, lake, or another river or ends on land as bed seepage and evapotranspiration exceed water supply.
"There are no official definitions for the generic term river as applied to geographic features, although in some countries or communities a stream is defined by its size. Many names for small rivers are specific to geographic location; examples are "run" in some parts of the United States, "burn" in Scotland and northeast England, and "beck" in northern England. Sometimes a river is defined as being larger than a creek, but not always: the language is vague."
A watercourse which is linear and flows across the solid portion of a planetary surface.
streamlet
An artificial body of water, often contained by a dam, constructed for the purpose of water storage.
A cylindrical hole, pit, or tunnel drilled or dug down to a depth from which water, oil, or gas can be pumped or brought to the surface.
A surface landform which provides an egress for groundwater or steam to flow out of the ground.
Springs are typically where an aquifer surface meets the ground surface or where there is a fissure.
An area of water bordered by land on three sides.
A body of water, usually of smaller size than a lake.
A small, human-made channel which has been dug for draining or irrigating the land.
Artificial watercourse with no flow or a controlled flow used drainage.
An vegetated area which overlaps a wetland ecosystem.
Place or area with clustered or scattered buildings and a permanent human population.
An accumulation of water of varying size.
The term body of water most often refers to large accumulations of water, such as oceans, seas, and lakes, but it includes smaller pools of water such as ponds, wetlands, or more rarely, puddles. A body of water does not have to be still or contained; Rivers, streams, canals, and other geographical features where water moves from one place to another are also considered bodies of water.
Naturally formed, subterranean open area or chamber.
A construction that has been assembled by deliberate human effort.
A permanent walled and roofed construction.
A barrier constructed across a watercourse to control the flow or raise the level of water.
An excavation in the Earth for the purpose of extracting earth materials.
As with other classes that are "features", the subclasses of this class are being moved to more informative locations. Their relation to agriculture will be modelled by something more akin to a quality or relation to an agricultural process.
An area of land which is used for the cultivation of crops or grazing of livestock, including any agricultural constructions therein.
A range of mounts which is dominated by mountains.
A region of general uniform slope, comparatively level, and of considerable extent.
A landform consisting of loose rock particles such as sand, gravel, shingle, pebbles, cobble, or even shell fragments along the shoreline of a body of water.
A region rendered barren or partially barren by environmental extremes, especially by low rainfall.
Area of dry or relatively dry land surrounded by water or low wetland.
A hydrographic feature which is located below the surface of a marine water body.
An area in which grasses (Graminae) are a significant component of the vegetation.
Land having a cover of trees, shrubs, or both.
An area with a high density of trees. A small forest may be called a wood.
The definitions of forest can vary greatly, and different classes will be needed to support the major categories. Tree cover alone is not enough to distinguish between forests and plantations. The international definition proposed by the 2010 FAO Forestry Resource Assessment: "land spanning more than 0.5 ha with trees higher than 5 metres and canopy cover of more than 10 percent, or trees able to reach these thresholds in situ . It does not include land that is predominantly under agricultural or urban land use." - FAO. 2010. Global forest resources assessment 2010, Main report, FAO Forestry Paper 163. Rome.
A vegetated area which is part of a tundra ecosystem.
A field which is located on land and used for agricultural purposes, such as the grazing of livestock or the cultivation of crops.
An intentional planting of a crop, on a large scale, usually for uses other than cereal production or pasture. The term is currently most often used for plantings of trees and shrubs. The term tends also to be used for plantings maintained on economic bases other than that of subsistence farming.
A channel of a watercource which has been constructed by humans or their technologies.
A geographical region whose affairs and population are administered by an authority.
An arid terrain with clay-rich soil that has been extensively eroded by wind and water.
A ridge of rocks, lying near the surface of the sea, which may be visible at low tide, but is usually covered by water.
A ditch that supplies water to surrounding land.
A ditch that collects water from the surrounding land.
A part of an astronomical body which is primarily composed of solid material.
An island that does not sit on a continental shelf, and is of volcanic origin.
A grassland ecosystem which is used for grazing of ungulate livestock as part of a farm or ranch.
The separation between neighbouring drainage basins (catchments). In hilly country, the divide lies along topographical peaks and ridges, but in flat country or on a high plateau (especially where the ground is marshy) the divide may be invisible - just a more or less notional line on the ground on either side of which falling raindrops will start a journey to different rivers, and even to different sides of a country or continent.
A facility in which fish are raised commercially in tanks or enclosures, usually for food.
A hatchery in which the eggs of fish are hatched under artificial conditions.
A flooded parcel of arable land used for growing rice and other semiaquatic crops.
Area covered with low-growing or stunted perennial vegetation and usually not mixed with trees.
A landform sunken or depressed below the surrounding area.
depression
A depressed landform which physically confines a river, slough or ocean strait, and which consists of a bed and banks.
A biome is an ecosystem which is undergoing climactic ecological succession.
In this definition, there is an assumption that no major perturbations are occurring or have occurred in a time frame affects the successional dynamics of the ecosystem. A "major" perturbation is one which disrupts the community's ability to restore its (near) equilibrium. Usually, pioneer or early secondary successional processes would be in effect in such scenarios.
A tract of land which has few or no trees and is surrounded by more heavily wooded areas.
There should be a better superclass than "field" which should indicate that there are no woody plants in growth form "tree" around.
A biome which is primarily or completely situated on a landmass.
An aquatic biome which is determined by a marine water body.
This biome includes open-ocean and unprotected coastal ecosystems, characterized by exposure to wave action, tidal fluctuation, and ocean currents as well as systems that largely resemble these. Water in the marine biome is generally within the salinity range of seawater: 30 to 38 ppt.
A reservoir constructed for the purpose of providing water for irrigation.
irrigation pond
A facility, permanent or temporary, on land, in air, space or water, where scientific research or measurements can be undertaken.
An opening of the sea into the land, or of a lake into its shore.
A field which includes at least two mounts connected by high ground and arranged in an approximately linear fashion.
A step-like feature between higher and lower ground: a relatively flat or gently inclined shelf of earth, backed and fronted by steep slopes or manmade detaining walls.
A terrace which is used for agricultural activities.
Lake sediment is sediment which covers the bottom of a lake. Lake sediments are comprised mainly of clastic material (sediment of clay, silt, and sand sizes), organic debris, chemical precipitates, or combinations of these.
A field which is composed primarily of gravel.
A bounded area of land, or water, usually in its natural or semi-natural (landscaped) state and set aside for some purpose, usually to do with recreation or conservation.
A raised walkway over water, supported by piles or pillars.
A building or region where sports activities can be carried out.
An aquatic biome which is determined by a body of freshwater.
A rock is a naturally occurring solid aggregate of one or more minerals or mineraloids.
From https://en.wikipedia.org/wiki/ [A mineral] is different from a rock, which can be an aggregate of minerals or non-minerals and does not have a specific chemical composition. The exact definition of a mineral is under debate, especially with respect to the requirement a valid species be abiogenic, and to a lesser extent with regards to it having an ordered atomic structure.
An environmental material which is primarily composed of minerals, varying proportions of sand, silt, and clay, organic material such as humus, interstitial gases, liquids, and a broad range of resident micro- and macroorganisms.
'In engineering terms, soil is referred to as regolith, or loose rock material that lies above the 'solid geology'. Soil is commonly referred to as "earth" or "dirt"; technically, the term "dirt" should be restricted to displaced soil.' https://en.wikipedia.org/wiki/Soil " The upper limit of soil is the boundary between soil and air, shallow water, live plants, or plant materials that have not begun to decompose. Areas are not considered to have soil if the surface is permanently covered by water too deep (typically more than 2.5 meters) for the growth of rooted plants. The lower boundary that separates soil from the nonsoil underneath is most difficult to define. Soil consists of horizons near the Earth's surface that, in contrast to the underlying parent material, have been altered by the interactions of climate, relief, and living organisms over time. Commonly, soil grades at its lower boundary to hard rock or to earthy materials virtually devoid of animals, roots, or other marks of biological activity. For purposes of classification, the lower boundary of soil is arbitrarily set at 200 cm." Soil taxonomy, 2nd Ed., quoted in http://www.nrcs.usda.gov/wps/portal/nrcs/detail/soils/edu/?cid=nrcs142p2_054280
A lentic water body which is composed primarily of marine water.
A solid astronomical body part which is part of the planetary surface between the peak of an elevation or the bottom of a depression and relatively flat surrounding land.
Water that has been adversely affected in quality by anthropogenic influence.
An excreta material which is composed primarily of feces, an excreta consisting of waste products expelled from an animal's digestive tract through the anus (or cloaca) during defecation.
stool
ENVO bodily fluid classes differ from UBERON's treatment of bodily fluids. UBERON refers to the substance itself ("S"). We assert that UBERON's classes are the primary compositional component of the terms in ENVO ("S material"). Use of the ENVO terms is typically recommended when you wish to indicate that there may be other materials intermixed with S.
This is distinct from classes such as http://purl.obolibrary.org/obo/UBERON_0001988 in that it refers to the environmental material composed primarily of feces rather than 'just' feces.
The mixture of gases (roughly (by molar content/volume: 78% nitrogen, 20.95% oxygen, 0.93% argon, 0.038% carbon dioxide, trace amounts of other gases, and a variable amount (average around 1%) of water vapor) that surrounds the planet Earth.
An environmental material primarily composed of dihydrogen oxide in its liquid form.
Particulate environmental material which is formed as a result of the transport and deposition of particles by flowing liquid.
Sediment is typically deposited on the bed or bottom of a body of water or other liquid.
Particulate environmental material with diameters less than 500 micrometers.
Dust occurs in and may be deposited from the atmosphere.
Water which has a low concentration of dissolved solutes, particularly that of sodium chloride.
The lower bound of solute concentration required for water to be considered freshwater is variable, but is always less than that of seawater, and often cited as less than 1 gram of solutes per 1 litre of water.
Wastewater that is contaminated with feces or urine,
A biome which is determined by a water body and which has ecological climax communities adapted to life in or on water.
Sediment that accumulates in the flat or very gently sloping areas of the deep ocean basin floor. The three main types of deep marine sediment, also known as pelagic sediment, are siliceous oozes, calcareous oozes, and red clays.
Revise adjacent to. Consider sampled stream sediment. Dry stream sediment.
Manure which has been derived from the aerobically decomposed remnants of organic materials.
A hospital is a building in which health care services are provided by specialized staff and equipment.
Straw or other material strewn in an animal's enclosure (e.g. a stable) for it to sleep on and to absorb its faeces and urine.
straw bedding
A building in which a business presents a selection of goods and offers to trade or sell them to customers for money or other goods.
A shop in which a business offers food products for sale or trade.
Whether food is the primary product offered by the business or simply one of the products it offers is not specified in this class.
A soil which is composed of approximately equal proportions of sand and silt, with a smaller proportion of clay.
Some authorities consider loam to be any soil material that contains 7 to 27% clay, 28 to 50% silt, and less than 52% sand.
Soil which is part of an ecosystem used for agricultural activities.
A portion of soil which is found in a garden.
A material which is not the desired output of a process and which is typically the input of a process which removes it from its producer (e.g. a disposal process).
Manure which is derived from the waste products of animals.
This is interesting in that the "role" aspect of "waste" is (or can be) replaced by another role "fertilizer". Thus, the positioning of "manure" under waste may not be totally correct.
A house used for sheltering non-human animals.
While humans are animals, this class does not refer to human houses.
An animal house which is used to house pigs.
A waste treatment plant which equipped to treat sewage such that its potential for environmental contamination is reduced.
sewage treatment plant
Drinking water is water which may be consumed by humans with no adverse effects on their health.
A material entity that has been processed by humans or their technology in any way, including intermediate products as well as final products.
Manure which is primarily composed of pig feces.
An industrial building is a building within which goods are produced and, optionally, stored or within which services are rendered.
It's possible that this will become an inferred class in the future. The United Nations' International Standard Industrial Classification should be referred to when expanding this branch. ISIC can also be used to identify processes. See http://unstats.un.org/unsd/cr/registry/regcst.asp?Cl=27&Lg=1.
A dairy is a building in which animal milk is harvested and, optionally, processed for human consumption.
'Terminology differs between countries. For example, in the United States, the entire dairy farm is commonly called a "dairy." The building or farm area where milk is harvested from the cow is often called a "milking parlor" or "parlor." The farm area where milk is stored in bulk tanks is known as the farm's "milk house." Milk is then hauled (usually by truck) to a "dairy plant," also referred to as a "dairy", where raw milk is further processed and prepared for commercial sale of dairy products. In New Zealand, farm areas for milk harvesting are also called "milking parlours", and are historically known as "milking sheds."' https://en.wikipedia.org/wiki/Dairy
A food processing building is a building in which materials that contain or consist of essential body nutrients - such as carbohydrates, fats, proteins, vitamins, or minerals - and may be ingested and assimilated by an organism to produce energy, stimulate growth, and maintain life are converted alternative forms.
The semantics of food are being handled by FOODON http://purl.obolibrary.org/obo/foodon.owl
A bakery is a building in which raw flour-based food is baked in an oven to produce food products such as bread, cakes, pastries, and pies. These products are often sold from the bakery itself.
A bakery is a food processing building and a 'food shop' at the same time. This needs to be resolved.
A brewery is a building in which alcoholic beverages are produced by brewing, that is, steeping a starch source (commonly cereal grains) in water and fermenting the resulting sweet liquid with yeast. At times, the products are also sold from the brewery.
A product which is composed primarily of paper.
A paper product which is used as legal tender in economic or other monetary trasactions.
bank note
An air filter is a device that removes some substance from air.
This is a general definition derived from the definitions for particulate, chemical, and other air filters. Subclasses should be created if needed.
A building within which logs are cut into lumber products.
A portion of soil which is part of a cropland or a rangeland biome.
A material entity which other material entities in an environmental system are primarily or partially composed of.
Everything under this parent must be a mass noun (i.e. not countable). All subclasses are to be understood as being composed primarily of the named entity, rather than restricted to that entity. For example, "ENVO:water" is to be understood as "environmental material composed primarly of some CHEBI:water".
Instances of this class are portions of environmental materials, such as seawater in bucket, a water parcel in the photic zone of a lake, or the concrete that composes a building part. Instances of these portions may have fiat or non-fiat boundaries. For example, a water parcel has not physical boundaries, while the seawater in a bucket is bounded by the internal surfaces of the bucket.
A layer of some material entity which is adjacent to one or more of its external boundaries and directly interacts with its immediate surroundings.
This class is distinct from a geometric surface, which is two-dimensional. The idea of "uppermost" may be problematic. Further, the definition of layer (the superclass of surface in rev 133) references surface. This may be another issue. Perhaps this can be made into an inferred class using 'bounding layer of' some material entity, note that 'bounding layer' implies containment, which may not be valid here.
A facility in which animals are confined within enclosures and displayed to the public, and in which they may also be bred.
Anthropogenic material in or on which organisms may live.
An environmental material which is a liquid or semi-liquid mixture of water and some combination of soil, silt, and clay particles.
A well which provides access to groundwater held in an aquifer.
Particulate environmental material which is composed primarily of particles of sand with only minor proportions of other substances.
This definition is intentionally ambiguous to support the multiple thresholds set by different authorities. Some authorities consider as sands soil material that contains 85% or more sand; the percentage of silt plus 1.5 times the percentage of clay does not exceed 15. coarse sand (sable grossier) 25% or more very coarse and coarse sand, and less than 50% any other one grade of sand.
An environmental material which is composed primarily of pieces of gravel.
As with all size-based classifications, there is considerable variation in what is considered gravel.
A marine biome which is determined by an ocean.
Ocean biomes are determined by major bodies of saline water, principal components of the hydrosphere. Approximately 71% of the Earth's surface is covered by ocean, a continuous body of water that is customarily divided into several principal oceans and smaller seas. More than half of this area is over 3,000 metres (9,800 ft) deep. Average oceanic salinity is around 35 parts per thousand (ppt) (3.5%), and nearly all seawater has a salinity in the range of 30 to 38 ppt.
An environmental material which is composed primarily of particles.
particulate matter
particulate environmental material
Environmental material derived from living organisms and composed primarily of one or more biomacromolecules.
A forest ecosystem which is undergoing climactic ecological succession.
A woodland biome is a terrestrial biome which includes, across its entire spatial extent, woody plants spaced sufficiently far apart to allow light penetration to support communities of herbaceous plants or shrubs living closer to the woodland floor.
A shrubland biome is a terrestrial biome which includes, across its entire spatial extent, dense groups of shrubs.
A grassland ecosystem in which dominant ecological communities have reached their climax successional state.
A desert ecosystem which is undergoing climactic ecological succession.
A tundra ecosystem which is undergoing climactic ecological succession.
A mangrove biome is a terrestrial biome which includes, across its spatial extent, mangrove plants (Rhizophoraceae). Mangrove plants are able to withstand high levels of salinity as well as regions of anoxia and frequent tidal inundation. Mangrove biomes often occur near tropical and sub-tropical estuaries and depositional marine coastal environments where fine sediments (often with high organic content) collect in areas protected from high energy wave action.
Preliminary definition. Depending on whether mangrove trees or shrubs are present, this class could be a child of shrubland biome or woodland biome. Consider creating the appropriate classes.
An anthropogenic terrestrial biome is a terrestrial biome which has community structures determined by human activity.
A cropland ecosystem which is undergoing climactic ecological succession.
A village biome is an anthropogenic terrestrial biome which contains settlements such as villages, towns, and/or small cities and which is primarily used for agricultural activity.
Villages are also described as agricultural settlements with greater than 100 persons per square kilometre; however, no upper limit is defined.
A rangeland biome is an anthropogenic terrestrial biome which is primarily used for the rearing and grazing of livestock.
A dense settlement biome is an anthropogenic terrestrial biome which is primarily used for human habitation, recreation, and industry within built structures with little other land use.
A biome which is determined by a freshwater lake.
A freshwater biome which is determined by a freshwater river.
A system which has the disposition to environ one or more material entities.
In ENVO's alignment with the Basic Formal Ontology, this class is being considered as a subclass of a proposed BFO class "system". The relation "environed_by" is also under development. Roughly, a system which includes a material entity (at least partially) within its site and causally influences that entity may be considered to environ it. Following the completion of this alignment, this class' definition and the definitions of its subclasses will be revised.
A material entity which 1) is spatially continuous, 2) is composed of material of comparable thickness, composition, and physical properties, and 3) is physically distinct from adjacent portions of environmental material.
An anthropogenic environment is an environmental system which is the product of human activity.
Unsatisfactory definition here. Must consider the threshold that makes an environmental system anthropogenic.
A marine environment and enviroment which is determined by a marine water body.
A planetary surface is a surface layer where the solid or liquid material of a planet comes into contact with an atmosphere or outer space.
a useful class: this can be used to define sub-terrestrial and sub-marine entities
A field used for the cultivation of corn or related crop plants.
Requested in Issue 112 as part of the curation of metagenome submissions in the European Nucleotide Archive.
This class was created to accommodate "fields" from agricultural fields to marine mesoscale eddy fields. Thus, it has a very broad definition which makes it less than informative when annotating. Please consider using or requesting an appropriate subclass.
A site which has its extent determined by the presence or influence of one or more components of an environmental system or the processes occurring therein.
Formerly, this class was an experimental class and a subclass of "environmental feature". It is now aligned to BFO. The class was not obsoleted as the core semantics maintained their stability through its transition.
A house is a building that provides a dwelling-place for a living entity.
The provisioning of a dwelling-place can perhaps be modelled as a role.
A human house is a house which provides a dwelling-place for humans.
A building part is a construction which is part of a building.
Not recommended for annotation. This class is likely to be made into an inferred class as its subclasses are distributed among more meaningful superclasses (i.e. ceiling is_a surface layer). See for example, "building floor". The boundaries between building parts may be bona fide or fiat.
A bathroom is a room which contains a washbasin or other fixture, such as a shower or bath, used for bathing by humans.
A building part which is separated from other building parts by one or more interior walls and, optionally, outdoor areas by one or more exterior walls.
A constructed barrier is a freestanding wall, berm, or fence built to limit movement of entities across a boundary.
Glass is an amorphous (non-crystalline) solid which is often transparent.
This class refers to all forms of glass. For the familiar form present in window panes and drinking glasses, consider silica-based glass.
Silica-based glass is a glass composed primarily of silicon dioxide, the primary constituent of sand.
Silica-based glasses are the most common manufactured variety of glass.
A building floor is a surface layer which is part of a building and used for walking.
To be more precise, a subfloor and a floor covering may be specified. Please request these classes and propose definitions if they are needed.
A solid, cylindrical object or column with its length greater than its diameter.
This was created in response to a user request, but it is an odd class in that it specifies a shape rather than a particular material entity. It may, therefore, be deprecated when more meaningful or sensible alternatives become apparent.
A factory (previously manufactory) or manufacturing plant is an industrial site, usually consisting of buildings and machinery, or more commonly a complex having several buildings, where workers manufacture goods or operate machines processing one product into another.
A table is a form of furniture with a flat horizontal upper surface used to support objects, for storage, show, and/or manipulation.
table
A desk is a table which is intended for information-manipulation tasks, including writing and use of interactive electronics.
The intentional nature of this definition is problematic, but the restricted range of activities visited upon a desk is of interest.
desk
A piece of furniture is a movable object intended to support various human activities such as seating (e.g., chairs, stools and sofas) and sleeping (e.g., beds).
The assumption is that furniture is manufactured, which is arguable. Further, according to Black's Law Dictionary (http://thelawdictionary.org/furniture/) many classes can be subclasses of 'piece of furntiure': "This term includes that which furnishes, or with which anything is furnished or supplied; whatever must be supplied to a house, a room, or the like, to make it habitable, convenient, or agreeable; goods, vessels, utensils, and other appendages necessary or convenient for housekeeping; whatever is added to the interior of a house or apartment, for use or convenience. Bell v. Holding, 27 Ind. 173.The term “furniture” embraces everything about the house that has been usually enjoyed there, including plate, linen, china, and pictures. 1 Endicott v. Endicott, 41N. J. Eq. 96, 3 Atl. 157.The word “furniture” made use of in the disposition of the law. or in the conventions or acts of persons, comprehends only such furniture as is intended for use and ornament of apartments, but not libraries which happen to be there, nor plate. Civ.Code La. art. 477." However, this would eventually be absurd and limit other groupings. Perhaps some sort of 'furnishing' BFO:function would be a better way to handle this.
piece of furniture
A motor vehicle is a vehicle which is propelled by an engine or motor and that does not operate on rails.
motor vehicle
A truck is a motor vehicle which, as its primary funcion, transports cargo rather than human passangers.
truck
A vehicle is a mobile machine which transports people or cargo.
vehicle
A lentic water body is a water body in which the accumulated water, in its totality, has very little to no directed flow.
lentic water body
A lotic water body is a water body in which the accumulated water, in its totality, is flowing.
lotic water body
A manufactured structure made of interspaced structural elements such as metal or wooden bars or wires held together such that they may be used to confine, contain, or protect something.
manufactured cage
A drylot is an enclosure of limited size usually bare of vegetation and used for fattening livestock.
drylot
A feedlot is a plot of land on which livestock are fattened for market
feedlot
planetary landmass
A settlement with a high density of buildings and inhabitants.
The thresholds for what makes a settlment "dense" can be determined as needed. If there is a specific threshold that should be added to ENVO, please make a new class request.
dense settlement
water mass
Hydrological precipitation is a process during which any product of the condensation of atmospheric water vapour is pulled to the planetary surface by gravity.
"process" is included in the label to make it clear that we are not referring to the precipitated material (e.g. snow, rain, sleet)
hydrological precipitation process
An area of a planet's surface which is primarily composed of bedrock, desert pavement, scarp rock, talus, material exposed by slides, volcanic material, glacial debris, sand, material exposed during strip mining, gravel, and other accumulations of earthen material in contact with an atmospheric column extending from the planetary boundary layer to the planet's exosphere with little to no physical obstruction.
According to the NLCD 2011, areas of barren land generally have less than 15% cover of vegetation. A specific threshold is not asserted in this definition.
area of barren land
A temperature that inheres in some portion of air.
obsolete air temperature
A village is a clustered human settlement or community, larger than a hamlet but smaller than a town, with a population ranging from a few hundred to a few thousand. Though often located in rural areas, the term urban village is also applied to certain urban neighbourhoods. Villages are normally permanent, with fixed dwellings; however, transient villages can occur. Further, the dwellings of a village are fairly close to one another, not scattered broadly over the landscape, as a dispersed settlement.
village
A material entity which is composed of one or more chemical entities and has neither independent shape nor volume but tends to expand indefinitely.
gaseous environmental material
A material part of an astronomical body.
Material parts of astronomical bodies generally have boundaries formed by discontinuities in qualities, composition, or other physical characterisitcs. These boundaries are sometimes sharp, and sometimes diffuse, with different classification systems and communities declaring varying thresholds (e.g. for where a shoreline, forest, or other entity begins and ends). However, some boundaries are declared by fiat - that is, by arbitrary human convention or decree - particularly by regulatory or other authorities and communities of practice. The classes in this hierarchy attempt to offer generalisable definitions that allow multiple classfiication systems to map to and interoperate through. If desired, we can create classes that declare thresholds used by a given authority or community under the more generic ones, annotated with source information.
astronomical body part
An environmental material which is in a solid state.
This is a defined class: its subclasses will not be asserted, but filled by inference.
solid environmental material
An environmental material which is in a liquid state.
This is a defined class: most of its subclasses will not be asserted, but filled by inference.
liquid environmental material
A precipitation process is a process in which a portion of some substance segregates from a material in which that substance or its precursors were dissolved or suspended in and settles due to a force such as gravity or centrifugal force.
precipitation process
An animal house which is only partially surrounded by a building envelope.
open animal house
An animal house which has a complete building envelope.
closed animal house
A manufactured cage which may be used to confine, contain, or protect an animal.
chicken cage
animal cage
A petting zoo is a zoological garden which contains domesticated non-human animals and some wild non-human animals that are docile enough for humans to touch and feed.
Petting zoos are often nested within a zoological garden featuring wild non-human animals, not docile enough for humans to touch.
petting zoo
An artificial channel which transports unwanted water or waste liquids away from their source, either to a more useful area, a receptacle, or into sewers or stormwater mains as waste discharge to be released or processed.
plumbing drain
A facility in which non-human animals are slaughtered and processed for human consumption.
slaughter plant
abattoir
A building which is used to care for a human child during the working day by a person, outside the child's immediate family, other than that child's legal guardians.
daycare building
This is a kind of day care facility. A facility need not be a building.
day care building
A building in which fish are subject to a series of operations to prepare them for human consumption.
This is a kind of fish processing facility. Facilities need not be buildings, factory ships may be considered fish processing facilities.
fish processing building
A building in which nursing aides and skilled nurses provide care and treatment to residents who have significant difficulty coping with the required activities of daily living.
old people's home
nursing home
A human house which serves as a long-term shelter for its inhabitants and within which they store personal property.
This term is not to be used for hotels, hostels, inns and the like, which provides shorter-term stays.
residential building
A building within which food and drink are prepared and served to customers in exchange for money or other goods and/or services.
restaurant
A part of an ecosystem which may be or has been used for one or more overnight stays by humans sheltering in tents, camper vans, caravans, or improvised shelters.
campground
A campground which has been modified by humans to provide and maintain facilities for camping such as fire pits, road access, latrines, and garbage bins.
dedicated campground
A campground which has no pre-existing facilities installed or maintained by humans, usually found outside of anthropised ecosystems.
impromptu campground
A manufactured product which may hold a volume of heated water suitable for one or more humans to bathe in, usually for the purposes of hydrotherapy or pleasure.
hot tub
Wastewater which is produced by industrial activity and which contains chemical contaminants other than those associated with urine and fecal matter.
industrial wastewater
A construction which is designed to hold water in which humans may swim or perform other leisure activities.
constructed swimming pool
A hydraulic-engineering installation which transports water - in specified amounts, of a specified quality, and in accordance with a water-consumption plan - from a source of supply into a conduit.
Sources of water include rivers, lakes, reservoirs, and other water bodies. Conduits include canals, pipelines, and tunnels. Water intakes typically transport water for purposes of hydroelectric power engineering, water supply, or irrigation.
water intake
A building which provides the site for food services with little or no waiting staff furnishing table service.
cafeteria
A food shop which sells a selection of food products that are not typical dietary components of the human population it is co-located with.
deli
The food products sold in a delicatessen are often considered unusual by the majority of its customers and may come from foreign food supplies which are not widely imported into its region of operation.
delicatessen
A truck which is equipped to cook and sell food.
Due to the facilities on board, food trucks are often larger than other trucks with comparable mechanics.
food truck
A restaurant which provides prepared meals or other food products that the purchaser must eat off its premises.
take-out restaurant
A booth with an open window on one side.
This definition of kiosk is characteristic of the Western hemisphere and used in English-speaking countries.
kiosk
A kiosk from which food products are sold.
food kiosk
A food shop in which food products are the primary offer for sale or trade.
grocery store
A part of an ecosystem which has been allocated to host a gathering of people for multiple entertainment or commercial activities.
Fairgrounds, or parts thereof, may be constructed (e.g. concreted over) or be natural (e.g. clearings or heaths), thus land use is the key differentia.
fairground
A fairground which is used to exhibit agricultural technology, livestock, and farm-related activity.
agricultural fairground
A part of an ecosystem where people gather for the purchase and sale of provisions, livestock, and other goods.
public market
As with campgrounds and fairgrounds, land use is the key differentia here. The regularity of marketplace activities may provide a differentia for further growth of this branch.
market
A food shop in which the food products on offer are restricted to those produced in a region and cultural setting other than that of the shop's locality.
ethnic food shop
An exchangeable device which can be connected to a plumbing system to deliver and drain water.
plumbing fixture
A plumbing fixture which is bowl-shaped and used for washing hands, dishwashing, and other purposes.
sink fixture
A plumbing fixture which may serve as a container for water in which humans or other animals may bathe.
Of course, there are other uses for bathtubs.
bathtub fixture
A plumbing fixture within which a human or other animal may bathe under a spray of water.
Indoors, there is a drain in the floor. Most showers have temperature, spray pressure and adjustable showerhead nozzle. Showering is common in Western culture due to the efficiency of using it compared with a bathtub. Its use in hygiene is, therefore, common practice. A shower uses less water on average than a bath: 80 litres for a shower compared with 150 litres for a bath.
shower fixture
An environmental system which is determined by materials bearing roughly homogeneous qualities.
Organisational class. Not intended for annotation.
environmental system determined by a quality
An environmental system which is determined by a living organism.
environmental system determined by an organism
An environmental system determined by an animal.
animal-associated environment
An environmental system determined by part of a living or dead animal, or a whole small animal.
environment associated with an animal part or small animal
An environmental system which includes both living and non-living components.
This class will be primarily filled by inference, any environmental system which necessarily includes living parts should be autoclassified here.
ecosystem
An environmental zone which is bounded by material parts of a land mass or the atmosphere or space adjacent to it.
terrestrial environmental zone
An ecosystem in which grasses (Graminae) are the dominant form of vegetation and determine the system's structure and dynamics.
grassland ecosystem
A building which is primarily used to facilitate the buying or selling of goods or services.
"Commerce includes legal, economic, political, social, cultural and technological systems that are in operation in any country or internationally."
commercial building
An ecosystem which is determined by communities of plants with a tree growth form and in which members of those communities form continuous or discontinuous regions of canopy cover.
forest ecosystem
An ecosystem which 1) is determined by communities of annual crops, perennial woody crops, or by actively tilled land, 2) is primarily used for agricultural activity, and 3) contains no village or larger human settlement.
cropland ecosystem
A layer which is primarily composed of some solid material, allowing for non-solid parts such as interstitial pockets of gas or liquid.
solid layer
A vegetated area is a geographic feature which has ground cover dominated by plant communities.
A surface layer which is composed primarily of solid environmental material.
solid surface layer
A body of water which is primarily composed of saline water.
This class has its subclasses populated by inference.
saline water body
An ecosystem which 1) typically has monthly average temperatures below 10 degrees Celsius 2) has a low evapotranspiration ratio 3) is dominated by treeless terrain, covered by communities of low-growing vegetation such as dwarf shrubs, sedges and grasses, mosses, and lichens, 4) contains areas of soil underlain by permafrost with a thin active layer and 5) occurs in both polar and alpine regions (i.e., both high latitudes and high altitudes), and 5) does not have permanent snow or ice cover.
Tundra ecosysems are often underlaid by permafrost, with the result that drainage is bad and the soil may be saturated for long periods. It does not have a permanent snow-ice cover. Productivity is low in this biome because of the extremes of climate.
tundra ecosystem
A research facility in which systems of manufactured products control internal conditions and in which scientific or technological research, experiments, and measurement may be performed.
research laboratory
laboratory facility
A liquid astronomical body part which is continuous and is delimited by physical discontinuities or non-liquid boundaries.
body of liquid
A part of an astronomical body which is primarily composed of liquid material.
liquid astronomical body part
A part of an astronomical body which is primarily composed of fluid.
fluid astronomical body part
A building which is primarily used for the long-term habitation of humans.
domestic building
A surface layer where the solid or liquid material of an astronomical body comes into contact with an atmosphere or outer space.
surface of an astronomical body
A layer which separates two portions of environmental material which possess 1) differing compositions, 2) a discontinuity of some property, or 3) some derivative of some property in a direction normal to the interface.
interface layer
An ecosystem in which the composition, structure, and function of resident ecological assemblages are primarily determined by a desert.
desert ecosystem
A large continuous area of land, either surrounded by sea or contiguous with another landmass.
landmass
A part of an astronomical body which is composed of a continuous medium bearing liquid, gaseous, and solid material in variable quantities.
compound astronomical body part
A surface layer of an astronomical body which is primarily composed of solid material and is not covered by oceans or other bodies of water.
land
aquatic ecosystem
marine ecosystem
freshwater ecosystem
An ecosystem which primarily occurs on land.
terrestrial ecosystem
A material entity which has been assembled through the intentional, instinctual, or deliberately programmed efforts of an organism or machine.
construction
An ecosystem which is formed as a result of human activity or impact.
anthropised ecosystem
An anthropised ecosystem which is determined by the presence of humans and their constructions.
human settlement
A construction in which eggs are hatched under artificial conditions.
hatchery
A landform which occurs on the surface of an astronomical body.
The usage of "surface" here aligns with that of planetary surface: in contact with the atmosphere or space. The extent of the "surface" can vary. For rocky planets like Earth, astrogeologists consider the crust as the surface.
surface landform
A solid astronomical body part which has been formed from and is composed primarily of the matter of that astronomical body.
Landforms may be natural or anthropogenic. This term has often has loose usage when referencing entities which are either subterranean or submerged below water bodies. In some cases, oceans themselves are considered landforms. Here, we have provided subclasses to resolve this ambiguity, but place oceans and other water bodies elsewhere.In later revisions, this hiearchy is likely to be reordered based on the formation processes of the entities within it.
landform
reef
A textile is a manufactured product comprised of a network of natural or artificial fibers (often referred to as thread or yarn).
An organic material which is primarily composed of some natural bodily fluid or secretion such as blood, semen, saliva, blood plasma, intracellular and interstitial fluids.
A bodily fluid material which is composed primarily of excreta, bodily fluids consisting of matter which contains the waste products of biological processes, including urine or feces, discharged from an organism's body.
Food material which can be used to meet nutritional requirements of animals, particularly livestock such as cattle, goats, sheep, horses, chickens and pigs.
Most animal feed is from plants but some is of animal origin. Fodder refers particularly to food given to the animals (including plants cut and carried to them), rather than that which they forage for themselves. It includes hay, straw, silage, compressed and pelleted feeds, oils and mixed rations, and also sprouted grains and legumes.
Contaminated animal feed is an animal feed that has become contaminated with or come contact with microorganisms or toxic chemicals.
A mixture of crushed and coarsely ground bones that is used as an organic fertilizer for plants and formerly in animal feed.
Food material which can be used to meet nutritional requirements of plants.
A textile comprised of a pliable material made usually by weaving, felting, or knitting natural or synthetic fibers and filaments.
An environmental material which is unable to resist shear forces and continuously deforms when subject to them.
fluid environmental material
A process in which includes the components of an environmental system as participants.
This is a convenience class for organisation and should not be used for annotation.
environmental system process
A process during which material is displaced from its original location and transported either to a new location or back to the original location.
Experimental class for structural purposes not recommended for annotation.
material transport process
Sediment which has been transported through the marine water column, settling on the seafloor.
Particles of marine sediment are primarily generated by 1) processes in terrestrial systems and transported to the marine realm by the action of rivers or aeolian processes (amongst other routes) , 2) marine organisms, 3) chemical processes in seawater, or 4) cosmogeneous input.
marine sediment
A structure which traverses a mass of one or more environmental materials, and encloses a roughly tubular site.
channel
A vehicle which locomotes using rails and consists of a series of connected compartments used to transport passengers or cargo.
train
A train which is capable of and used for passenger transport.
passenger train
A passenger train which runs along an undergroud rail system.
subway
tube train
underground train
London Underground
SkyTrain
Tube
U-Bahn
Underground
metropolitana
subway train
A building part which is a narrow hall or passage in a building with rooms leading off it.
hall
passage
hallway
building corridor
A building which accomodates conferences.
conference center
conference centre
conference venue
A human construction in which people are educated.
educational facility
An institutional building in which students are educated.
school
school building
An institutional building which temporarily houses homeless people.
homeless shelter
A human construction in which healthcare is provided.
health facility
medical facility
healthcare facility
A healthcare facility which is used for short-term patient care.
ACC
ACF
acute care center
acute care facility
A healthcare facility in which patients are medically assessed.
CAC
clinical assessment centre
clinical patient assessment center
clinical patient assessment centre
clinical patient assessment facility
A healthcare facility which 1) is located in part of a hospital and 2) is used by an organizational unit within a hospital.
hospital ward
hospital unit facility
A room in which emergency medical care is provided.
A&E room
ER room
EW room
accident & emergency department room
casualty department room
emergency department room
emergency room room
emergency ward room
emergency unit room
A hospital unit facility which is used to provide intensive medical care.
ICU
ICW
ITU
critical care unit
critical care ward
intensive care ward
intensive therapy unit
intensive treatment unit
intensive treatment ward
intensive care unit facility
A room which is used for patient care during a patient's visit or stay in a healthcare facility.
patient-care room
examination room
patient bed room
patient room
A healthcare facility which is used to provide outpatient health care services.
clinic
ambulatory care clinic
outpatient clinic
medical clinic
A medical clinic which is used to provide family medicine services.
GP clinic
GP office
family care clinic
family doctor clinic
family doctor office
family medicine clinic
family medicine office
general medicine clinic
general practice clinic
general practice office
family practice clinic
A residential building which is used to provides long-term care for residents.
LTC center
LTC centre
LTC facility
long-term care center
long-term care centre
long-term care facility
A long-term care facility which is used to provide care for people with complex health needs, and which typically has at least one caregiver in attendance twenty four hours a day.
residential care facility
group home facility
A building which is used by an organization which serves a long-established role in human society.
This term needs further consideration and development as semantics of institution are ambiguous at scale - e.g. are hotels institutional buildings?
institutional building
A market which is used for the sale and purchase of perishable goods.
wet market
A human construction which is used to forcibly confine humans.
correctional center correctional centre
correctional facility
detention center
detention centre
gaol
jail
lock-up
penitentiary
remand center
remand centre
prison facility
A manufactured product consisting of a duct opening which allows air to circulate.
vent
air vent
A poll which is attached to the head, foot, or side of a bed frame.
adult portable bed rail
assist bar
bed handle
bed rail
bed side rail
grab bar
half rail
hospital bed rail
safety rail
side rail
bedrail
A manufactured product consisting of a panel on which control or monitoring instruments are set.
console
control board
control unit
display board
display panel
indicator panel
instrument board
instrument panel
panel
control panel
A manufactured product consisting of a handle used to open or close a door.
door knob
door handle
A pole which provides stability or support when grasped by the hand.
rail, railing
hand rail
handrail
A switch which turns a light on or off.
switch, dimmer switch
lightswitch
light switch
A manufactured product which is a storage compartment with a lock.
lockable cabinet
lockable cupboard
locking cabinet
locking cupboard
locker
A switch which allows patients in health care settings to alert a nurse or other health care staff member.
nurse call cord
nurse call button
Steel which is composed primarily of a corrosion resistant alloy of iron and chromium.
inox steel
stainless
stainless steel
A paper product which is thin translucent paper.
tissue
Tissue paper is often used for wrapping or for protecting delicate articles.
tissue paper
A plumbing fixture which is bowl-shaped, part of a toilet fixture, and capable of contain human waste until it is disposed of.
lavatory bowl
toilet bowl
A manufactured product which is composed of one or more glass or other transparent or semi-transparent materials set inside a frame, and installed in wall, door, roof or vehicle surfaces to allow the passage of light, and sometimes air.
casement
casement window
pane
sash
sash window
windowpane
window
A manufactured product which is composed of a hinged, sliding, or revolving barrier which is installed at the entrance to a building, room, vehicle, or in the framework of a cabinet.
door
A paper product which is a thin sheet material made of processed cellulose fibres.
paper
paper sheet
sheet of paper
An environmental material consisting of organic matter from plants and/or animals that is used in agriculture as fertilizer.
animal manure
compost
farm slurry
green manure
liquid manure
Most manure consists of animal feces; other sources include compost and green manure.
manure
A device which can connect, disconnect, or divert current in an electrical circuit.
switch
A manufactured product which is an alloy of iron and which typically contains a few tenths of a percent of carbon.
steel
An environnmental material which 1) is composed primarily of polymers with high molecular mass and 2) once deformed does not spontaneously return to its original shape.
Plastik
plastica
塑膠
Kunststoff
envoPlastics
"High molecular mass" can be ambiguous as it does not set a threshold for what is considered "high". Here we make no commitment to a threshold.
plastic
A plastic which is composed primarily of polymers produced by a manufacturing process.
manufactured plastic
synthetic plastic
Transmission of a disease agent (infectious pathogen, toxic chemical, etc.) from a source that is common to those who acquire the disease. Common vehicles include air, water, food, injected substances. Legionellosis is an example of common vehicle spread in air that has passed through air conditioning equipment contaminated by the causal organism. HIV disease and hepatitis B and C can be spread among illicit drug users by the common vehicle of contaminated needles and syringes. Cholera and many other waterborne diseases are spread by the common vehicle of contaminated water.
common vehicle transmission
A role that inheres in a material that is input as the subject of interest in a scientific technique - either as an entity about which data is generated in an assay or study, or an entity that is transformed or modified in a material processing technique (e.g. the source from which a biological sample is taken)
An interaction between an exposure stressor and an exposure_receptor.
The condition of an organism in all aspects (e.g., functional or metabolic efficiency).
See technical discussion about logic of assigning health status: https://www.w3.org/2001/sw/BestPractices/OEP/Lists-of-values-20040625/
condition
medical condition
medical state
Damion Dooley note: GenEpiO includes various health status descriptors here; many are annotated as included in the American AHA HIPPA or United Kingdom NHS terminologies. The challenge is to map them or order them in such a way that merged data can be analyzed.
subject health status
Condition
The process of drawing in by breathing.
inhalation
Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential
MIxS
A symptom onset date is a date-time entity that marks the start of one or more reported symptoms pertaining to an episode of human or animal illness
symptom onset date
A substance, usually composed primarily of carbohydrates, fats, water and/or proteins, that can be eaten or drunk by an animal or human being for nutrition or pleasure.
Food material for humans and animals which is processed with the intention that it be consumable as a whole or added to other food products.
food product
foodon product type
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
This class includes food products which are derived from or produced by a plant.
plant food product
A food product made from domestic pig meat (Sus domesticus or Sus scrofa scrofa).
pork meat food product
A food product that is derived from some cow.
cow food product
A cut of meat (a meat chop) cut perpendicularly to the spine of the pig and usually containing a rib or part of a vertebra, served as an individual portion.
pork chop food product
A food product which is derived from or produced by an animal that has a vertibrae.
vertebrate animal food product
A food product made from domesticated bird meat.
poultry meat 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
A food product derived from one or more microorganisms including bacteria, mold, and yeast.
microbial food product
invertebrate animal 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
A food product which is an output of a food cooking process.
food (cooked)
This food product type includes food products which are derived from a large, diverse group of photosynthetic organisms.
algal 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 animal food product
Beef that has been ground.
beef (ground)
A food product from a category of domestic birds kept for meat, eggs, and feathers including fowl such as chickens, turkeys, and waterfowls such as domestic ducks and geese and other meat birds such as pigeons and doves and games birds including pheasants.
A food product that is derived from some poultry.
poultry food product
A turkey meat food product is any food product made predominantly of turkey parts.
turkey meat food product
A fermentation process in which either carbohydrates, proteins or fats are modified through microbial, enzymatic and/or other biological process.
food fermentation
A cut of meat that is initially separated from the carcass of an animal during butchering.
animal primal cut
A product deriving from mahi-mahi or common dolphinfish (Coryphaena hippurus) also widely called dorado and dolphin.
dolphinfish food product
herring food product
Lamb meat food product is a meat product taken from a lamb, a sheep less than a year old.
lamb meat food product
food product by consumer group
sheep meat food product
tuna food product
A food product consisting of food material derived primarily from a single organism.
food product by organism
Any substance that can be consumed by an organism to satisfy nutritional or other health needs, or to provide a social or organoleptic food experience
food
foodstuff
nourishment
sustenance
This class is the top of FOODON's main food product hierarchy which is described in the https://www.foodon.org website, and can be searched in lookup services like https://www.ebi.ac.uk/ols/
food material
Roasting is a baking process when the food being baked is meats
meat roasting
A food evaporation process is the process of removing water from a food.
food evaporation process
A process involving the physical transformation of a food source or food product into some derived organic material or food product
food transformation process
Invertebrates are animals that neither possess nor develop a vertebral column (commonly known as a backbone or spine), derived from the notochord. This includes all animals apart from the subphylum Vertebrata.
invertebrate animal
Food material which has been categorized by a characteristic such as granularity or temperature.
food material by characteristic
A form of frying characterized by the use of minimal cooking oil or fat (compared to shallow frying or deep frying); typically using just enough oil to lubricate the pan. A pan fry takes place at lower heat than does a sauté.
shallow frying
A physical object quality which describes a characteristic of some food material.
food material characteristic
A cut of meat from a pig, that comes from the tissue along the dorsal side of the rib cage.
pork loin
cut of beef, british
beef rump cut (british)
A butchery cut of beef that is primal, sub-primal or a retail cut.
butchery cut of beef
A food product organized by the process which it results from.
food product by process
A method of precooking food where a liquid is heated to just below the boiling point. Often used to retard the spoiling of milk.
food scalding
A food product that is derived from some pig.
pig food product
pork food product
A fish fillet, from the French word filet meaning a thread or strip, is the flesh of a fish which has been cut or sliced away from the bone by cutting lengthwise along one side of the fish parallel to the backbone.
fish fillet
mahi mahi fillet
Pet food is plant or animal material intended for consumption by pets.
pet food
A whole breast that is obtained from a turkey.
turkey breast
barramundi food product
barramundi fillet
A herring fillet is a fillet cut of herring
herring fillet
A fillet cut of a tuna fish.
tuna fillet
A beef cut that is derived from the 6th, 7th and 8th rib of the rib primal.
beef short rib
Synbiotic claim refers to food ingredients or dietary supplements combining probiotics and prebiotics in a form of synergism that beneficially affect the host.
synbiotic claim
A cut of beef from the primal rib, one of the nine primal cuts of beef. While the entire rib section comprises ribs six through 12, a standing rib roast may contain anywhere from two to seven ribs.
beef prime rib roast
A fish steak, alternatively known as a fish cutlet, is a cut of fish which is cut perpendicular to the spine and can either include the bones or be boneless.
fish steak
A thin slice of meat from the leg or ribs of veal, pork, chicken, or mutton.
cutlet
A whole animal.
animal
A beef meat cut that has a flat-cut appearance.
beef steak
A beef primal cut that comes from the area below the backbone .
A portion of meat from either the short loin, the sirloin, or the tenderloin muscle area.
beef loin
A cut of beef corresponding to the psoas major muscle, which is very tender.
beef tenderloin
A boneless steak cut from the sirloin region
beef top loin steak
A beef steak that is prepared from the beef short loin. The maximum width of the tenderloin must be at least 1/2 inch (13mm) when measured parallel to the length of the backbone.
A steak of beef cut from the front of the short loin area.
beef T-bone steak
A beef steak that is prepared from the beef short loin. The maximum width of the tenderloin must be atleast 1.25 inches (3.2cm) when measured parallel to the length of the backbone.
A steak of beef cut from the back of the short loin area.
beef porterhouse steak
A steak cut of beef taken from the smaller end of the tenderloin, or psoas major of the cow carcass, usually a steer or heifer.
filet mignon (North America)
A butchery cut of chicken that is typically boneless.
chicken fillet
A fruit ripeness characteristic in which a fruit has surpassed ripeness and is undergoing decomposition.
overripe
A fruit ripeness characteristic in which a fruit has some ripe part(s) or is about to achieve full maturity.
slightly ripe
A pet food that has not been heat treated or otherwise preserved.
pet food (raw)
A food item intended to provide pleasure or reward to an animal, and which might not be nutritious.
pet treat
Food contact materials are materials that are intended to be in contact with food. These can be things that are quite obvious like a glass or a can for soft drinks as well as machinery in a food factory or a coffee machine.
food contact material
Cultivation of plants within a polytunnel or similar tunnel.
tunnel farming
The rearing of domesticated animals for food.
food animal rearing
An approach to animal husbandry designed to maximize production, while minimizing costs by keeping livestock such as cattle, poultry, and fish at high stocking densities, at large scale, and using automated feeding systems.
industrial livestock production
A technology-based approach toward food production that aims to provide optimal growing conditions throughout the development of a crop located within an enclosed growing structure such as a greenhouse or building.
controlled environment agriculture (CEA) production
aquaculture production
Aquatic farmed food production located offshore, in coastal areas or in freshwater lakes, open-net pens, or “cages”, that allow for free exchange between the farm and the surrounding environment.
aquaculture open-pen rearing
aquaculture closed containment pen rearing
The flesh of fish
fish meat
A meat made up from the beef cut is known as sirloin. Ground sirloin is ground sirloin meat.
ground sirloin
A Japanese cooking method in which food is broiled or grilled with a glaze of soy sauce, mirin, and sugar.
teriyaki cooking method
An animal meat (cut) and an output of simple random sampling.
random sample animal meat cut
A heating container process in which the container conducts heat by being in proximity to an open flame, a hot surface or an oven.
direct heating of container
A heating container process in which the temperature of contained liquid is raised to a threshold.
heating liquid in container
cut of beef, mexican
A cut of beef and part of the sub-prime cut known as the chuck.
diezmillo
A Japanese term to describe a uniformly cut block of skinless and boneless seafood.
saku
A food product that is derived from some animal.
animal food product
A cut of meat which is long, narrow and boneless.
meat strip
A cutlet made from chicken breast.
chicken breast cutlet
A piece or pieces or amount of substance derived from one or more organisms.
organism piece
A severed part of an animal.
piece of animal
One or more pieces of animals.
piece(s) of animal
A smaller cut of meat that is obtained from the larger primal cut of an animal.
animal sub-primal cut
An animal meat cut that is derived from a sub-primal, individual muscle cut or minor primal cut.
animal retail cut
An organ that derives from an animal.
animal organ
A cut of beef that is initially separated from the carcass of a{n} {organism} during butchering.
beef primal cut
A retail cut of meat from an elk that is of a size for slicing into more than one portion and is suitable for roasting.
elk roast
A smaller cut of beef that is obtained from the larger primal cut of beef.
beef sub-primal cut
A retail cut of meat from a beef that is of a size for slicing into more than one portion and is suitable for roasting.
beef roast
A cut of beef that is derived from a sub-primal, individual muscle cut or minor primal cut.
beef retail cut
A retail cut of meat from a lamb that is of a size for slicing into more than one portion and is suitable for roasting.
lamb roast
A retail cut of meat from a pork that is of a size for slicing into more than one portion and is suitable for roasting.
pork roast
A retail cut of meat from a veal that is of a size for slicing into more than one portion and is suitable for roasting.
veal roast
A cut of meat that is initially separated from the carcass of a lamb during butchering.
lamb primal cut
A cut of meat that is initially separated from the carcass of a pork during butchering.
pork primal cut
A cut of meat that is initially separated from the carcass of a veal during butchering.
veal primal cut
A smaller cut of meat that is obtained from the larger primal cut of a lamb.
lamb sub-primal cut
A smaller cut of meat that is obtained from the larger primal cut of a pork.
pork sub-primal cut
A smaller cut of meat that is obtained from the larger primal cut of a veal.
veal sub-primal cut
A pork meat cut that is derived from a sub-primal, individual muscle cut or minor primal cut.
pork retail cut
A retail cut of meat from a lamb that is perpendicular to the spine, and usually containing a rib or riblet part of a vertebra.
lamb chop
A retail cut of meat from a pork that is perpendicular to the spine, and usually containing a rib or riblet part of a vertebra.
pork chop
A severed part of a pork.
piece of pig
A severed part of a beef.
piece of cow
One or more pieces of cows.
piece(s) of cow
A cut of meat that is initially separated from the carcass of a bison during butchering.
bison primal cut
A smaller cut of meat that is obtained from the larger primal cut of a bison.
bison sub-primal cut
A cut of meat that is initially separated from the carcass of a buffalo during butchering.
buffalo primal cut
A smaller cut of meat that is obtained from the larger primal cut of a buffalo.
buffalo sub-primal cut
A buffalo meat cut that is derived from a sub-primal, individual muscle cut or minor primal cut.
buffalo retail cut
A buffalo meat cut that has a flat-cut appearance.
buffalo steak
A food product containing a quantity of iron large enough to make a significant contribution to nutritional needs.
iron rich label claim
A food product containing a quantity of vitamin A large enough to make a significant contribution to nutritional needs.
vitamin A rich label claim
A beef cut that comes from the 'round', the rear leg of the beef.
beef round
A raw beef round cut.
beef round (raw)
A beef cut that comes from the outside of the rear leg.
beef bottom round
A raw beef bottom round cut.
beef bottom round (raw)
A steak cut from the beef bottom round.
beef bottom round steak
A raw beef bottom round steak.
beef bottom round steak (raw)
A boneless beef bottom round steak.
beef bottom round steak (boneless)
A raw and boneless beef bottom round steak.
beef bottom round steak (boneless, raw)
A roast cut from the beef bottom round.
beef bottom round roast
A raw beef bottom round roast.
beef bottom round roast (raw)
A boneless beef bottom round roast.
beef bottom round roast (boneless)
A raw and boneless beef bottom round roast.
beef bottom round roast (boneless, raw)
A beef cut that comes from the inside of the rear leg.
beef top round
A raw beef top round cut.
beef top round (raw)
A steak cut from the beef top round.
beef top round steak
A raw beef top round steak.
beef top round steak (raw)
A boneless beef top round steak.
beef top round steak (boneless)
A raw and boneless beef top round steak.
beef top round steak (boneless, raw)
A beef top round steak in which the top cap portion has been separated off.
beef top round steak (cap off)
A raw beef top round steak in which the top cap portion has been separated off.
beef top round steak (cap off, raw)
A raw and boneless beef top round steak in which the top cap portion has been separated off.
beef top round steak (cap off, boneless, raw)
A roast cut from the beef top round.
beef top round roast
A raw beef top round roast.
beef top round roast (raw)
A boneless beef top round roast.
beef top round roast (boneless)
A raw and boneless beef top round roast.
beef top round roast (boneless, raw)
A beef cut that comes from the round primal, and is found on the front end of the rear leg.
beef sirloin tip
A raw beef sirloin tip cut.
beef sirloin tip (raw)
A roast cut from the beef sirloin tip.
beef sirloin tip roast
A raw beef sirloin tip roast.
beef sirloin tip roast (raw)
A steak cut from the beef sirloin tip.
beef sirloin tip steak
A raw beef sirloin tip steak.
beef sirloin tip steak (raw)
A roast that derives from beef sirloin tip and only consists of M.vastus lateralis.
beef sirloin tip side roast
A raw beef sirloin tip side roast.
beef sirloin tip side roast (raw)
A steak cut from the beef sirloin tip side roast.
beef sirloin tip side steak
A raw beef sirloin tip side steak.
beef sirloin tip side steak (raw)
A roast that derives from beef sirloin tip and only consists of M.rectus femoris.
beef sirloin tip center roast
A raw beef sirloin tip center roast.
beef sirloin tip center roast (raw)
A steak cut from the beef sirloin tip center roast.
beef sirloin tip center steak
A raw beef sirloin tip center steak.
beef sirloin tip center steak (raw)
A beef cut that is an elongated muscle located in the center of the beef round cut, and thus is named “Eye.”
beef eye of round
A raw beef eye of round cut.
beef eye of round (raw)
A roast cut from the beef eye of round.
beef eye of round roast
A raw beef eye of round roast.
beef eye of round roast (raw)
A steak cut from the beef eye of round.
beef eye of round steak
A raw beef eye of round steak.
beef eye of round steak (raw)
A beef cut that extends from the neck to the fifth rib and includes the shoulder blade and upper arm.
beef chuck
A steak cut from the beef chuck tender.
beef chuck tender steak
A raw beef chuck tender steak.
beef chuck tender steak (raw)
A roast cut from the beef chuck tender.
beef chuck tender roast
A raw beef chuck tender roast.
beef chuck tender roast (raw)
A large, boneless cut that comes from between the ribs and backbone. It contains a mix of tender and somewhat tough muscles, which are fabricated into smaller cuts known as the chuck eye roll and the chuck under blade.
beef chuck roll
A raw beef chuck roll cut.
beef chuck roll (raw)
The top portion of the chuck roll that is separated from the under-blade section.
beef chuck eye roll
A raw beef chuck eye roll cut.
beef chuck eye roll (raw)
A roast cut from any portion of the chuck eye roll, typically the center.
beef chuck eye roast
A raw beef chuck eye roast.
beef chuck eye roast (raw)
A steak cut from the rib end only of the chuck eye roll.
beef chuck eye steak
A raw beef chuck eye steak.
beef chuck eye steak (raw)
A cut made by splitting a chuck eye roll in half lengthwise, resulting in two boneless, country-style ribs.
beef country-style rib
A raw beef country-style rib.
beef country-style rib (raw)
A meat cut that is the flatter portion of the Chuck Roll and is under the Chuck Eye Roll.
beef under blade
A thin muscle that lays in the seam between the chuck eye roll and under blade.
beef sierra steak
A raw beef sierra steak.
beef sierra steak (raw)
A beef cut from the center of the under blade.
beef denver steak
A raw beef denver steak.
beef denver steak (raw)
A roast cut in which under blade with other muscles and connective tissue are removed and either left whole or portioned.
beef denver roast
A beef denver roast that is raw.
beef denver roast (raw)
A large muscle system which lies dorsal and posterior to the elbow joint, ventral and posterior to the ridge of the scapula (blade bone) and is anterior to the 6th rib.
beef shoulder clod
A raw beef shoulder clod.
beef shoulder clod (raw)
The largest section of the shoulder clod that consist of the large muscle system of the thick end of the shoulder.
beef shoulder clod arm roast
A raw beef shoulder clod arm roast.
beef shoulder clod arm roast (raw)
A steak cut across the grain from the shoulder clod arm roast.
beef shoulder steak
A raw beef shoulder steak.
beef shoulder steak (raw)
A roast cut from the beef shoulder clod.
beef shoulder roast
A raw beef shoulder roast.
beef shoulder roast (raw)
A steak cut across the grain from the shoulder clod arm roast similar to the shoulder steak. Visible connective tissue and associated lean must be removed to qualify as a Ranch Steak.
beef ranch steak
A raw beef ranch steak.
beef ranch steak (raw)
The second most tender muscle in the animal that is derived from the shoulder clod. However, internal connective tissue should be removed to preserve that tenderness.
beef top blade
A raw beef top blade cut.
beef top blade (raw)
A beef steak cut that is end-to-end from the whole top blade.
beef top blade steak
A raw beef top blade steak.
beef top blade steak (raw)
A steak cut from the top blade, where the cutting method removes internal connective tissue from the whole Top Blade.
beef flat iron steak
A raw beef flat iron steak.
beef flat iron steak (raw)
A cut that is derived from the beef chuck and must include rib 2 through 5.
beef chuck short rib
A raw beef chuck short rib.
beef chuck short rib (raw)
A cut from beef chuck short rib that is an individual muscle and is boneless.
beef chuck short rib (boneless)
A raw and boneless beef chuck short rib.
beef chuck short rib (boneless, raw)
A beef cut that is the portion of the forequarter after removal of the rib, shortplate, foreshank and brisket.
beef square cut chuck
A raw beef square cut chuck.
beef square cut chuck (raw)
A beef steak cut that is identified by its 7-shaped bone. The 7-bone is made by cutting steaks across the scapula or blade bone.
beef 7-bone chuck steak
A raw beef 7-bone chuck steak.
beef 7-bone chuck steak (raw)
A beef roast cut that is identified by its 7-shaped bone. The 7-bone is made by cutting roasts across the scapula or blade bone.
beef 7-bone chuck roast
A raw beef 7-bone chuck roast.
beef 7-bone chuck roast (raw)
A steak cut from the flat bone portion of the blade that comes from ribs 4 through 5.
beef blade chuck steak
A raw beef blade chuck steak.
beef blade chuck steak (raw)
A roast cut from the flat bone portion of the blade that comes from ribs 4 through 5.
beef blade chuck roast
A raw beef blade chuck roast.
beef blade chuck roast (raw)
A beef roast that comes from the center portion of the Chuck Roll.
beef chuck roast
A raw beef chuck roast.
beef chuck roast (raw)
A beef steak that comes from the center portion of the Chuck Roll.
beef chuck steak
A raw beef chuck steak.
beef chuck steak (raw)
A beef cut that is adjacent to the arm and includes ribs 2 through 5.
beef cross-rib roast
A raw beef cross-rib roast.
beef cross-rib roast (raw)
A steak cut from the arm bone (humerus) of the upper forelimb.
beef chuck arm steak
A raw beef chuck arm steak.
beef chuck arm steak (raw)
A roast cut from the arm bone (humerus) of the upper forelimb.
beef chuck arm roast
A raw beef chuck arm roast.
beef chuck arm roast (raw)
A beef cut that is derived from the anterior end of the untrimmed chuck roll.
beef chuck neck roast
A raw beef chuck neck roast.
beef chuck neck roast (raw)
A roast cut is made during fabrication to square off the chuck roll.
beef chuck flap/edge roast
A raw beef chuck flap/edge roast.
beef chuck flap/edge roast (raw)
A raw beef loin cut.
beef loin (raw)
beef short loin
A raw beef short loin cut.
beef short loin (raw)
A raw beef T-bone steak.
beef T-bone steak (raw)
A cut refers to the group of muscles that extends the length of the Top Loin adjacent to the spine bone and on top of the finger bone.
beef strip loin (bone-in)
A raw beef strip loin that contains bone.
beef strip loin (bone-in, raw)
A group of muscles that extends the length of the top loin adjacent to the spine bone and on top of the finger bone.
beef strip loin (boneless)
A raw and boneless beef strip loin.
beef strip loin (boneless, raw)
A roast cut that comes from boneless beef strip loin.
beef strip roast (boneless)
A raw beef strip roast.
beef strip roast (boneless, raw)
A cut that comes from the top loin or strip loin into uniform steak.
beef strip steak (boneless)
A raw and boneless beef strip steak.
beef strip steak (boneless, raw)
A beef strip steak that contains bone material.
beef strip steak (bone-in)
A raw beef strip steak that contains bone material.
beef strip steak (bone-in, raw)
A smaller roasting option than Strip Roast.
beef strip petite roast
A raw beef strip petite roast.
beef strip petite roast (raw)
A thick cut but smaller diameter than beef strip steak.
beef strip fillet
A raw beef strip fillet.
beef strip fillet (raw)
A meat cut that is an inside muscle of the beef loin.
beef tenderloin (bone-in)
A raw beef tenderloin that contains bone material.
beef tenderloin (bone-in, raw)
A raw beef tenderloin steak.
beef tenderloin steak (bone-in)
beef tenderloin steak (bone-in, raw)
A cut that is a long, narrow, and lean muscle located within the loin, and is the most tender cut of beef.
beef tenderloin (boneless)
A raw and boneless beef tenderloin.
beef tenderloin (boneless, raw)
A roast cut from the larger tenderloin.
beef tenderloin roast
A raw beef tenderloin roast.
beef tenderloin roast (raw)
A boneless steak cut from the tenderloin.
beef tenderloin steak
beef tenderloin steak (raw)
A beef primal cut that is contained within the larger cut 'beef loin'. It is located between the short loin and the round and includes the hip section and ends at the socket of the pelvis.
beef sirloin
A raw beef sirloin cut.
beef sirloin (raw)
A beef cut that is located behind the beef short loin on the top back end of the animal.
beef top sirloin butt
A raw beef top sirloin butt.
beef top sirloin butt (raw)
A steak cut from the beef top sirloin butt that is flavourful and juicy.
beef top sirloin steak
A raw beef top sirloin steak.
beef top sirloin steak (raw)
A roast cut from the beef top sirloin.
beef top sirloin roast
A raw beef top sirloin roast.
beef top sirloin roast (raw)
A roast cut that is a smaller version of the larger {animal top sirloin roast
beef top sirloin petite roast
A raw beef top sirloin petite roast.
beef top sirloin petite roast (raw)
A cut that is portioned from a top sirloin steak.
beef top sirloin fillet
A raw beef top sirloin fillet.
beef top sirloin fillet (raw)
A beef steak cut from the triangle-shaped muscle that caps or covers the top sirloin.
beef culotte steak
A raw beef culotte steak.
beef culotte steak (raw)
A beef roast cut from the triangle-shaped muscle that caps or covers the top sirloin.
beef culotte roast
A raw beef culotte roast.
beef culotte roast (raw)
A beef sub-primal cut that is the lower portion of the sirloin section of the loin that contains three muscles that vary in tenderness.
beef bottom sirloin butt
A raw beef bottom sirloin butt.
beef bottom sirloin butt (raw)
A beef roast cut that is triangular shaped and is located at the tip of the sirloin.
beef tri-tip roast
A raw beef tri-tip roast.
beef tri-tip roast (raw)
A steak cut from the beef tri-tip section.
beef tri-tip steak
A raw beef tri-tip steak.
beef tri-tip steak (raw)
A small-sized sirloin steak.
beef petite sirloin steak
A raw beef petite sirloin roast.
beef petite sirloin steak (raw)
A small roast section of the bottom sirloin opposite the sirloin tip in the beef round.
beef petite sirloin roast
beef petite sirloin roast (raw)
A boneless cut with a hearty texture that’s a good source for fajita meat.
beef sirloin bavette flap
A raw beef sirloin bavette flap cut.
beef sirloin bavette flap (raw)
A steak cut from the beef sirloin bavette flap.
beef sirloin bavette steak
A raw beef sirloin bavette steak.
beef sirloin bavette steak (raw)
A beef cut that is located below the loin primal.
beef flank
A raw beef flank.
beef flank (raw)
A steak cut from the beef flank.
beef flank steak
A raw beef flank steak.
beef flank steak (raw)
A beef cut that is located on the underside of the animal below the rib primal. The end of the sixth through the twelfth rib is contained within the plate primal cut.
beef short plate
A raw beef short plate cut.
beef short plate (raw)
A beef steak that is a trimmed, boneless portion of the diaphragm muscle attached to the 6th through 12th rib on the underside of the short plate.
beef inside skirt steak
A raw beef outside skirt steak.
beef inside skirt steak (raw)
beef outside skirt steak
beef outside skirt steak (raw)
A beef steak that is a thick strip of meat located on the underside of the carcass and hangs between the last rib and the loin.
beef hanger steak
A raw beef hanger steak.
beef hanger steak (raw)
A beef cut that is usually taken from the flat end of ribs 6 through 9.
beef plate short rib
A raw beef plate short rib.
beef plate short rib (raw)
A beef cut that is located on the underside of the animal, below the chuck primal, which extends from between the forelegs to the plate.
beef brisket
A raw beef brisket.
beef brisket (raw)
A beef cut that is the leaner half of the whole brisket.
beef brisket flat half
A raw beef brisket flat half cut.
beef brisket flat half (raw)
A boneless beef brisket flat half cut.
beef brisket flat half (boneless)
A raw and boneless beef brisket flat half cut.
beef brisket flat half (boneless, raw)
A beef sub-primal cut that is the less lean half of the whole Brisket.
beef brisket point half
A raw beef brisket point half.
beef brisket point half (raw)
A portion of the beef leg, which is used extensively for movement.
beef shank
A raw beef shank.
beef shank (raw)
A cross-section of beef leg.
beef shank cross-cut
A raw beef shank cross-cut.
beef shank cross-cut (raw)
A center-cut cross-section of a beef leg
beef shank center cut
A raw beef shank center-cut.
beef shank center cut (raw)
A beef cut that is situated under the front section of the backbone and used primarily for support.
beef rib
A raw beef rib cut.
beef rib (raw)
A boneless cut from the rib primal.
beef ribeye roll (lip on)
A raw beef ribeye roll cut.
beef ribeye roll (lip on, raw)
A beef rib roast that has had the sixth through the twelfth rib bones removed leaving just the rib-eye muscle.
beef ribeye roast
A raw beef ribeye roast.
beef ribeye roast (raw)
A beef steak that is a cut from the rib-eye roast.
beef ribeye steak
A raw beef ribeye steak.
beef ribeye steak (raw)
A meat cut that is located above the short rib in the rib primal between the Chuck and Loin primal.
beef ribeye roll
beef ribeye roll (raw)
A smaller alternative to the ribeye roast.
beef ribeye petite roast
A raw beef ribeye petite roast.
beef ribeye petite roast (raw)
A smaller ribeye steak
beef ribeye fillet
A raw beef ribeye fillet.
beef ribeye fillet (raw)
A steak cut that is portioned from the ribeye cap roll by slicing at a right angle to the grain or muscle fibre direction.
beef ribeye cap steak
A raw beef ribeye cap steak.
beef ribeye cap steak (raw)
A cut that is portioned by slicing at a right angle to the grain or direction of muscle fibre.
beef ribeye cap roll
A beef ribeye cap roll cut that is raw.
beef ribeye cap roll (raw)
A beef cut that is situated under the front section of the backbone.
beef rib sub-primal
A raw beef rib sub-primal cut.
beef rib sub-primal (raw)
A raw beef short rib cut.
beef short rib (raw)
A beef cut that is portioned by the number of rib bones.
beef back rib
A raw beef back rib cut.
beef back rib (raw)
A beef steak that is a cut from the rib roast.
beef rib steak
A raw beef rib steak.
beef rib steak (raw)
A raw beef prime rib roast.
beef prime rib roast (raw)
A rib roast that includes ribs 9 or 10 through 12 and is next to the loin.
beef small end rib roast
A raw beef small end rib roast.
beef small end rib roast (raw)
A rib roast that includes ribs 6 through 8 or 9 and is next to the chuck.
beef large end rib roast
A raw beef large end rib roast.
beef large end rib roast (raw)
A tender, bone-in steak with a frenched rib presentation.
beef cowboy steak
A raw beef cowboy steak.
beef cowboy steak (raw)
A tender bone-in steak from the rib with a long bone and marbling that adds flavour.
beef tomahawk steak
A raw beef tomahawk steak.
beef tomahawk steak (raw)
A thin strip of beef cut from between individual ribs in the rib primal.
beef rib finger
A raw beef rib finger cut.
beef rib finger (raw)
A lamb primal cut that is the upper foreleg extending from elbow to blade bone.
lamb shoulder
A raw lamb shoulder cut.
lamb shoulder (raw)
A whole cut from the Shoulder. The cut location is the full length of the Scapula or blade bone and includes the muscle groups above and below the Scapula.
lamb shoulder blade
A raw lamb shoulder blade cut.
lamb shoulder blade (raw)
A roast that is derived from the blade portion of the lamb shoulder primal. The cut location is from either the flat bone or the center portion of the Blade
lamb shoulder blade roast
A raw lamb shoulder blade roast.
lamb shoulder blade roast (raw)
A lamb chop that is derived from the blade portion of the lamb shoulder primal.
lamb shoulder blade chop
A raw lamb shoulder blade chop.
lamb shoulder blade chop (raw)
A whole cut from the shoulder. The shoulder arm consists of the muscle groups that extend from the elbow joint to the shoulder joint and includes the first three ribs.
lamb shoulder arm
A raw lamb shoulder arm cut.
lamb shoulder arm (raw)
A roast that is derived from the arm portion of the Shoulder primal. Arm Roasts come from the shaft of the Humerus and includes the surrounding muscles that extends from the Elbow joint to the Shoulder joint.
lamb shoulder arm roast
A raw lamb shoulder arm roast.
lamb shoulder arm roast (raw)
A lamb chop that is derived from the arm portion of the lamb shoulder primal.
lamb shoulder arm chop
A raw lamb shoulder arm chop.
lamb shoulder arm chop (raw)
A primal cut that comes from the area which extends from groin to ankle.
lamb leg
A raw lamb leg.
lamb leg (raw)
A boneless lamb leg.
lamb leg (boneless)
A leg half that is derived from a whole leg. The anatomical location is the “half” that comes from the shank or lower section of the Leg. The half includes the center section with muscles from the bottom, eye, tip, and top.
lamb shank half
A raw lamb shank half cut.
lamb shank half (raw)
A lamb leg half that is derived from a whole leg. The anatomical location is the “Half” that comes from the Pelvic region of the Leg known as the Sirloin. The half includes the center section with muscles from the bottom, eye, tip, and top.
lamb sirloin half
A raw lamb sirloin half cut.
lamb sirloin half (raw)
A lamb sirloin half that has bones removed except for the femur and humerus bone and the designated shank (i.e. hindshank, or foreshank) is removed.
lamb sirloin half (shank off, semi-boneless)
A cut from lamb sirloin half (shank off, semi-boneless) that is raw.
lamb sirloin half (shank off, semi-boneless, raw)
A boneless cut that comes from the outside and sirloin tip portion of any boneless leg cut.
lamb leg bottom
A boneless cut that comes from the inside portion of any boneless leg cut and shall consist of the semimembranosus, adductor and firmly attached muscles. The inside is separated from the bottom and knuckle portion along the natural seams.
lamb leg top
A lamb chop that derives from the sirloin portion of the leg. The cut location extends from the anterior end of the Pelvic bone to the hip socket.
lamb sirloin chop
A raw lamb sirloin chop.
lamb sirloin chop (raw)
A boneless lamb sirloin chop.
lamb sirloin chop (boneless)
A raw and boneless lamb sirloin chop.
lamb sirloin chop (boneless, raw)
A whole rear leg containing the eye, bottom, sirloin, sirloin tip and top.
leg of lamb
A raw leg of lamb.
leg of lamb (raw)
A leg of lamb that has the shank and sirloin removed leaving only the “center” section of the leg thus the name “center cut.”
leg of lamb center cut
A raw leg of lamb center cut.
leg of lamb center cut (raw)
A lamb primal cut that is between the shoulder and loin.
lamb rib
A raw lamb rib.
lamb rib (raw)
A lamb minor primal cut that is the lower chest cavity underneath the rack that includes ribs 5-8.
lamb breast
A minor lamb primal cut that is meat lower shank from front leg with no hock bones.
lamb foreshank
A raw lamb foreshank.
lamb foreshank (raw)
A lamb cut that comes from the anatomical body location on either side of the spine that is located posterior to the Rack and anterior to the Sirloin or hip.
lamb loin
A raw lamb loin cut.
lamb loin (raw)
A whole cut that is derived from the short loin or any loin item that includes the sirloin. Because of its anatomical location, the tenderloin is the least exercised muscle in the carcass thus the name “Tender” Loin. The cut location is from underneath the finger bones in the short loin and the hipbone in the sirloin.
lamb tenderloin
A raw lamb tenderloin cut.
lamb tenderloin (raw)
A boneless and fatty cut from the belly of a pig.
pork belly
A raw pork belly.
pork belly (raw)
A primal skeletal area of a pig that extends from groin to ankle.
pork leg
A raw pork leg.
pork leg (raw)
A leg half that is derived from a whole pork leg. The anatomical location is the “Half” that comes from the Rump or Pelvic region of the Leg.
pork leg sirloin half
A raw pork leg sirloin half cut.
pork leg sirloin half (raw)
A leg half that is derived from a whole pork leg. The anatomical location is the “Half” that comes from the Shank or lower section of the Leg
pork leg shank half
A raw pork leg shank half cut.
pork leg shank half (raw)
A raw pork loin cut.
pork loin (raw)
Pork loin chop that is derived from the blade end of the pork loin and must include the blade bone/cartilage.
pork loin blade chop
A raw pork loin blade chop.
pork loin blade chop (raw)
A roast derived from the loin blade.
pork loin blade roast
A raw pork loin blade roast.
pork loin blade roast (raw)
A pork loin chop from the center cut loin. The cut location is adjacent to but after the T-Bone chop and before the Sirloin portion on the Loin.
porterhouse chop
A raw porterhouse chop.
porterhouse chop (raw)
A pork loin chop that is derived from the center cut rib section of the loin.
ribeye chop
A raw ribeye chop.
ribeye chop (raw)
A roast that is derived from the center cut rib section of the loin.
ribeye roast
A raw ribeye roast.
ribeye roast (raw)
A pork chop that is derived from the whole loin. The Sirloin is the last 5 to 7 inches of the posterior end of the Loin. Sirloin Chop comes after but is adjacent to, the posterior end of the center-cut loin.
pork sirloin chop
A raw pork sirloin chop.
pork sirloin chop (raw)
A pork chop that is derived from boneless sirloin.
pork sirloin chop (boneless)
A raw and boneless pork sirloin chop.
pork sirloin chop (boneless, raw)
A pork roast that is derived from the whole loin. The Sirloin is the last 5 to 7 inches of the posterior end of the Loin. The Sirloin Roast comes after but is adjacent to the posterior end of the Center Cut Loin.
pork sirloin roast
A raw pork sirloin roast.
pork sirloin roast (raw)
The whole tenderloin. Because of its anatomical location, the tenderloin is the least exercised muscle in the carcass, thus the name “tender” loin. The tenderloin is located underneath the Finger bones and the Hipbone in the Loin.
pork tenderloin
A boneless pork chop that is derived from the center-cut top loin.
New York chop (boneless)
A raw and boneless New York chop.
New York chop (boneless, raw)
A boneless roast that is derived from the center-cut top loin.
New York roast (boneless)
A raw New York roast.
New York roast (boneless, raw)
A meat cut that is derived from the blade end of a pork loin and must include not less than three (3) or more than six (6) ribs.
pork loin country-style ribs
Raw pork loin country-style ribs.
pork loin country-style ribs (raw)
Boneless pork loin country-style ribs.
pork loin country-style ribs (boneless)
A meat cut that is derived from the boneless blade end of the pork loin.
pork loin country-style ribs (boneless, raw)
Back Ribs that are derived from the pork loin.
pork loin back ribs
Raw pork loin back ribs.
pork loin back ribs (raw)
A slice that is derived from a whole pork leg.
pork leg center slice
A raw pork leg center slice that is raw.
pork leg center slice (raw)
A raw and cured pork leg center slice.
pork leg center slice (cured, raw)
Ribs derived from the pork belly. Spareribs are the longer rib bones and intercostal meat located below the back ribs. They begin with the second rib and extend downward to the sternum and costal cartilage, spanning the length of the Rib cage.
pork spareribs
Raw pork spareribs.
pork spareribs (raw)
Upper foreleg of a pig that extends from elbow to blade bone.
pork shoulder
A boneless pork shoulder.
pork shoulder (boneless)
Forelimb from a shoulder.
pork picnic
A raw pork picnic cut.
pork picnic (raw)
A pork roast that is derived from the picnic sub-primal of the shoulder primal.
pork arm roast
A raw pork arm roast.
pork arm roast (raw)
The section of a pork shoulder that includes the blade and 7-bone.
pork shoulder blade
A raw pork shoulder blade cut.
pork shoulder blade (raw)
A pork steak that is derived from the Shoulder Blade. The cut location is just above the shoulder joint adjacent to the picnic.
pork butt steak
A raw pork butt steak.
pork butt steak (raw)
The sirloin tip also known as the Knuckle is the muscle group of a pig that runs parallel with the (Femur) Leg bone that extends upward from the (Patella) Kneecap to the Ball of the Femur.
pork sirloin tip
A raw pork sirloin tip cut.
pork sirloin tip (raw)
A pork roast that is derived from the leg tip.The Sirloin Tip also known as the Knuckle is the muscle group that runs parallel with the (Femur) Leg bone that extends upward from the (Patella) Kneecap to the Ball of the Femur.
pork sirloin tip roast
A raw pork sirloin tip roast.
pork sirloin tip roast (raw)
A pork steak that is derived from the Top Leg, also known as an Inside Leg; the individual muscle Gracilis. It is the cap that covers the center portion of the Top Leg.
pork leg cap steak
A raw pork leg cap steak.
pork leg cap steak (raw)
A veal cut that is the portion of hindquarter remaining after the removal of loin.
veal leg
A raw veal leg.
veal leg (raw)
A cut that comes from the inside of the rear leg of a calf.
veal top round
A raw veal top round cut.
veal top round (raw)
A meat cut from the upper part of a hind leg.
veal hindshank
A raw veal hindshank cut.
veal hindshank (raw)
A veal primal cut that comes from the area below the backbone .
veal loin
A raw veal loin cut.
veal loin (raw)
A veal primal cut that is situated under the front section of the backbone and used primarily for support.
veal rib
A raw veal rib.
veal rib (raw)
A veal roast that is derived from the rib section.
veal rib roast
A raw veal roast.
veal rib roast (raw)
A veal primal cut that consist of the plate and brisket portion of the forequarter (intact) and shall contain 11 ribs.
veal breast
A raw veal breast.
veal breast (raw)
A boneless veal breast.
veal breast (boneless)
A raw and boneless veal breast.
veal breast (boneless, raw)
A veal primal cut that is the foreleg portion from the chuck.
veal foreshank
A raw veal foreshank cut.
veal foreshank (raw)
A veal primal cut that is contained within the larger primal cut 'veal loin'. It is located between the short loin and the leg (round) and includes the hip section and ends at the socket of the pelvis.
veal sirloin
A raw veal sirloin.
veal sirloin (raw)
A veal primal cut that is the upper foreleg extending from elbow to blade bone.
veal shoulder
A raw veal shoulder.
veal shoulder (raw)
A veal meat cut in which the cut location is the full length of the Scapula or blade bone and includes the muscle groups above and below the Scapula.
veal shoulder blade
A raw veal shoulder arm cut.
veal shoulder blade (raw)
A veal meat cut in which shoulder arm consists of the muscle groups that extend from the elbow joint to the shoulder joint and includes the first three ribs.
veal shoulder arm
A raw veal shoulder blade cut.
veal shoulder arm (raw)
A cut of meat that is found between the top and bottom round roast located on both hindquarters of the elk.
elk eye of round roast
A raw elk eye of round roast.
elk eye of round roast (raw)
A raw beef porterhouse steak.
beef porterhouse steak (raw)
A raw beef tenderloin.
beef tenderloin (raw)
A piece of animal meat that is derived from cow.
piece of beef
A piece of boneless beef.
piece of beef (boneless)
One or more pieces of beef.
piece(s) of beef
A raw butchery cut of beef.
butchery cut of beef (raw)
A bison meat cut that is derived from a sub-primal, individual muscle cut or minor primal cut.
bison retail cut
A bison meat cut that has a flat-cut appearance.
bison steak
A bison primal cut that is contained within the larger cut 'bison loin'. It is located between the short loin and the round and includes the hip section and ends at the socket of the pelvis.
bison sirloin
A raw bison sirloin cut.
bison sirloin (raw)
A bison cut that is located behind the short loin on the top back end of the animal.
bison top sirloin butt
A raw bison top sirloin butt.
bison top sirloin butt (raw)
A steak cut from the bison top sirloin butt.
bison top sirloin steak
A raw bison top sirloin steak.
bison top sirloin steak (raw)
A bison cut that comes from the 'round', the rear leg of the bison.
bison round
A raw bison round cut.
bison round (raw)
A bison cut that comes from the inside of the rear leg.
bison top round
A raw bison top round cut.
bison top round (raw)
A steak cut from the bison top round.
bison top round steak
A raw bison top round steak.
bison top round steak (raw)
A bison steak that is a cut from the rib-eye roast.
bison ribeye steak
A raw bison ribeye steak.
bison ribeye steak (raw)
A bison cut that extends from the neck to the fifth rib and includes the shoulder blade and upper arm.
bison chuck
A raw bison chuck cut.
bison chuck (raw)
bison shoulder clod
A raw bison shoulder clod.
bison shoulder clod (raw)
A buffalo cut that comes from the 'round', the rear leg of the buffalo.
buffalo round
A raw buffalo round cut.
buffalo round (raw)
A buffalo cut that comes from the inside of the rear leg.
buffalo top round
A raw buffalo top round cut.
buffalo top round (raw)
A steak cut from the buffalo top round.
buffalo top round steak
A raw buffalo top round steak.
buffalo top round steak (raw)
A raw beef primal cut.
beef primal cut (raw)
A raw beef sub-primal cut.
beef sub-primal cut (raw)
A raw beef retail cut.
beef retail cut (raw)
A butchery cut of animal that is typically boneless.
animal fillet
A raw animal fillet cut.
animal fillet (raw)
A raw piece of animal.
piece of animal (raw)
A piece of animal that contains skin.
piece of animal (with skin)
A piece of animal that is skinless.
piece of animal (skinless)
A piece of animal that contains the skin and is raw.
piece of animal (with skin, raw)
A raw skinless piece of animal.
piece of animal (skinless, raw)
A raw animal organ that is obtained from an animal during a butchery process.
animal organ (raw)
A piece of an animal organ.
piece of animal organ
A raw piece of an animal organ.
A raw piece of animal organ.
piece of animal organ (raw)
A piece of meat that is derived from an animal.
piece of animal meat
A raw piece of animal meat.
piece of animal meat (raw)
A piece of skinless animal meat.
piece of animal meat (skinless)
A raw piece of skinless animal meat.
piece of animal meat (skinless, raw)
A piece of animal meat that contains skin.
piece of animal meat (with skin)
A raw piece of animal meat that contains skin.
piece of animal meat (with skin, raw)
A piece of boneless animal meat.
piece of animal meat (boneless)
A piece of animal meat that contains bone material.
piece of animal meat (with bone)
A raw piece of animal meat that contains bone material.
piece of animal meat (with bone, raw)
A whole thigh that is obtained from an animal.
animal thigh
A whole breast that is obtained from an animal.
animal breast
A whole wing that is obtained from an animal.
animal wing
A whole neck that is obtained from an animal.
animal neck
A whole leg that is obtained from an animal.
animal leg
A whole raw animal breast.
animal breast (raw)
A whole raw animal wing.
animal wing (raw)
A whole raw animal neck.
animal neck (raw)
A whole raw animal leg.
animal leg (raw)
A piece of an animal breast.
piece of animal breast
A raw piece of an animal breast.
piece of animal breast (raw)
A piece of skinless animal breast.
piece of animal breast (skinless)
A raw piece of skinless animal breast.
piece of animal breast (skinless, raw)
A piece of animal breast that contains skin.
piece of animal breast (with skin)
A raw piece of animal breast that contains skin.
piece of animal breast (with skin, raw)
A piece of skinless and boneless animal breast.
piece of animal breast (skinless, boneless)
A raw piece of skinless and boneless animal breast.
piece of animal breast (skinless, boneless, raw)
A piece of light meat that comes from an animal breast or wing.
piece of light animal meat
A raw piece of light animal meat.
piece of light animal meat (raw)
A piece of light animal meat that contains skin.
piece of light animal meat (with skin)
A raw piece of light animal meat that contains skin.
piece of light animal meat (with skin, raw)
A piece of skinless light animal meat.
piece of light animal meat (skinless)
A raw piece of skinless light animal meat.
piece of light animal meat (skinless, raw)
A raw cut of animal meat.
butchery cut of animal (raw)
A raw animal primal cut.
animal primal cut (raw)
A raw animal sub-primal cut.
animal sub-primal cut (raw)
A raw animal retail cut.
animal retail cut (raw)
An animal meat cut that has a flat-cut appearance.
animal steak
A raw animal steak.
animal steak (raw)
A retail cut of meat from an animal that is of a size for slicing into more than one portion and is suitable for roasting.
animal roast
A raw animal roast.
animal roast (raw)
A boneless animal roast.
animal roast (boneless)
A raw and boneless animal roast.
animal roast (boneless, raw)
A retail cut of meat from an animal that is perpendicular to the spine, and usually containing a rib or riblet part of a vertebra.
animal chop
A raw animal chop.
animal chop (raw)
A boneless animal chop.
animal chop (boneless)
A raw and boneless animal chop.
animal chop (boneless, raw)
A raw piece of boneless animal meat.
piece of animal meat (boneless, raw)
A skinless animal breast.
animal breast (skinless)
A raw skinless animal breast.
animal breast (skinless, raw)
An animal breast that contains skin.
animal breast (with skin)
A raw animal breast that contains skin.
animal breast (with skin, raw)
A skinless and boneless animal breast.
animal breast (skinless, boneless)
A raw, skinless and boneless animal breast.
animal breast (skinless, boneless, raw)
A boneless, seasoned and freshly frozen animal roast.
animal roast (boneless, seasoned, fresh frozen)
Material that derives from some avian animal.
avian animal material
A severed part of an avian animal.
piece of avian animal
A raw piece of avian animal.
piece of avian animal (raw)
A piece of meat that is derived from an avian animal.
piece of avian animal meat
A raw piece of avian animal meat.
piece of avian animal meat (raw)
Material that derives from some chicken.
chicken material
A raw chicken fillet cut.
chicken fillet (raw)
A severed part of a chicken.
piece of chicken
A piece of chicken meat which has been cut according to butchery practice.
butchery cut of chicken
Material that derives from some turkey.
turkey material
A severed part of a turkey.
piece of turkey
A raw piece of turkey.
piece of turkey (raw)
A piece of turkey that contains skin.
piece of turkey (with skin)
A piece of turkey that is skinless.
piece of turkey (skinless)
A piece of turkey that contains the skin and is raw.
piece of turkey (with skin, raw)
A raw skinless piece of turkey.
piece of turkey (skinless, raw)
An organ that derives from a turkey.
turkey organ
A raw animal organ that is obtained from a turkey during a butchery process.
turkey organ (raw)
A piece of a turkey organ.
piece of turkey organ
A raw piece of a turkey organ.
A raw piece of turkey organ.
piece of turkey organ (raw)
A piece of meat that is derived from a turkey.
piece of turkey meat
A raw piece of turkey meat.
piece of turkey meat (raw)
A piece of skinless turkey meat.
piece of turkey meat (skinless)
A raw piece of skinless turkey meat.
piece of turkey meat (skinless, raw)
A piece of turkey meat that contains skin.
piece of turkey meat (with skin)
A raw piece of turkey meat that contains skin.
piece of turkey meat (with skin, raw)
A piece of boneless turkey meat.
piece of turkey meat (boneless)
A piece of turkey meat that contains bone material.
piece of turkey meat (with bone)
A raw piece of turkey meat that contains bone material.
piece of turkey meat (with bone, raw)
A skinless turkey breast.
turkey breast (skinless)
A raw skinless turkey breast.
turkey breast (skinless, raw)
A turkey breast that contains skin.
turkey breast (with skin)
A raw turkey breast that contains skin.
turkey breast (with skin, raw)
A skinless and boneless turkey breast.
turkey breast (skinless, boneless)
A raw, skinless and boneless turkey breast.
turkey breast (skinless, boneless, raw)
A piece of a turkey breast.
piece of turkey breast
A raw piece of a turkey breast.
piece of turkey breast (raw)
A piece of skinless turkey breast.
piece of turkey breast (skinless)
A raw piece of skinless turkey breast.
piece of turkey breast (skinless, raw)
A piece of turkey breast that contains skin.
piece of turkey breast (with skin)
A raw piece of turkey breast that contains skin.
piece of turkey breast (with skin, raw)
A piece of skinless and boneless turkey breast.
piece of turkey breast (skinless, boneless)
A raw piece of skinless and boneless turkey breast.
piece of turkey breast (skinless, boneless, raw)
Material that derives from some poultry.
poultry material
A severed part of a poultry.
piece of poultry
A raw piece of poultry.
piece of poultry (raw)
A raw piece of poultry meat.
piece of poultry meat (raw)
A piece of boneless poultry meat.
piece of poultry meat (boneless)
A piece of poultry meat that contains bone material.
piece of poultry meat (with bone)
A raw piece of poultry meat that contains bone material.
piece of poultry meat (with bone, raw)
A whole raw poultry breast.
poultry breast (raw)
A whole raw poultry wing.
poultry wing (raw)
A whole raw poultry neck.
poultry neck (raw)
A whole raw poultry leg.
poultry leg (raw)
Material that derives from some bison.
bison material
A severed part of a bison.
piece of bison
A raw piece of bison.
piece of bison (raw)
A piece of bison meat which has been cut according to butchery practice.
butchery cut of bison
A raw bison primal cut.
bison primal cut (raw)
A raw bison sub-primal cut.
bison sub-primal cut (raw)
A raw bison retail cut.
bison retail cut (raw)
A raw bison steak.
bison steak (raw)
A retail cut of meat from a bison that is of a size for slicing into more than one portion and is suitable for roasting.
bison roast
A raw bison roast.
bison roast (raw)
A boneless bison roast.
bison roast (boneless)
A raw and boneless bison roast.
bison roast (boneless, raw)
A retail cut of meat from a bison that is perpendicular to the spine, and usually containing a rib or riblet part of a vertebra.
bison chop
A raw bison chop.
bison chop (raw)
Material that derives from some cow.
cow material
A raw piece of beef.
piece of cow (raw)
A raw beef roast.
beef roast (raw)
A boneless beef roast.
beef roast (boneless)
A raw and boneless beef roast.
beef roast (boneless, raw)
A boneless, seasoned and freshly frozen beef roast.
beef roast (boneless, seasoned, fresh frozen)
A retail cut of meat from a beef that is perpendicular to the spine, and usually containing a rib or riblet part of a vertebra.
beef chop
A raw beef chop.
beef chop (raw)
A boneless beef chop.
beef chop (boneless)
A raw and boneless beef chop.
beef chop (boneless, raw)
Material that derives from some buffalo.
buffalo material
A severed part of a buffalo.
piece of buffalo
A raw piece of buffalo.
piece of buffalo (raw)
A piece of buffalo meat which has been cut according to butchery practice.
butchery cut of buffalo
A raw buffalo primal cut.
buffalo primal cut (raw)
A raw buffalo sub-primal cut.
buffalo sub-primal cut (raw)
A raw buffalo retail cut.
buffalo retail cut (raw)
A raw buffalo steak.
buffalo steak (raw)
A retail cut of meat from a buffalo that is of a size for slicing into more than one portion and is suitable for roasting.
buffalo roast
A raw buffalo roast.
buffalo roast (raw)
A boneless buffalo roast.
buffalo roast (boneless)
A raw and boneless buffalo roast.
buffalo roast (boneless, raw)
A retail cut of meat from a buffalo that is perpendicular to the spine, and usually containing a rib or riblet part of a vertebra.
buffalo chop
A raw buffalo chop.
buffalo chop (raw)
A food product that is derived from some lamb.
lamb food product
Material that derives from some lamb.
lamb material
A severed part of a lamb.
piece of lamb
A raw piece of lamb.
piece of lamb (raw)
A piece of lamb meat which has been cut according to butchery practice.
butchery cut of lamb
A raw lamb primal cut.
lamb primal cut (raw)
A raw lamb sub-primal cut.
lamb sub-primal cut (raw)
A lamb meat cut that is derived from a sub-primal, individual muscle cut or minor primal cut.
lamb retail cut
A raw lamb retail cut.
lamb retail cut (raw)
A raw lamb roast.
lamb roast (raw)
A boneless lamb roast.
lamb roast (boneless)
A raw and boneless lamb roast.
lamb roast (boneless, raw)
A boneless, seasoned and freshly frozen lamb roast.
lamb roast (boneless, seasoned, fresh frozen)
A boneless lamb chop.
lamb chop (boneless)
A raw and boneless lamb chop.
lamb chop (boneless, raw)
Material that derives from some veal.
veal material
A severed part of a veal.
piece of veal
A raw piece of veal.
piece of veal (raw)
A piece of veal meat which has been cut according to butchery practice.
butchery cut of veal
A raw veal primal cut.
veal primal cut (raw)
A raw veal sub-primal cut.
veal sub-primal cut (raw)
A veal meat cut that is derived from a sub-primal, individual muscle cut or minor primal cut.
veal retail cut
A raw veal retail cut.
veal retail cut (raw)
veal roast (raw)
A boneless veal roast.
veal roast (boneless)
A raw and boneless veal roast.
veal roast (boneless, raw)
A boneless, seasoned and freshly frozen veal roast.
veal roast (boneless, seasoned, fresh frozen)
Material that derives from some deer.
deer material
A severed part of a deer.
piece of deer
A raw piece of deer.
piece of deer (raw)
Material that derives from some elk.
elk material
A severed part of an elk.
piece of elk
A raw piece of elk.
piece of elk (raw)
A piece of elk meat which has been cut according to butchery practice.
butchery cut of elk
An elk meat cut that is derived from a sub-primal, individual muscle cut or minor primal cut.
elk retail cut
Material that derives from some pig.
pig material
A raw piece of pork.
piece of pig (raw)
A piece of pork meat which has been cut according to butchery practice.
butchery cut of pork
A raw pork primal cut.
pork primal cut (raw)
A raw pork sub-primal cut.
pork sub-primal cut (raw)
A raw pork retail cut.
pork retail cut (raw)
A pork meat cut that has a flat-cut appearance.
pork steak
A raw pork steak.
pork steak (raw)
A raw pork roast.
pork roast (raw)
A boneless pork roast.
pork roast (boneless)
A raw and boneless pork roast.
pork roast (boneless, raw)
A boneless, seasoned and freshly frozen pork roast.
pork roast (boneless, seasoned, fresh frozen)
A boneless pork chop.
pork chop (boneless)
A raw and boneless pork chop.
pork chop (boneless, raw)
An animal fillet that is skinless.
animal fillet (skinless)
A raw skinless animal fillet
animal fillet (skinless, raw)
An animal fillet that contains skin.
animal fillet (with skin)
A raw animal fillet that contains skin.
animal fillet (with skin, raw)
An animal breast that has the bone attached to it.
animal breast (bone-in)
A raw bone-in animal breast.
animal breast (bone-in, raw)
A raw bone-in turkey breast.
turkey breast (bone-in, raw)
A turkey breast that has the bone attached to it.
turkey breast (bone-in)
fish (whole or pieces)
Fish meat that has not been cooked or preserved other than perhaps by freezing. If previously frozen, it has subsequently been thawed.
fish meat (raw)
meat (cooked)
fish fillet (frozen)
mahi mahi fillet (raw)
herring fillet (pickled)
fish fillet (raw)
meat (raw)
A whole raw turkey breast.
turkey breast (raw)
fish fillet (smoked)
herring fillet in tomato sauce
tuna fillet (light meat, raw)
fish fillet (with skin, raw, breaded, frozen)
fish fillet (stuffed with crabmeat and shrimp)
fish (portion cut)
fish steak (raw)
fish fillet (breaded, precooked)
fish fillet (in tomato sauce)
tuna fillet (raw)
fish fillet (breaded)
fish fillet (whitemeat, skinless, raw)
herring fillet (smoked, and vegetables)
herring fillet (pickled, skinless)
fish fillet (breaded, frozen)
herring fillet (raw)
herring fillet in lemon-flavored sauce
A raw pork tenderloin cut.
pork tenderloin (raw)
Food product for animal covers foods intended for consumption by domesticated animals.
food product for animal
A beef steak product which is raw and is cut from the outer part of the round of a cow.
beef round steak (raw)
poultry (whole or pieces)
A raw beef chuck cut.
beef chuck (raw)
A raw pork shoulder.
pork shoulder (raw)
A raw pork chop.
pork chop (raw)
A raw lamb chop.
lamb chop (raw)
A food product that is raw.
food (raw)
beef sirloin steak (cooked)
turkey breast (roasted)
A raw beef steak is a flat cut of beef, with parallel faces spaced to a thickness of 1 to 5 centimetres (1⁄2 to 2 in), usually cut perpendicular to the muscle fibers, with a raw mass in common restaurant service ranging from 120 to 600 grams (4 to 21 oz). Beef steaks are usually grilled, pan fried, or broiled.
A raw beef steak.
beef steak (raw)
processed food product
A raw piece of chicken.
piece of chicken (raw)
meat (prepared)
A piece of meat that is derived from a poultry.
Meat from a poultry bird.
piece of poultry meat
fish fillet (quick-frozen in blocks)
fish fillets and minced fish (quick-frozen in blocks)
A meat product is a product organized by the form of - or processing done to - its meat component (a skeletal meat part of an animal or crustacean).
meat (whole or pieces)
fish fillet (unprocessed, frozen)
fish fillet (deep-frozen, unprocessed)
fish fillet (deep-frozen)
An agency food product type is a class of food product defined by an agency or consortium.
agency food product type
Any chemical or chemical mixture that exists in a food material or was added to a food material.
chemical food component
A member of the group of eukaryotic organisms in the kingdom Fungi that includes unicellular microorganisms such as yeasts and molds, as well as multicellular fungi that produce familiar fruiting forms known as mushrooms.
fungus
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
An informal term for a large, diverse group of photosynthetic eukaryotic organisms that are not necessarily closely related, and is thus polyphyletic.
algae
This is a hierarchy of organisms, grouped minimally in a combination of taxonomy and consumer-oriented food groups.
organism by alternate grouping
A composite organism that arises from algae or cyanobacteria living among filaments of multiple fungi species in a mutualistic relationship.
lichen
A chemical food component in liquid form.
liquid chemical food component
Anatomical or other part(s) or substances derived from plant or animal or fungal organisms.
organism material
Material that derives from some animal.
animal material
Poultry, game bird or turtle eggs.
egg or egg component
divided into pieces, thickness <0.3 cm.
medium ground and sifted (bolted)
whole and pieces
whole, shape achieved by forming, thickness 1.5-7 cm.
finely ground
divided into segments or wedges
physical state, shape or form, multiple
cut into short pieces
The physical state of the food product (liquid, semiliquid, semisolid, or solid). Solid food products are further subdivided by shape or form. Terms are provided for products that have both liquid and solid components or that incorporate air or other gases. [FDA CFSAN 1995]
food physical quality
divided into pieces, thickness 0.3-1.5 cm.
divided into halves
medium ground
divided or disintegrated
sliced, thick, between 0.5 and 1.5 cm.
divided into pieces, thickness more than 1.5 cm.
Refers to natural or formed shape as appropriate, regardless of size, which may vary from very large (e.g., beef carcass) to very small (e.g., poppy seed, yeast cell).
whole
Divided into pieces whose shape is defined in relation to the shape of the whole, i.e., halves, quarters, or segments. It is used regardless of the size of the whole.
divided into halves, quarters or segments
disintegrated or ground
sliced
whole, shape achieved by forming, thickness 0.3-1.5 cm.
cut into long pieces
sliced, thin, below 0.5 cm.
whole, shape achieved by forming, thickness bigger than 7 cm.
whole, shape achieved by forming
divided into quarters
whole, natural shape
Divided into pieces whose shape bears little or no relation to the shape of the whole. If all dimensions are below 0.2 cm., use *DISINTEGRATED OR GROUND*. Examples are: bread slice, cubed beef, sliced carrot, cut green beans, apple ring, shredded cabbage or cheese.
divided into pieces
whole, shape achieved by forming, thickness <0.3 cm.
not heat-treated
Used to broadly characterize a food product based on the extent of heat applied. Heat treatment affects the flavor and textural characteristics of a food and thus consumer preparation time. Heat treatment causes chemical changes and/or reduction of enzyme and of microbial activity and thus affects food safety and shelflife. Specifics of preparation are covered by *G. COOKING METHOD* and *H. TREATMENT APPLIED*. [FDA CFSAN 1995]
extent of food heat treatment
fully heat-treated
partially heat-treated
heat-treated
heat-treated, multiple components, different degrees of treatment
food cooking
Cooked at moderate to high levels of heat in which no liquid is added and only small amounts of fat may be added to prevent sticking.
cooking by dry heat
Cooked without moisture, covered or uncovered, in an oven.
food baking
Cooked without moisture under or over intense direct heat.
broiling or grilling
Cooked without moisture over direct heat from a charcoal fire.
charcoal broiling
Cooking on a flat surface at medium heat with only a sufficient amount of fat used to prevent sticking.
griddle cooking
Cooking by agitating the food over a dry, high heat source, resulting in exploding.
cooked by popping
Cooking with direct heat until the surface of the food is browned, usually associated with bread or sandwiches.
food toasting
Cooking in a microwave oven.
cooking by microwave
Cooking in varying amounts of water, water-based liquid or steam.
cooking by moist heat
A process of cooking by moist heat which is effected by hot water or water-based liquid in a container.
cooking in water or water-based liquid
A cooking in water or water-based liquid process in which the liquid is boiling.
boiling in container
Cooked in boiling water at 212 degrees F.; water that is not absorbed into the food product is discarded after cooking.
boiling and then draining
Cooked in boiling water at 212 degrees F. Liquid to solid ratio is greater than 2:1.
boiling in large amount of liquid
boiling in small amount of liquid
Cooked in boiling water at 212 degrees F. The water incorporates itself into the product being cooked or is not discarded when cooking is complete.
boiling without draining
Browned initially in fat and then tightly covered and cooked over low heat in a small amount of water.
cooking by braising
Cooking in a moderate amount of liquid at just below the boiling point.
cooking by simmering
cooking in steam
Cooked in a pressure cooker.
steaming with pressure
Cooked suspended above boiling water.
steaming without pressure
cooking with fat or oil
Cooked by adding fat or oil to those foods that do not contain fat or oil that would render during the cooking process.
cooking with added fat or oil
Cooked with sufficient fat or oil to coat and moisten the food being prepared, but not cooked in enough fat or oil to immerse the food.
cooking in small amount of fat or oil
Cooking in a very small amount of very hot fat, turning and browning the food on all sides.
sautéing
Cooked by frying foods quickly over high heat, stirring constantly. Only enough cooking oil is used to coat the bottom of the pan.
stir-frying
Cooked in hot fat or oil deep enough to immerse the food entirely.
deep-frying process
Cooked in fat or oil rendered from the food being prepared.
cooking with inherent fat or oil
heating container by immersion in water or steam
A food cooking method in which heat is transferred to the outside of a container.
heating container
Heating a container that is placed in another container filled with boiling water.
heating container in double boiler
Heating a container that is placed in another container filled with water kept near the boiling point.
heating container by water bath
A chinese cooking technique similar to sauteing in which thick slices or chunks of floured or battered ingredients are slow seared over moderate to low heat.
shallow frying process
Extracting flavor and other components from food sources by immersion in water, usually at near-boiling temperature.
steeping
A process to bring an already fully cooked product to serving temperature.
food reheating
food reheating by microwave
food reheating by dry heat
food reheating by boil-in-bag
food reheating in pan or cooking utensil
A Chinese cooking technique to prepare delicate food such as bird nests, shark fins, etc. The food is covered with water and put in a covered ceramic jar and the jar is then steamed for several hours.
double steaming
Rotisserie is a style of roasting where meat is skewered on a spit and revolves over a flame or other heat source.
rotisserie roasting
Searing is a technique used in grilling, roasting, braising, sautéing, etc. that cooks the surface of the food at high temperature so that a brownish crust forms by Maillard reaction and denaturation of proteins.
searing
blind baking
pressure frying process
lactic acid fermentation
proteolytic fermentation
lactic acid-other agent fermentation
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
A food modification process by microbial or enzymatic action which results in molecular changes in any food component.
microbial/enzymatic modification process
alcohol-acetic acid fermentation
lipolytic fermentation
A food fermentation process in which significant amounts of two or more components (i.e. carbohydrate and protein, carbohydrate and fat, protein and fat, or all three) are modified through microbial processes. Enzymatic or other biological processes may also be involved.
multi-component food fermentation
A food modification process where physical or chemical changes are effected in any food ingredient through a physical or non-enzymatic chemical process.
physical/chemical modification process
food modification process
A claim that sodium has been added to an edible product.
sodium added claim
A claim that a mineral has been added to an edible product.
mineral added claim
A claim that calcium has been added to an edible product.
calcium added claim
A claim that iron has been added to an edible product.
iron added claim
A claim that potassium has been added to an edible product.
potassium added claim
A claim that chloride has been added to an edible product.
chloride added claim
acidification process
Treated with moist heat to soften the grain and to transfer nutrients from the bran to the endosperm.
food parboiling process (grain)
A claim that phosphorus has been added to an edible product.
phosphorus added claim
food component addition process
single component food fermentation
alcohol fermentation
A component separation process at the very least removes one component from an initial entity. The removed component may be captured as a process output for reuse if not destroyed in the process of removal.
food component separation process
Modified through complex enzymatic or microbial processes resulting in physicochemical changes in particular with respect to texture, flavor, color or shelf life of the food product. Such changes may be induced by the introduction of certain chemicals, such as sodium sulfite, salt, sugar, or other substances, such as phenolics, in dry or liquid form and often aided by smoke. Cheese should always be indexed by the appropriate narrower term under *LACTIC ACID-OTHER AGENT FERMENTED*.
curing or aging
carbohydrate fermentation
A claim that a zinc has been added to an edible product.
zinc added claim
curing or aging < 2 weeks
curing or aging 2 weeks to 1 month
curing or aging 1 to 2 months
curing or aging 2 to 4 months
curing or aging 4 to 6 months
curing or aging 6 to 12 months
curing or aging 12 months or over
acetic acid fermentation
bacterial food-curing process
food surface bacterial curing
food interior bacterial curing
mold food-curing process
food surface mold curing
food interior mold curing
seed roasting
marinading
A claim that magnesium has been added to an edible product.
magnesium added claim
A claim that copper has been added to an edible product..
copper added claim
A claim that manganese has been added to an edible product.
manganese added claim
A claim that selenium has been added to an edible product.
selenium added claim
A claim that chromium has been added to an edible product.
chromium added claim
A claim that molybdenum has been added to an edible product.
molybdenum added claim
A claim that fluoride has been added to an edible product.
fluoride added claim
Preservation by adding chemical preservatives (e.g., sorbic acid, sodium benzoate, BHT, calcium proprionate) to suppress or inhibit undesirable microorganisms or enzyme activity.
preservation by adding chemicals
food sterilization before filling
food salting
Smoking is the process of flavoring, browning, cooking, or preserving food by exposing it to smoke from burning or smoldering material, most often wood.
food smoking
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
Preservation by immersing in or spraying with liquids (e.g., sulfite solutions) or surrounding with gases (e.g., ethylene oxide, propylene oxide or sulfur dioxide) to destroy undesirable microorganisms or inactivate enzymes. Diffusion and chemical reaction may create a residue in the food product that contributes to continuing preservation.
preservation by treatment with chemicals
Preservation by use of chemical to destroy, suppress or inhibit undesirable microorganisms or enzyme activity.
chemical food preservation process
food sterilization after filling
Preservation by storage in an atmosphere in which the concentrations of oxygen and carbon dioxide are different from those in air. This reduces microbial and enzymatic activity; often used commercially in conjunction with refrigeration (e.g., refrigerated rail cars) for fresh meat and produce.
preservation by storage in modified atmosphere
drying under reduced pressure
sterilization by irradiation
food sterilization by hot filling and cooling
surface pasteurization or disinfection by ultraviolet irradiation
dehydration or drying
Drying by heat.
heat drying process
pasteurization by irradiation
Preservation by the use of high temperature for a time sufficient to reduce or destroy undesirable microorganisms and enzyme activity. [FDA CFSAN 1995]
heat treatment food preservation
Preservation by filtering out yeasts and molds, generally followed by aseptic packaging. FDA CFSAN 1995
food filtration
Preservation by irradiation, primarily by gamma radiation.
preservation by ionizing radiation
food sterilization by heating
Reduction of water in the product by osmosis.
osmotic dehydration
aseptic filling and sealing of food
food slow freezing
food sterilization by hot filling, held hot and cooling
Dehydration by sublimation under reduced pressure while frozen. Usually the product is not stored frozen.
freeze-drying
Cooling and keeping at a temperature between 30°F and 45°F (-1°C and 7°C). Regarding food preservation regulations, the temperature range depends on national legislation.
food chilling
food quick freezing
spray-drying
shelf-drying under normal pressure
pasteurization by heating
Preservation by freezing a food product and keeping it at a temperature below the freezing point (20-30 degrees F) without regard to the product's physical state.
food freezing
Immersed in a salt brine strong enough to suppress enzyme activity and growth of undesirable organisms.
food brining
Preservation by the use of radiation to destroy or suppress undesirable microorganisms or enzyme activity.
preservation by irradiation
Packed in dry salt in sufficient quantity to suppress enzyme activity or growth of undesirable organisms.
food dry salting
drum-drying
Dried by natural heat, usually through exposure to the sun. Includes field-dried products such as grains and dry beans. These products are included also if they have been artificially dried to return them to normal dry state, e.g. grain that has been artificially dried after harvest.
natural heat drying
Preservation by cooling and storage at low temperature (chilling at around 0-5°C (32 to 41°F), freezing at -18°C (0°F)) to prevent or retard microbial or enzymatic spoilage.
chilling or freezing
drying under normal pressure
Drying by the application of artificial heat.
artificial heat drying
Preservation method that lowers the water activity (relative humidity) of a food product. This is accomplished by using mechanical dehydration equipment, by natural drying, by adding salt, sugar or other agents to the food or by surface drying during a refrigeration or freezing operation. This method of preservation may be used in conjunction with other preservation methods such as preservation by thermal processing.
preservation by reducing water activity
Preservation by adding sugar, sugar syrup or by partial inversion of disaccharides until the sugar concentration is high enough to prevent growth of microorganisms.
preservation by adding sugar
food sterilization at ultra high temperature (UHT)
When used to describe a dairy product, means that such product shall have been thermally processed at or above 138° C (280° C) for at least 2 seconds, either before or after packaging so as to produce a product that has extended shelf life under refrigerated conditions (21 CFR 131.3 (c)). Used to describe liquid egg products that also have been thermally processed, but at a different temperature than for milk products. The egg product will have an extended shelf life under refrigerated conditions.
ultra pasteurization (UP) by heat
preservation by adding acid
Sous-vide, French for "under vacuum", is a method of cooking that is intended to maintain the integrity of ingredients by heating them for an extended period of time in vacuum sealed plastic pouches at relatively low temperatures. Food is cooked for a long time, sometimes well over 24 hours. Unlike cooking in a slow cooker, sous-vide cooking uses airtight plastic bags placed in hot water well below boiling point (usually around 60°C or 140°F).
sous vide cooking
preservation of food component by heat treatment
ingredient preservation by irradiation
Preservation by adding spices or extracts (e.g. garlic, onion, horseradish, paprika) to suppress or inhibit undesirable micro-organisms, enzyme activity, or oxidative changes.
preservation by adding spices or extracts
Preservation by adding inorganic acids or salts (e.g. SO2, H2SO4, KNO4, NaNO3) to suppress or inhibit undesirable micro-organisms or enzyme activity.
preservation by adding inorganic acids or salts
Preservation by adding organic acids or salts (e.g. lactic acid, acetic acid, salicylic acid) to suppress or inhibit undesirable micro organisms or enzyme activity.
preservation by adding organic acids or salts
Preservation by adding antibiotics (e.g. nisin, tylosine, subtlin, bacitracin, chlorotetracyclin, oxytetracyclin) to kill micro organisms or stop their growth.
preservation by adding antibiotics
Separation of colloidal or very fine solid materials by filtration through microporous or semipermeable mediums. Membranes have pores in the range 2-20 nm diameter.
food ultra-filtration
pasteurization by heat after filling
pasteurization by heat before filling
The process of holding food at a high pressure, normally greater than 1000 bar, which leads to sterilization. Example: Fruit juice, jam.
ultra high pressure sterilization
Treated by electron accelerator radiation, for example to kill insects in cereals.
preservation by electron accelerator radiation
disinfection by irradiation
drying by radiation
drying by microwave radiation
drying by infrared heat radiation
drying under increased pressure
concentration by reverse osmosis
Drying by exposure to the sun. Example: cereals, spices, vegetables.
sun drying
Frozen very rapidly by means of refrigerating agents such as liquid nitrogen or carbon dioxide. Example: lobster frozen in liquid nitrogen.
food cryogenic freezing
The process of food storage involving an accompanying refrigerating agent.
food storage with refrigerating agent process
Preservation by storage in inert gases (e.g. nitrogen) to suppress or inhibit undesirable micro-organism growth, oxidation activity, etc.
inert atmosphere storage process
Storing under reduced pressure (e.g. 1.3-2 kPa) in order to suppress or inhibit undesirable micro organism growth, oxidation activity, etc.
vaccume storage process
Blanching is a cooking process wherein a food, usually a vegetable or fruit, is scalded in boiling water, removed after a brief, timed interval, and finally plunged into iced water or placed under cold running water (shocking or refreshing) to halt the cooking process. Blanching foods helps reduce quality loss over time. People often use blanching as a pre-treatment prior to freezing, drying, or canning—heating vegetables or fruits to inactivate enzymes, modify texture, remove the peel, and wilt tissue. Blanching is also utilized to preserve color, flavor, and nutritional value. The process has three stages: preheating, blanching, and cooling. The most common blanching methods for vegetables/fruits are hot water and steam, while cooling is either done using cold water or cool air.
food blanching
Storage of fruits and vegetables in an atmosphere in which the concentrations of oxygen, carbon dioxide (and often nitrogen) are different from those in air and at a low temperature. All three (four) factors are controlled at the desired levels in order to suppress the fruits' and vegetables' natural respiration.
controlled atmosphere storage process
Microfiltration is used to remove undesirable micro-organisms and molecules. The membranes have pore diameters from 10 to 10000 nm. Micro-filtration is often used instead of pateurisation, e.g. in the brewing industry.
food micro-filtration
High Temperature Short Time (HTST) pasteurization is one of the most common methods of pasteurization , which uses metal plates and hot water to raise milk temperatures to at least 72° C (161° F) for not less than 15 seconds, followed by rapid cooling.
high temperature short time (HTST) pasteurization
Higher Heat Shorter Time (HHST) is a process similar to HTST pasteurization, but it uses slightly different equipment and higher temperatures (83 - 127° C) for a shorter time.
higher heat shorter time (HHST) pasteurization
Typically involves heating milk or cream to 135° to 150° C (275° to 302° F) for 1 or 2 seconds. The milk is then packaged in sterile, hermetically-sealed (airtight) containers (aspetic filling) and can be stored without refrigeration for up to 90 days. After opening, spoilage times for UHT products are similar to those of conventionally pasteurized products.
ultra high temperature (UHT) pasteurization
filling conditions for pasteurization
A pasteurization by heating process which uses low heat for a longer time to kill pathogenic bacteria.
low-temperature-long-time (LTLT) pasteurization
In the U.S., grain strength is calculated as 10 times the acid content expressed as acetic acid. For example, 40 grain vinegar = 4% acetic acid; 120 grain vinegar = 12% acetic acid. [Technically Speaking about Vinegar - A food technologist's guide to vinegar, The Vinegar Institute, 5775 Peachtree-Dunwoody Road, Atlanta, Georgia 30342, USA].
packed in vinegar with sugar
Packed in a medium that is also a food product. Ingredients that are introduced through the packing medium are indexed as appropriate under *INGREDIENT OR FOOD ADDED* found in *H. TREATMENT APPLIED*.
packed in edible medium
packed in heavily sweetened liquid
packed in lightly sweetened water or juice
Packed in a modified atmosphere that contributes to preservation (e.g., applesauce packed with nitrogen in the head space or tuna salad sandwich packed in nitrogen-containing polyethylene wrapper). Also applicable to large-scale applications in shipping or storage (e.g., meat under carbon dioxide in a rail car).
packed in gas other than air
Packed with a gas that is liquified under pressure and that upon release of the pressure propels and aerates the food product. See 21 CFR 173.345 and 173.360 for substances used.
packed with aerosol propellant
packed in vegetable juice
packed in water
packed in salt brine
packed in sweetened brine
food packing medium
The medium in which the food is packed for preservation and handling or the medium surrounding homemade foods, e.g., peaches cooked in sugar syrup. The packing medium may provide a controlled environment for the food. It may also serve to improve palatability and consumer appeal.
packed in vegetable oil
packed in acidified salt brine
Packed in sweetened water or in sweetened and/or concentrated fruit juice. For single-strength unsweetened fruit juice, use *PACKED IN FRUIT JUICE*. When the specific terms under *PACKED IN SWEETENED LIQUID* are used, the statement seen on the product label should be used for indexing. For additional information, see 21 CFR 145.
packed in sweetened liquid
packed in extra heavily sweetened liquid
packed in fat or oil
Packed in a container under high vacuum (26-29 in.).
vacuum-packed
packed in carbon dioxide
packed in vinegar
packed in slightly sweetened water or juice
packed in nitrogen
packed in gas mixture
packed in gravy or sauce, dairy or egg component
packed in gravy or sauce
packed in gelatin
packed in gravy or sauce, meat
packed in gravy or sauce, vegetable
packed in olive oil
Packed in unsweetened single strength juice or juice prepared from concentrated fruit juice and water; if sweetener is added to the fruit juice, use the appropriate term under *PACKED IN SWEETENED LIQUID*.
packed in fruit juice
packed in vinegar and oil
Packed in broth; includes meat, poultry or seafood packed in its' own juice.
packed in broth
packed in cream or milk
Packed in squid or octopus ink.
packed in ink
packed in gravy or sauce, fruit
packed in animal fat or oil
packed in vinegar with sugar and salt
A food contact material which encloses the food and can be in the type of a container, packaging or wrapping.
food packaging
plastic squeeze bottle or tube, top lined with foil
plastic squeeze bottle or tube
plastic squeeze bottle or tube, top lined with laminate
plastic squeeze bottle or tube, unlined top
plastic squeeze bottle or tube, top lined with cork
glass container, tinless steel lid
bimetal container
glass container, plastic lid, paper lining
laminate tube, ends lined with laminate
laminate tube, ends lined with foil
laminate tube, ends lined with cork
paperboard tube with lid or ends
textile or fabric stocking or casing
ceramic or earthenware bottle
ceramic or earthenware crock or jar
ceramic or earthenware container
paper bag, sack or pouch, plastic liner
paper bag, sack or pouch, foil liner
paper bag, sack or pouch, laminate liner
A soft-sided paper container that is used as a bag.
paper bag, sack or pouch
glass container, cork stopper
plastic tray or pan, laminate cover or wrapping
plastic tray or pan, aluminum foil cover or wrapping
plastic tray or pan, plastic cover or wrapping
plastic tray or pan, paper wrapping
A flat plastic container with raised edges that is used to carry things.
plastic tray or pan
laminate tube, unlined aluminum ends
plastic wrapper
paperboard tray with wrapper
glass container
plastic tray or pan, cardboard cover
glass container, aluminum lid
glass container, plastic lid, laminate lining
glass container, plastic lid or stopper
glass container, aluminum lid, plastic lining
glass container, plastic lid, plastic lining
A thin, transparent plastic film that adheres to the surface and itself, and is used to wrap objects and materials in an air-tight manner.
plastic shrink-pack
laminate tube, unlined plastic ends
aluminum tube, unlined plastic top
glass container, plastic lid, aluminum foil lining
paper bag, sack or pouch, paper liner
paperboard container with laminate liner
glass container, tin-plated steel lid
laminate bag or pouch
plastic boil-in-bag
paperboard container with plastic liner
paperboard container with aluminum foil liner
paperboard container with paper liner
tinless steel plate container
paperboard molded pack
metal container
paperboard container, waxed
paperboard container, plastic coated
paperboard container with window
paperboard container with liner
paperboard container
textile or fabric container
textile or fabric bag
paperboard or paper container
aluminum tray or pan, plastic cover or wrapping
aluminum tray or pan, cardboard cover
aluminum tray or pan, laminate cover or wrapping
aluminum tray or pan, aluminum foil cover or wrapping
aluminum tray or pan, paper wrapping
aluminum tray or pan
plastic bag or pouch
laminate tube
aluminum tube
aluminum tube, top lined with laminate
aluminum tube, top lined with foil
aluminum tube, top lined with cork
Corresponds to FSTA Thesaurus Packaging 2.2.1 Plastic container.
plastic container
paper wrapper
wood container
aluminum can, drum or barrel
tin plate container
wood box
wood drum
wood barrel, cask or wheel
plastic container, molded or bubble pack
laminate container
aluminum container
plastic container, rigid or semirigid, tin-plated steel lid
plastic container, rigid or semirigid
plastic container, rigid or semirigid, tinless steel lid
plastic container, flexible or film
plastic container, rigid or semirigid, plastic lid
plastic container, rigid or semirigid, aluminum lid
steel plate container
aluminum foil wrapper
paperboard container with foil or liner overwrap
plastic container, blow-molded
can, bottle or jar
Classification corresponding to FSTA Thesaurus Packaging 3.1 Package Types
container or wrapping by form
ampul
According to FSTA Thesaurus Packaging 3.1 package types, includes boil-in bag, carrier bag, flat bag, inner bag, retort pouch, shipping bag, valve bag, and valve sack
bag, sack or pouch
drum (container)
A flexible container of distinctive construction and closure features used in the dispensing of tablet or powdered prescription medication; it is typically constructed of film or paper that may be coated or laminated to protect the contents [CFSAN Thesaurus].
envelope
tube
vial
Classification corresponding to FSTA Thesaurus Packaging 2.1.2 Material
container or wrapping by material
A container which is a bottle or a jar.
bottle or jar
A container which is made of a thin metal and and is used for the distribution or storage of goods.
can (container)
leaf wrapper
husk wrapper
capsule
multicontainer package
wax container
glass container, metal lid
wrapper, material unspecified
edible container
box
A narrow-necked container typically made of glass or plastic that is used to store and transport liquids.
bottle
jar
drawn can
three-part can
jug or demijohn
pail
Classification corresponding to FSTA Thesaurus Packaging 3.2.4 Sealing/closing means
sealing/closing element
adhesive
multicomponent adhesive
multicomponent adhesive, no solvent
multicomponent adhesive, organic solvent
multicomponent adhesive, water soluble
one component adhesive
one component adhesive, organic solvent
one component adhesive, water soluble
thermoplastic adhesive
glass stopper
plastic stopper
polyethylene plug
polypropylene plug
polyvinyl chloride plug
plastic screw cap or lid
plastic screw cap/pilfer proof
crown cap
metal screw cap or lid
metal screw cap/pilfer proof
wooden cork
seal/gasket
cork wood gasket
metal gasket
plastic gasket
rubber gasket
steel solder
tin solder
ceramic or earthenware bottle, coloured
ceramic or earthenware bottle, uncoloured
ceramic or earthenware jar, coloured
ceramic or earthenware jar, uncoloured
glass container, uncoloured
glass container, uncoloured, light weight
glass container, uncoloured, normal weight
glass container, uncoloured, strengthened
glass container, uncoloured, covered/protected
glass container, coloured
glass container, coloured, light weight
glass container, coloured, normal weight
glass container, coloured, strengthened
glass container, coloured, covered/protected
aluminum box
aluminium box, plastic-coated
aluminium box, varnished
aluminium can, drum or barrel, plastic coated
aluminium can, drum or barrel, varnished
aluminium foil wrapper, coated for heat sealing
aluminium foil-paper wrapper
aluminum coextruded with paper
aluminum combined with paper and plastic
aluminum combined with regenerated cellulose
laminated aluminum combination with paper
stainless steel container
steel plate container tinned one side
steel plate container tinned both sides
varnished tin-plate container
natural polymer container
casein resin
cellulose film
acetate cellulose film
butyrate cellulose film
propyonate cellulose film
regenerated cellulose film
regenerated cellulose film, coated
regenerated cellulose film, coloured
rubber container
A paper container that has been treated with an antimicrobial agent or preservative chemical.
paper container, treated
lacquered paper container
saturated (immersed) paper container
waxed paper container
A paper container that has not been treated with any agents.
paper container, untreated
bleached paper container
kraft or brown paper container
grease proof paper container
imitation grease proof paper container
Porous, wet-strength paper, e.g. tea bag.
tissue paper container
paperboard container, untreated
paperboard container, surface treated
paperboard container, surface treated both sides
paperboard container, surface treated inside
paperboard container, surface treated outside
paper combined material
impregnated/micro waxed paper
metalized paper wrapper
metalized paper coextruded with plastic
metalized paper laminated with plastic
metalized paper laminated with treated paper
paper-aluminium foil-plastic wrapper
coextruded paper-aluminium-plastic wrapper
laminated paper-aluminium-plastic wrapper
paper-paper combination
paper-plastic combination
laminate paper coextruded with plastic
Corresponds to FSTA Thesaurus Packaging 2.2.1 'Type of plastic'
plastic container, according to type of plastic
thermoplastic sheet or container
polyamide container
acryl-nitrile container
nylon 11 container
nylon 6,6 container
polycarbonate container
polyester container
polyester container, glass fibre strengthened
linear polyester container
polyethylene container
high density polyethylene container
low density polyethylene container
linear low density polyethylene container
low density polyethylene container, treated
polymethylmethacrylate container
polypropylene container
biaxial oriented polypropylene container
oriented polypropylene container
polystyrene container
polyvinyl chloride container
unplasticized polyvinyl chloride container
plasticized polyvinyl chloride container
polyvinylidene chloride container
thermosetting polymer container
alkyd resin container
amin resin container
aniline-formaldehyde container
carbamide-formaldehyde container
diciandiamide-formaldehyde container
epoxy resin container
phenonile resin container
polyester resin container
plastic container, combined material
metallized polymer container
metallized polyamide container
metallized polyester container
polyethylene (high density) - polyamide container
polyethylene (high density) - nylon 11 container
polyethylene (high density) - polyester container
polyethylene (high density) - polypropylene container
polyethylene (low density) - polyamide container
polyethylene (low density) - nylon 11 container
polyethylene (low density) - polyester container
polyethylene (low density) - polyethylene (high density) container
polyethylene (low density) - polyethylene (low density) container
polyethylene (low density) - polypropylene container
polyethylene - regenerated cellulose container
polyethylene - vinyl copolymer container
polyvinyl chloride - polyvinylidene chloride container
natural textile container
animal hair container
bass fibre container
asbestos container
cotton container
leaf fibre container
polymer base textile container
polyamide textile container
polyester textile container
polyolefin textile container
boil-in bag
inner bag
closing cap or lid
closing capsule
screw cap or lid
peel-off lid
stopper
Example: egg box.
recycled paperboard container
polyethylene terephthalate (pet) container
polyolefin container
The specific container or coating materials in direct contact with the food. [FDA CFSAN 1995]
food product contact surface
beverage can enamel surface
noncarbonated beverage can enamel surface
carbonated beverage can enamel surface
beer beverage can enamel surface
Wax may be applied directly as a coating to the food product or may be used as a container material. Examples include wax-coated cheese, wax-coated cucumber, waxed fiberboard container, etc.
food-grade wax surface
enamel surface for fruit (f-enamel)
polyethylene surface
enamel surface for citrus fruit
milk enamel surface for milk
enamel surface for meat
polypropylene surface
polystyrene surface
enamel surface for seafood
A surface consisting of a coating that contains a specially prepared vehicle, instead of raw oil. Sometimes referred to as varnish or lacquer.
food-grade enamel-coated surface
Trade name of polyvinylidene chloride copolymer film. Chief packaging uses are in film and in coatings for other flexible substrates such as cellophane and paper.
saran surface
Trade name of polyester used in the usa.
mylar surface
A generic term for a class of polyamides containing repeating amide groups connected by methylene units. The most common types used in food industry are ny-lon-66 and nylon-11.
nylon surface
A surface of a Cryovac bag, a shrinkable version of pvdc used for vacuum packaging, e.g. of red meat.
Cryovac bag plastic surface
Polyvinylidene chloride surface
enamel surface for corn (c-enamel)
Cellophane is a thin, transparent sheet made of regenerated cellulose.
cellophane
A rubber hydrochloride, first introduced as a packaging film in 1936 in the U.S.A.
pliofilm surface
polyester surface
CA: thermoplastic material made by the esterification of cellulose with acetic anhydride and acetic acid.
cellulose acetate surface
A surface made out of food-grade wood.
food-grade wood surface
food-grade plastic surface
PVC
polyvinyl chloride surface
food-grade ceramic surface
food-grade paper product surface
A surface made of food-grade glass.
food-grade glass surface
A surface made of food-grade metal
food-grade metal surface
A surface made out of aluminum metal
aluminum surface
A surface made out of food-grade tin metal.
food-grade tin surface
A surface made of food-grade steel.
food-grade steel surface
A surface of a food-grade textile
food-grade textile surface
food-grade cork surface
Ash which is incorporated into the surface of a food such as cheese.
food-grade ash
A plant leaf used as a food contact surface.
leaf food contact surface
A plant husk used as a food contact surface.
husk food contact surface
food contact surface from natural material
food contact surface from human-made material
latex surface
A surface of Teflon, a trade name for a polymer used to provide better protection and longer life to porous metals (nickel alloys) in coextruded sheets and films.
teflon surface
A very thin edible covering, either natural or some form of a synthetic, that is used to enclose ground meat and other ingredients.
edible casing
A surface made of polymer extracted from nature.
food-grade natural-based polymer surface
laboratory animal as food consumer
food fish as consumer
pet fish as consumer
non-food animal as food consumer
sheep or goat as consumer
food animal as consumer
All narrower term definitions extracted from 58 Federal Register 2302, January 6, 1993, part 101.62(b).
fat special claim
poultry as consumer
cattle as consumer
Food produced and marketed to supply the particular dietary needs of normal infants (21 CFR 105.65) or normal toddlers (age 1 to 2 years). Junior foods are included with the strained foods for infants up to one year. Foods fall in this category only if the label bears a statement such as 'baby food', 'strained food', 'junior food' or 'toddler food'.
infant or toddler as food consumer
animal as food consumer
Renamed from *FOOD FOR SPECIAL DIETARY USE* [LanguaL 2008]. These descriptors are used either for foods intended for special dietary use as defined in 21 CFR 105 or for foods that have special characteristics indicated in the name or labeling. Such claims would include 'low calorie', 'low cholesterol', 'diet' or 'dietetic', etc. Prior to february 1992, this category of descriptors was limited solely to food for adult humans. The category is now used in conjunction with any appropriate *CONSUMER GROUP* descriptor(s), for example, 'low sugar baby food' would be indexed by *INFANT OR TODDLER FOOD* as well as by *LOW SUGARS FOOD*.
dietary claim
horse as consumer
Food produced and marketed for human use.
human as food consumer
pig as consumer
pet cat as consumer
Pet animals as a consumer group; products are labeled accordingly.
pet animal as consumer
pet bird as consumer
pet dog as consumer
A claim that a food is low in energy, and any claim likely to have the same meaning for the consumer, may only be made where the product does not contain more than 40 kcal (170 kJ)/100 g for solids or more than 20 kcal (80 kJ)/100 ml for liquids. For table-top sweeteners the limit of 4 kcal (17 kJ)/portion, with equivalent sweetening properties to 6 g of sucrose (approximately 1 teaspoon of sucrose), applies [REGULATION (EC) No 1924/2006 Corrigendum 2007-01-18]. Food having 40 calories or less per amount customarily consumed (and per 50 grams of food if the amount customarily consumed is small). Meals and main dishes contain 120 calories or less per 100 grams of food [US FDA]
low energy food claim
A claim that a food is energy-reduced, and any claim likely to have the same meaning for the consumer, may only be made where the energy value is reduced by at least 30 %, with an indication of the characteristic(s) which make(s) the food reduced in its total energy value [REGULATION (EC) No 1924/2006 Corrigendum 2007-01-18]. Food having at least 25% fewer calories per amount customarily consumed from the calories of a comparable food product. The complarable food may not be 'low calorie' [US FDA].
reduced energy food claim
A claim that a food is sodium-free or salt-free, and any claim likely to have the same meaning for the consumer, may only be made where the product contains no more than 0,005 g of sodium, or the equivalent value for salt, per 100 g. [REGULATION (EC) No 1924/2006 Corrigendum 2007-01-18]. Food having less than 5 milligrams of salt or sodium per amount customarily consumed (or for meals and main dishes, less than 5 miligrams of salt or sodium per labeled serving). Such foods must not contain an ingredient that is salt or sodium or generally understood to comtain salt or sodium except where the ingredient listed is footnoted '*adds a trivial amount of {salt or sodium}' [US FDA]
salt or sodium free claim
A claim that a food is very low in sodium/salt, and any claim likely to have the same meaning for the consumer, may only be made where the product contains no more than 0,04 g of sodium, or the equivalent value for salt, per 100 g or per 100 ml. This claim shall not be used for natural mineral waters and other waters [REGULATION (EC) No 1924/2006 Corrigendum 2007-01-18]. Food having 35 milligrams or less salt or sodium per amount customarily consumed (and per 50 grams if the amount customarily consumed is small). Meals and main dishes contain 35 milligrams or less salt or sodium per 100 grams of food [US FDA]
very low salt or sodium claim
reduced salt or sodium claim
A claim that a food is low in sodium/salt, and any claim likely to have the same meaning for the consumer, may only be made where the product contains no more than 0,12 g of sodium, or the equivalent value for salt, per 100 g or per 100 ml. For waters, other than natural mineral waters falling within the scope of Directive 80/777/EEC, this value should not exceed 2 mg of sodium per 100 ml [REGULATION (EC) No 1924/2006 Corrigendum 2007-01-18]. Food having 140 milligrams or less salt or sodium per amount customarily consumed. Meals and main dishes have 140 milligrams or less salt or sodium per 100 grams food [US FDA]
low salt or sodium claim
A claim that a food is low in fat, and any claim likely to have the same meaning for the consumer, may only be made where the product contains no more than 3 g of fat per 100 g for solids or 1,5 g of fat per 100 ml for liquids (1,8 g of fat per 100 ml for semi-skimmed milk). [REGULATION (EC) No 1924/2006 Corrigendum 2007-01-18]. Food having 3 grams of fat or less per amount customarily consumed (and per 50 grams of food if the amount customarily consumed is small). Meals and main dishes contain 3 grams or less fat per 100 grams of food and not more than 30% of calories from fat [US FDA].
low fat food
Food containing at least 25% less fat per amount customarily consumed from the fat content of a comparable food product. The comparable food may not be 'low fat'.
reduced fat food
All narrower term definitions extracted from 58 Federal Register 2302, January 6, 1993, part 101.62(d).
cholesterol special claim
Food having less than 2 milligrams cholesterol per amount customarily consumed (or for meals and main dishes, less than 2 milligrams cholesterol per labeled serving). Such food must contain no ingredient that contains cholesterol except where the ingredient listed has been footnoted '*adds a trivial amount of cholesterol'. If the food contains less than 2 milligrams cholesterol per amount customarily consumed by special processing and the total fat exceeds 13 grams cholesterol per amount or labeled serving, the amount of cholesterol must be 'Substantially less' (25%) than in a comparable food with significant market share (5% of market).
cholesterol free claim
Food having 20 miligrams or less cholesterol per amount customarily consumed (and per 50 grams of food if the amount customarily consumed is small). Meals and main dishes contain 20 milligrams or less cholesterol per 100 grams of food. If the food qualifies by special processing and total fat exceeds 13 grams per amount and labeled serving, the amount of cholesterol must be 'substantially less' (25%) than in a comparable food with significant market share (5% of market).
low in cholesterol claim
Food having at least 25% less cholesterol per amount customarily consumed from the cholesterol content of a comparable food product. The comparable food may not be 'low cholesterol'.
reduced cholesterol claim
All narrower term definitions are extracted from 58 Federal Register 2302, January 6, 1993, part 101.60(b) and from Corrigendum to Regulation (EC) No 1924/2006 of the European Parliament and of the Council of 20 December 2006 on nutrition and health claims made on foods.
energy special claim
All narrower term definitions extracted from 58 Federal Register 2032, January 6, 1993, part 101.61.
salt or sodium special claim
A claim that a food is high in fibre, and any claim likely to have the same meaning for the consumer, may only be made where the product contains at least 6 g of fibre per 100 g or at least 3 g of fibre per 100 kcal [REGULATION (EC) No 1924/2006 Corrigendum 2007-01-18]. Food that is promoted as a source of or as high in dietary fiber (often called simply 'fiber').
high fiber food
Food that is promoted as being either high or low in dietary fiber (often called simply 'fiber'). If the food is not low in total fat, total fat must be stated in conjunction with claim such as 'more fiber'.
fiber special claim
A claim that a food is fat-free, and any claim likely to have the same meaning for the consumer, may only be made where the product contains no more than 0,5 g of fat per 100 g or 100 ml. However, claims expressed as "X % fat-free" shall be prohibited [REGULATION (EC) No 1924/2006 Corrigendum]. Food having less than 0.5 grams fat per amount customarily consumed. Meals and main dishes have less than 0.5 grams fat per labeled serving. Such foods must contain no ingredient that is fat or understood to contain fat except when the ingredient listed has been footnoted '*adds a trivial amount of fat'.
fat free food
A claim that a food is energy-free, and any claim likely to have the same meaning for the consumer, may only be made where the product does not contain more than 4 kcal (17 kJ)/100 ml. For table-top sweeteners the limit of 0.4 kcal (1.7 kJ)/portion, with equivalent sweetening properties to 6 g of sucrose (approximately 1 teaspoon of sucrose), applies [REGULATION (EC) No 1924/2006 Corrigendum 2007-01-18]. Food having less than 5 calories per amount customarily consumed. Calorie amount is not defined for meals or main dishes [US FDA]
energy free food claim
A claim that a food is sugars-free, and any claim likely to have the same meaning for the consumer, may only be made where the product contains no more than 0,5 g of sugars per 100 g or 100 ml [REGULATION (EC) No 1924/2006 Corrigendum 2007-01-18]. Food having less than 0.5 grams sugars per amount customarily consumed (or for meals and main dishes, less than 0.5 grams sugars per labeled serving). Such foods nust contain no ingredient that is a sugar or generally understood to contain sugars except where the ingredient listed is footnoted '*adds a trivial amount of sugars' [US FDA]
sugars free food
A claim that a food is low in saturated fat, and any claim likely to have the same meaning for the consumer, may only be made if the sum of saturated fatty acids and trans-fatty acids in the product does not exceed 1.5 g per 100 g for solids or 0.75 g/100 ml for liquids and in either case the sum of saturated fatty acids and trans-fatty acids must not provide more than 10 % of energy. [REGULATION (EC) No 1924/2006 Corrigendum 2007-01-18]. Food having one gram or less saturated fat per amount customarily consumed and 15% or less of calories from saturated fat. Meals and main dishes contain one gram or less saturated fat per 100 grams food and less than 10% of calories from saturated fat.
low in saturated fat food
general label claim
[REGULATION (EC) No 1924/2006 Corrigendum 2007-01-18]
high energy food claim
All narrower term definitions extracted from 58 Federal Register 2302, January 6, 1993, part 101.60(c).
sugars special claim
A claim that a food is low in sugars, and any claim likely to have the same meaning for the consumer, may only be made where the product contains no more than 5 g of sugars per 100 g for solids or 2,5 g of sugars per 100 ml for liquids [REGULATION (EC) No 1924/2006 Corrigendum 2007-01-18]. Not defined in U.S. Federal Register; no basis for a recommended intake.
low sugars food
low fiber food
As defined in Corrigendum to Regulation (EC) No 1924/2006 of the European Parliament and of the Council of 20 December 2006 on nutrition and health claims made on foods, "claim" means any message or representation, which is not mandatory under Community or national legislation, including pictorial, graphic or symbolic representation, in any form, which states, suggests or implies that a food has particular characteristics; specificly, "nutrition claim" means any claim which states, suggests or implies that a food has particular beneficial nutritional properties due to: (a) the energy (calorific value) it (i) provides; (ii) provides at a reduced or increased rate; or (iii) does not provide; and/or (b) the nutrients or other substances it (i) contains; (ii) contains in reduced or increased proportions; or (iii) does not contain.
nutrition-related claim
no or reduced energy claim
no or reduced fat claim
no fat added claim
All narrower term definitions extracted from 58 Federal Register 2302, January 6, 1993, part 101.62(c).
saturated fat-related claim
no animal fat added claim
no tropical oils added claim
no palm oil added claim
rich in fiber claim
naturally rich in fiber claim
no or reduced salt or sodium claim
no salt added claim
Food having less than 5 milligrams salt per amount customarily consumed (or for meals and main dishes less than 5 milligrams salt per labeled serving). Such food must contain no ingredient that is salt or generally understood to contain salt except where the ingredient listed is footnoted '*adds a trivial amount of salt'.
salt free claim
low salt claim
Food having less than 35 milligrams of salt per serving and per 100 grams of food. (U.S. proposed)
very low salt claim
reduced salt claim
naturally sodium-free food
no or reduced sugar claim
A claim stating that sugars have not been added to a food, and any claim likely to have the same meaning for the consumer, may only be made where the product does not contain any added mono- or disaccharides or any other food used for its sweetening properties. If sugars are naturally present in the food, the following indication should also appear on the label: "CONTAINS NATURALLY OCCURRING SUGARS" [REGULATION (EC) No 1924/2006 Corrigendum]. No added sugars and 'without added sugars' are allowed if no sugar or sugar containing ingredient is added during processing. (28 Federal Register 2302, January 6, 1993)
no sugars added claim
starch-related claim
no modified food starch added claim
no starch added claim
A claim about a vitamin or mineral with respect to an edible product.
vitamin- or mineral-related claim
color-related claim
no artificial colors claim
no color added claim
flavor- or taste-related claim
no artificial flavors claim
no flavor added claim
sweetener-related claim
no artificial sweeteners claim
unsweetened claim
artificial ingredient-related claim
no artificial ingredients claim
no artificial additives claim
preservative-related claim
no nitrite/nitrate added claim
no sulfite added claim
no artificial preservatives claim
no preservatives claim
other ingredient- or constituent-related claim
no msg added claim
caffeine free claim
naturally caffeine free claim
processing-related claim
A raw food that has not been frozen, heat processed or otherwise preserved.
"fresh" label claim
not pasteurized claim
unpurified or unrefined claim
unbleached claim
Health claim means any claim made on the label or in labeling of a food, including a dietary supplement, that expressly or by implication, including "third party" references, written statements (e.g., a brand name including a term such as "heart"), symbols (e.g., a heart symbol), or vignettes, characterizes the relationship of any substance to a disease or health-related condition. See also 21 CFR 101.14 [http://www.accessdata.fda.gov/scripts/cdrh/cfdocs/cfcfr/CFRSearch.cfm?fr=101.14]. A claim is a health claim if in the naming of the substance or category of substances, there is a description or indication of a functionality or an implied effect on health; examples: "contains antioxidants" (the function is an antioxidant effect); "containsprobiotics/prebiotics" (the reference to probiotic/prebiotic implies a health benefit). Equally, claims which refer to an indication of a functionality in the description of a nutrient or a substance (for instance as an adjective to the substance) should also beclassified as a health claim; examples: "with prebiotic fibres" or "contains prebiotic fibres". In Europe, a health claim is any statement about a relationship between food and health [http://ec.europa.eu/food/food/labellingnutrition/claims/health_claims_en.htm], and only authorized health claims are legal [see http://ec.europa.eu/food/food/labellingnutrition/claims/community_register/health_claims_en.htm]. COMMISSION REGULATION (EU) No 432/2012 of 16 May 2012 establishes a list of permitted health claims made on foods, other than those referring to the reduction of disease risk and to children"s development and health [http://eur-lex.europa.eu/LexUriServ/LexUriServ.do?uri=OJ:L:2012:136:0001:0040:en:PDF]
health-related claim
tooth decay-related claim
religion- or customs-related claim
kosher claim
USA: The 1990 Farm Act specifies that a food labeled 'organic' must meet four requirements: 1) the food must be raised by specified methods to replenish and maintain the fertility of the soil; 2) the food must be certified as having been produced with a nationally approved list of materials and practices; 3) to be eligible for certification at least three years must have elapsed between the first organic harvest and first use of nationally approved materials on land and crops;and 4) organic foods must meet all local, state and federal regulations governing the quality and safety of the food supply. Europe: Foods produced in accordance with Council Regulation (EC) No 834/2007 of 28 June 2007 on organic production and labelling of organic products and repealing Regulation (EEC) No 2092/91. [http://eur-lex.europa.eu/LexUriServ/LexUriServ.do?uri=OJ:L:2007:189:0001:0023:EN:PDF]
organic food claim
Considerations include amounts that are 'nutritionally trivial' and amounts that can be declared as zero on the nutrition label. An additional criterion based on amount per weight (e.g., per 100 grams) is not considered necessary because the amount of nutrient in a 'free' food is so low that even frequent and repeated consumption is unlikely to have physiological consequences. (U.S. proposed)
"free" label claim
An amount customarily consumed contains 20% or more of the daily nutritional value to describe protein, vitamins, minerals, dietary fiber, or potassium. May be used on meals or main dishes to indicate that product contains a food that meets the definition.
"high" label claim
"less" label claim
A claim stating that a product is "light" or "lite", and any claim likely to have the same meaning for the consumer, shall follow the same conditions as those set for the term "reduced", see *REDUCED {NAME OF NUTRIENT} NUTRITION CLAIM [P0132]*; the claim shall also be accompanied by an indication of the characteristic(s) which make(s) the food "light" or "lite" [REGULATION (EC) No 1924/2006 Corrigendum 2007-01-18]. Used for foods that have 33.3% fewer calories than a comparable product and a minimum reduction of more than 40 calories per serving. Any other use of 'light' must specify whether it refers to the look, taste or smell; for example, 'light in color'. (U.S. FDA proposed)
"light" label claim
"more" label claim
"source of" label claim
kosher for passover claim
A food consumer group is a class of organism based on their heterotrophic requirements or preferences.
food consumer group
no or reduced cholesterol claim
(percent) fat free claim
Food having less than 5 miligrams sodium per amount customarily consumed (or for meals and main dishes, less than 5 milligrams sodium per labeled serving). Such food must contain no ingredient that is sodium chloride or generally understood to contain sodium except where the ingredient listed is footnoted '*adds a trivial amount of sodium'.
sodium free claim
Food having 35 milligrams or less sodium per amount customarily consumed (and per 50 grams of food if the amount customarily consumed is small). Meals and main dishes contain 35 milligrams or less sodium per 100 grams food.
very low sodium claim
Food containing at least 25% less sodium per amount customarily consumed than the sodium content of a comparable food product. The comparable food may not be 'low sodium'.
reduced sodium claim
Foods having 140 milligrams or less sodium per amount customarily consumed (and per 50 grams of food if the amount customarily consumed is small). Meals and main dishes have 140 milligrams sodium per 100 grams of food.
low sodium claim
game as consumer
rabbit as consumer
other special claim
label claim in food name
label claim separate from food name
no water added claim
pareve claim
noncarbonated claim
lactose reduced food
lactose free food
unenriched claim
no vitamin or mineral added claim
gluten free claim
egg free claim
alcohol free claim
kosher milchlig claim
The food was quickly frozen while still fresh.
"fresh frozen" label claim
A claim that a food does not contain saturated fat, and any claim likely to have the same meaning for the consumer, may only be made where the sum of saturated fat and trans-fatty acids does not exceed 0,1 g of saturated fat per 100 g or 100 ml [REGULATION (EC) No 1924/2006 Corrigendum 2007-01-18]. Food having less than 0.5 grams saturated fat per amount customarily consumed (or for meals and main dishes, less than 0.5 grams saturated fat per labeled serving). Trans fatty acids are not more than 1% of total fat. Such foods contain no ingredient that is understood to contain saturated fat except where the ingredient listed has been footnoted '*adds a trivial amount of saturated fat' [US FDA].
saturated fat free food
Food containing at least 25% less saturated fat per amount customarily consumed than the saturated fat content of a comparable food product. The comparable food product may not be 'low saturated fat'.
reduced saturated fat food
Food having at least 25% less sugars per amount customarily consumed than the sugars content of a comparable food product.
reduced sugars food
Wild or semiwild foods consumed only during periods of famine when no other food is available.
aliment de disette
A food is 'enriched' when nutrients are added to it to replace those that are lost in processing.
enriched food claim
A food is 'fortified' when nutrients that were never present are added to it.
fortified food claim
A claim that iodine has been added to an edible product.
iodized claim
unfortified claim
Characterized by adherence to the dietary practices required by Islamic law (Webster's).
halal claim
adult human as food consumer
infant as food consumer, 0 - 3 months
infant as food consumer, 3 - 6 months
infant as food consumer, 6 - 12 months
toddler as food consumer, 12 months and onwards
low alcohol claim
probiotic claim
full fat claim
trans fat claim
Food Quality/Food Assurance Claim indicates, with reference to the product branding, labelling or packaging, whether the product is stamped with a quality mark, as approved by the governing authority, such as USDA for USA products [Source: GS1].
food quality claim
It should be noted that such claims are illegal in some countries, e.g. Denmark, and that other countries, e.g. United Kingdom, are calling for an end to the use of terms such as 'diabetic' or 'suitable for diabetics' on food labels. The European Commission is considering how foods intended specifically for people with diabetes can be controlled.
diabetic or suitable for diabetics claim
vegan/vegetarian or suitability for vegan/vegetarian claim
no pork added claim
no beef added claim
Food that is promoted as being either high or low in protein.
protein special claim
A claim that a food is high in protein, and any claim likely to have the same meaning for the consumer, may only be made where at least 20 % of the energy value of the food is provided by protein [REGULATION (EC) No 1924/2006 Corrigendum 2007-01-18].
high protein food
natural source of vitamins and or minerals claim
A claim that a food is a source of fibre, and any claim likely to have the same meaning for the consumer, may only be made where the product contains at least 3 g of fibre per 100 g or at least 1,5 g of fibre per 100 kcal [REGULATION (EC) No 1924/2006 Corrigendum 2007-01-18].
source of fibre
A claim that a food is a source of protein, and any claim likely to have the same meaning for the consumer, may only be made where at least 12 % of the energy value of the food is provided by protein. [REGULATION (EC) No 1924/2006 Corrigendum].
source of protein
A claim that a food contains a nutrient or another substance, for which specific conditions are not laid down in this Regulation, or any claim likely to have the same meaning for the consumer, may only be made where the product complies with all the applicable provisions of this Regulation, and in particular Article 5. For vitamins and minerals the conditions of the claim "source of" shall apply. [REGULATION (EC) No 1924/2006 Corrigendum 2007-01-18].
contains {name of the nutrient or other substance} nutrition claim
A claim stating that the content in one or more nutrients, other than vitamins and minerals, has been increased, and any claim likely to have the same meaning for the consumer, may only be made where the product meets the conditions for the claim "source of" and the increase in content is at least 30 % compared to a similar product. [Forordning (EF) nr. 1924/2006 Berigtigelse 2007-01-18].
increased {name of nutrient} nutrition claim
Where a food naturally meets the condition(s) laid down in this Annex for the use of a nutritional claim, the term "naturally/natural" may be used as a prefix to the claim [REGULATION (EC) No 1924/2006 Corrigendum2007-01-18].
"naturally/natural" label claim
A claim that a food is a source of vitamins and/or minerals, and any claim likely to have the same meaning for the consumer, may only be made where the product contains at least a significant amount as defined in the Annex to Directive 90/496/EEC or an amount provided for by derogations granted according to Article 6 of Regulation (EC) No 1925/2006 of the European Parliament and of the Council of 20 December 2006 on the addition of vitamins and minerals and of certain other substances to foods [REGULATION (EC) No 1924/2006 Corrigendum2007-01-18].
source of {name of vitamin/s} and/or {name of mineral/s} nutrition claim
A claim that a food is high in vitamins and/or minerals, and any claim likely to have the same meaning for the consumer, may only be made where the product contains at least twice the value of "source of [NAME OF VITAMIN/S] and/or [NAME OF MINERAL/S]" [REGULATION (EC) No 1924/2006 Corrigendum 2007-01-18].
high {name of vitamin/s} and/or {name of mineral/s} nutrition claim
A claim stating that the content in one or more nutrients has been reduced, and any claim likely to have the same meaning for the consumer, may only be made where the reduction in content is at least 30 % compared to a similar product, except for micronutrients, where a 10 % difference in the reference values as set in Directive 90/496/EEC shall be acceptable, and for sodium, or the equivalent value for salt, where a 25 % difference shall be acceptable. [REGULATION (EC) No 1924/2006 Corrigendum 2007-01-18].
reduced {name of nutrient} nutrition claim
food allergen labelling
Regulated by Directive 2003/89/EC of the European Parliament and of the Council of 10 November 2003 amending Directive 2000/13/EC as regards indication of the ingredients present in foodstuffs.
food allergen labelling about cereals containing gluten and products thereof
food allergen labelling about crustaceans and products thereof
food allergen labelling about eggs and products thereof
food allergen labelling about fish and products thereof
food allergen labelling about peanuts and products thereof
food allergen labelling about soybeans and products thereof
food allergen labelling about milk and products thereof, including lactose
food allergen labelling about nuts and products thereof
food allergen labelling about celery and products thereof
food allergen labelling about mustard and products thereof
food allergen labelling about sesame seeds and products thereof
Sulphur dioxide and sulphites are included in the EU list of allergens because they can cause adverse reactions in some people. Regulated by Directive 2003/89/EC of the European Parliament and of the Council of 10 November 2003 amending Directive 2000/13/EC as regards indication of the ingredients present in foodstuffs.
food allergen labelling about sulphur dioxide and sulphites
Contained in GS1 Allergen Code List.
food allergen labelling about cocoa and products thereof
Contained in GS1 Code List.
food allergen labelling about coriander and products thereof
food allergen labelling about lupine and products thereof
food allergen labelling about corn and products thereof
food allergen labelling about pod fruits and products thereof
food allergen labelling about carrot and products thereof
food allergen labelling about molluscs and products thereof
"no trans fat" claim
'Traditional" means proven usage on the Community market for a time period showing transmission between generations; this time period should be the one generally ascribed to one human generation, at least 25 years [COUNCIL REGULATION (EC) No 509/2006 of 20 March 2006 on agricultural products and foodstuffs as traditional specialities guaranteed]. A traditional food product is a product frequently consumed or associated to specific celebrations and/or seasons, normally transmitted from one generation to another, made with care in a specific way according to the gastronomic heritage, with little or no processing/manipulation, that is distinguished and known because of its sensory properties and associated to a certain local area, region or country. [http://www.truefood.eu/] Traditional means conforming to established practice or specifications prior to the Second World War. Traditional food is a food of a specific feature or features, which distinguish it clearly from other similar products of the same category in terms of the use of traditional ingredients (raw materials or primary products), traditional composition or traditional type of production and/or processing method. [Traditional Foods in Europe, EuroFIR Synthesis report No 6, 2009]
traditional food claim
Ethnic food is food from countries other than the home market contributing to a different food culture than the traditional cuisine of the host country. [Ethnic Groups and Foods in Europe, EuroFIR Synthesis report No 3, 2005] "Ethnic food" has been used colloquially for a wide variety of foodstuffs, virtually any that can be identified in the public mind with a foreign source or an ethnic minority group. In the narrower ethnographic meaning, it pertains only to food prepared or consumed by members of an ethnic group as a manifestation of its ethnicity. In the end ethnic food is food that members of an ethnic group consider their own and that others attribute to them. [http://www.answers.com/topic/ethnic-cuisines]
ethnic food claim
Raw material (species and/or varieties) or primary product either alone or as an ingredient that has been used in identifiable geographical areas and remains in use today (taking into account cases where use was abandoned for a time and then reinstated) and its characteristics are in accordance with current specifications of national and EU legislation. [Traditional Foods in Europe, EuroFIR Synthesis report No 6, 2009]
traditional ingredient claim
The uniquely identifiable composition (in terms of ingredients) that was first established prior to the Second World War and passed down through generations by oral or other means (taking into account cases where composition was abandoned for a time and then reinstated) and when necessary is differentiated from the composition defined by the generally recognized characteristics of the wider food group to which the product belongs. [Traditional Foods in Europe, EuroFIR Synthesis report No 6, 2009]
traditional composition claim
The production and/or processing of a food that has been transmitted from generation to generation through oral tradition or other means and has been applied prior to the Second World War and remains in use (taking into account cases where composition was abandoned for a time and then reinstated) despite its adjustment to binding rules from national or EU food hygiene regulations or the incorporation of technological progress, under the condition that production and/or processing remains in line with methods used originally and that the food"s intrinsic features such as its physical, chemical, microbiological or organoleptic features are maintained. [Traditional Foods in Europe, EuroFIR Synthesis report No 6, 2009]
traditional type of production and/or processing claim
Authentic ethnic food is food from countries other than the home market contributing to a different food culture than the traditional cuisine of the host country. Food may be adapted by combining local and imported ingredients. [Ethnic Groups and Foods in Europe, EuroFIR Synthesis report No 3, 2005]
authentic ethnic food claim
Modified ethnic food: a commercially-available version of a food that has been modified to suit the taste and preference of the host country. [Ethnic Groups and Foods in Europe, EuroFIR Synthesis report No 3, 2005]
modified ethnic food claim
COMMISSION REGULATION (EU) No 116/2010 of 9 February 2010 amending Regulation (EC) No 1924/2006 of the European Parliament and of the Council with regard to the list of nutrition claims.
monounsaturated fat claim
polyunsaturated fat claim
A claim that a food is high in monounsaturated fat, and any claim likely to have the same meaning for the consumer, may only be made where at least 45 % of the fatty acids present in the product derive from monounsaturated fat under the condition that monounsaturated fat provides more than 20 % of energy of the product [COMMISSION REGULATION (EU) No 116/2010 of 9 February 2010 amending Regulation (EC) No 1924/2006 of the European Parliament and of the Council with regard to the list of nutrition claims].
high monounsaturated fat
omega-3 fatty acids claim
A claim that a food is high in omega-3 fatty acids, and any claim likely to have the same meaning for the consumer, may only be made where the product contains at least 0,6 g alpha-linolenic acid per 100 g and per 100 kcal, or at least 80 mg of the sum of eicosapentaenoic acid and docosahexaenoic acid per 100 g and per 100 kcal [COMMISSION REGULATION (EU) No 116/2010 of 9 February 2010 amending Regulation (EC) No 1924/2006 of the European Parliament and of the Council with regard to the list of nutrition claims].
high omega-3 fatty acids
A claim that a food is high in polyunsaturated fat, and any claim likely to have the same meaning for the consumer, may only be made where at least 45 % of the fatty acids present in the product derive from polyunsaturated fat under the condition that polyunsaturated fat provides more than 20 % of energy of the product [COMMISSION REGULATION (EU) No 116/2010 of 9 February 2010 amending Regulation (EC) No 1924/2006 of the European Parliament and of the Council with regard to the list of nutrition claims].
high polyunsaturated fat
unsaturated fat claim
A claim that a food is high in unsaturated fat, and any claim likely to have the same meaning for the consumer may only be made where at least 70 % of the fatty acids present in the product derive from unsaturated fat under the condition that unsaturated fat provides more than 20 % of energy of the product [COMMISSION REGULATION (EU) No 116/2010 of 9 February 2010 amending Regulation (EC) No 1924/2006 of the European Parliament and of the Council with regard to the list of nutrition claims]..
high unsaturated fat
A claim that a food is a source of omega-3 fatty acids, and any claim likely to have the same meaning for the consumer, may only be made where the product contains at least 0,3 g alpha-linolenic acid per 100 g and per 100 kcal, or at least 40 mg of the sum of eicosapentaenoic acid and docosahexaenoic acid per 100 g and per 100 kcal [COMMISSION REGULATION (EU) No 116/2010 of 9 February 2010 amending Regulation (EC) No 1924/2006 of the European Parliament and of the Council with regard to the list of nutrition claims].
source of omega-3 fatty acids
US FDA Approved user group.
human as food consumer, four years and above
man as food consumer
woman as food consumer
pregnant or lactating woman as food consumer
senior as food consumer
teenager as food consumer
child as food consumer, less than four years
US FDA approved language lacking for the moment.
calcium and osteoporosis related claim
athlete as food consumer
bodybuilder as food consumer
menopaused woman as food consumer
weight-reducer as food consumer
infant as food consumer, 0 - 6 months
In the United States, these claims, usually referred to as "qualified health claims", are regulated by the Food and Drug Administration in the public interest, see 21 Code of Federal Regulations § 101.14 [http://www.accessdata.fda.gov/scripts/cdrh/cfdocs/cfcfr/CFRSearch.cfm?fr=101.14]
qualified health claim
Structure/function claims describe the role of a nutrient or dietary ingredient intended to affect normal structure or function in humans, for example, "calcium builds strong bones". In addition, they may characterize the means by which a nutrient or dietary ingredient acts to maintain such structure or function, for example, "fiber maintains bowel regularity," or "antioxidants maintain cell integrity," or they may describe general well-being from consumption of a nutrient or dietary ingredient. [http://www.fda.gov/Food/LabelingNutrition/LabelClaims/StructureFunctionClaims/default.htm]
structure/function claim
The term infant is typically applied to young children between the ages of 1 month and 12 months. [http://en.wikipedia.org/wiki/Infant]
infant as food consumer
Native American food claim
Alaskan Native food claim
Apache food claim
Navajo food claim
Shoshone Bannock food claim
Pacific food claim
Northern Plains food claim
Southwest Plains food claim
Hopi food claim
phytosterol claim
A data item consisting of a claim or record of a food product's origin or processing history or suitability for some purpose.
food datum
cut of meat, u.s.
A cut of meat from the breast or lower chest of beef or veal.
brisket
chuck
flank
rib (meat cut)
round or leg (meat cut)
fore shank
short loin
sirloin
short plate
loin
fat back
jowl, trimmed
foot (meat cut)
Meat cut from the area where the clod meets the edge of the pectoral muscle in an animal.
shoulder (meat cut)
breast (meat cut)
side (meat cut)
cut of meat, composite
A food plant physical characteristic about the ripening stage of development of a fruit.
fruit ripeness
A fruit ripeness characteristic in which a fruit has not achieved full maturity and is not slightly ripe.
unripe
A fruit ripeness characteristic in which a fruit has achieved full maturity and is ready for utilization.
ripe
Boneless skeletal meat from the lower sides of meat animals; usually belly meat is smoked and cured to produce bacon.
belly meat
The process of producing and/or retailing post-harvest food in a consumer or industrial context.
food facility preparation process
The process of preparing food at a human residence.
home food preparation process
The process of preparing and serving food in a restaurant.
restaurant food preparation process
The process of preparing and serving food in a fast food outlet.
fast food outlet preparation process
The process of preparing food in an industrial facility.
food industry preparation process
The process of preparing food in a commissary.
commissary food preparation process
The process of preparing and serving food in a restaurant or fast food outlet.
restaurant or fast food preparation process
The process of sourcing and selling food at a street vending establishment.
street vendor food retail process
cut of meat, french
quartier avant
caparacon
bavette
flanchet
hampe
plat-de-cote
poitrine
collier
basses-cotes
raquette
gite avant
jumeau
marcreuse
quartier arriere
cuisse
gite arriere
semelle
tranche (meat cut)
tranche grasse
aloyau
entre-cote
faux-filet
A boneless cut or slice of meat or fish.
filet
rumsteck
A piece of animal meat which has been cut according to butchery practice.
butchery cut of animal
A food production process involving the rearing of an organism.
agricultural food production
The hunting or foraging for wild food resources.
gathered
wild
wild food harvesting
An agricultural production process involving a domesticated organism.
domestic or cultivated food production
tail
cut of poultry meat
A whole wing that is obtained from a poultry.
The wing of a poultry bird.
poultry wing
A whole breast that is obtained from a poultry.
poultry breast
A whole leg that is obtained from a poultry.
poultry leg
A whole thigh that is obtained from a poultry.
The thigh cut of a poultry bird.
poultry thigh
An agricultural production process involving wild plants, insects or other organisms that are tended and protected.
semidomestic or semiwild food production
A planned process involving the rearing, manufacture or distribution of food material.
food production
The cultivation of plants for food.
food plant cultivation
outdoor/open-air plant cultivation
Open-air plant cultivation using non-organic fertilizer, pest and weed control treatments.
conventional outdoor/open-air cultivation
The organic cultivation of plants in an unsheltered area.
outdoor/open-air organic plant cultivation
under glass/protected plant cultivation
conventional under glass/protected cultivation
The organic cultivation of plants in a sheltered area.
under glass/protected organic plant cultivation
A method of growing plants, usually crops, without soil, by using mineral nutrient solutions in an aqueous solvent.
hydroponic cultivation
tenderloin
Plant cultivation according to organic food production methods including the use of fertilizers of organic origin such as compost manure, green manure, and bone meal and places emphasis on techniques such as crop rotation and companion planting, biological pest control and the fostering of insect predators.
organic plant cultivation
food plant physical quality
An agricultural production process that aims to produce food using natural substances and processes that have a limited negative environmental and human health impact as they encourage the responsible use of energy and natural resources like water, the maintenance of biodiversity, the preservation of regional ecological balances, enhancement of soil fertility, and animal welfare.
organic food production
A method of farming husbandry where the animals, for at least part of the day, can roam freely outdoors, rather than being confined in an enclosure for 24 hours each day. This term can be applied to egg, dairy, poultry, and meat production.
free-range food animal rearing
A meat shank or shin is the portion of meat around the tibia of the animal, the leg bone beneath the knee. [http://en.wikipedia.org/wiki/Shank_(meat)]
shank (meat)
A whole neck that is obtained from a poultry.
The neck cut of a poultry bird.
poultry neck
A food packaging type which is intended for the consumer to remove or open to access food material.
consumer-ready food packaging
A food packaging type which is used in bulk food packaging and is removed prior to retail distribution.
wholesale food bulk packaging
A saku which is derived from tuna fish.
tuna saku
A label claim that no natural or synthetic hormones were added during the production of a food product.
hormone-free food product claim
A label claim that no natural or synthetic antibiotics were added during the production of a food product.
antibiotic-free food product claim
A label claim that the animals which the food product derives from, were not raised in caged housing systems.
cage-free animal claim
A label claim that the animals which the food product derives from, were raised for some portion of their lives on or with access to a pasture.
pasture-raised food product claim
A label claim that the animals which the food product derives from, were fed a grass or forage-based diet.
grass-fed food product claim
A domestic or cultivated food production in which plant or animal from which the food product derives was raised on a farm.
farm-raised food product claim
label claim
GSCID-BRC standard
The GSCID-BRC Project and Sample Application Standard captures standardized human pathogen and vector sequencing metadata to support epidemiologic and genotype-phenotype association studies for human infectious diseases.
The NIAID page for specifications has a broken link for Core Project. This is the existing page: https://www.niaid.nih.gov/research/dmid-metadata-standards-core-project Link page is: https://www.niaid.nih.gov/research/human-pathogen-and-vector-sequencing-metadata-standards
This standard was developed by representatives of the Genome Sequencing Centers for Infectious Diseases (GSCIDs), the Bioinformatics Resource Centers (BRCs), and NIAID and informed by discussions and input with numerous collaborating scientists.
GSCID-BRC Project and Sample Application Standard
MIxS standard
MixS is a unified standard for describing sequence data provided by the Genomic Standards Consortium (GSC)
Minimum Information about any (x) Sequence (MIxS)
MIMARKS standard
The "minimum information about a marker gene sequence" (MIMARKS) is a standard developed by the Genomic Standards Consortium (GSC) for reporting marker gene sequences.
Minimum information about a marker gene sequence
A data item that indicates for the given categorical variable, a respondent has chosen an other or additional response not listed.
This class cannot be referred to directly as a subclass of more than one class without involving inference from the respective classes. Instances of it may exist as a kind of metadata. Usually a reference to a parent categorical class, but not a subordinate, carries the same information.
other (metadata value)
other relevance
other
Other: specify the sample scope that was used.
other specimen scope
other material
Other: specify the material that was used.
other material derived from specimen
A data item that is a free text description provided to indicate a target capture specification not covered by the other types.
other capture type
Specify the project method
other project method
This is an organizational category for grouping parameters relevant to a biomedical sample.
obsolete: draft GenEpiO BioSample standard
An NCBI antibiogram data item is an antimicrobial susceptibility and resistance datum related to drug resistant pathogens. This information is provided within an antibiogram table on BioSample records.
obsolete: NCBI antibiogram data item
HIPPA PHI guideline
The American HIPPA Protected Health Information (PHI) guidelines cover information, including demographic information, which relates to: - the individual’s past, present, or future physical or mental health or condition, - the provision of health care to the individual, or - the past, present, or future payment for the provision of health care to the individual, and that identifies the individual or for which there is a reasonable basis to believe can be used to identify the individual. Protected health information includes many common identifiers (e.g., name, address, birth date, Social Security Number) when they can be associated with the health information listed above."
American HIPPA Protected Health Information (PHI) guidelines
The natural (as opposed to laboratory) full scientific taxonomic name of a subject related to a given investigation, study and/or specimen.
obsolete: subject species
NCBI BioSample: intersex
obsolete: intersex
obsolete: isolation date
A culture isolation date is a date-time entity marking the end of a process in which a sample is isolated as a single colony or non-mixture culture
culture isolation date
year/month/day
A culture frozen date is a date-time entity marking the beginning of a process in which a sample culture is frozen for preservation.
culture frozen date
A date which describes when a laboratory received an isolate.
isolate received date
A date which describes when the isolate was entered into the database.
isolate upload date
gut, spine, tongue, lung
Name of body site where the specimen was obtained from, such as a specific organ or tissue.
Damion Dooley's note: Although term mentions "site" in label, this cannot be placed under "site" as it is intended to refer to organism material, and leads to unsatisfiable terms otherwise.
subject anatomical site
order: NCIT:C115935 # healthy NCIT:C25610 # pathologic NCIT:C28554 # deceased
Health or disease status of a given subject at time of specimen collection.
Currently this does not differ from the 'subject health status (GSCID-BRC)' item. It may be revised to have more options in the future.
subject health status at time of specimen collection
Describes the physical, environmental and/or local geographical source of the biological sample from which the sample was derived.
specimen source context
Substance produced by the body, e.g. stool, mucus, where the specimen was obtained from.
subject body product
Please refer to the definitions of depth in the environmental packages
collection depth datum
The environmental material level refers to the material that was displaced by the sample, or material in which a sample was embedded, prior to the sampling event. Environmental material terms are generally mass nouns. Examples include: air, soil, or water. EnvO (v 2013-06-14) terms can be found via the link: www.environmentontology.org/Browse-EnvO
obsolete: specimen source environmental material
A subject sex is the phenotypic sex of given subject (human or animal) related to a given investigation, study, and/or specimen.
Gender is not used because it is a term referencing human social and cultural convention.
subject sex specification
descriptive; type of human use (park, farm, urban)
Human use of land involving the management and modification of natural environment or wilderness into built environment.
URI: http://en.wikipedia.org/wiki/Land_use
specimen collection site land use
Number of indicator micro-organisms (colony forming units) present in a sample that have been used to suggest the presence of pathogens.
URI: http://www.who.int/water_sanitation_health/dwq/iwachap13.pdf
fecal indicator bacteria count
An environmental datum which describes the electrical conductivity of water.
An environmental datum which describes the concentration of dissolved oxygen in a sample.
GMI MDM standard
The Global Microbial Identifier "Minimum data for Matching" (MDM) standard is a standard that defines essential contextual data fields to be included in genomic sequence repository records.
the Global Microbial Identifier Minimum Data for Matching (MDM) Standard
soluble organic material name;measurement value
A test specification which describes the concentration of substances such as ammonia, road-salt, sea-salt, cyanide, hydrogen sulfide, thiocyanates and thiosulfate in a sample.
soluble inorganic material
soluble inorganic material concentration
An environmental datum which describes the concentration of nitrite of a sample.
An environmental datum which describes the concentration of nitrate of a sample.
An environmental datum which describes the total phosphorus concentration in a sample.
Total phosphorus concentration, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus. Can also be measured without filtering, reported as phosphorus.
Stream order is a measure of the relative size of streams (The smallest tributaries are referred to as first-order streams, while the largest river in the world, the Amazon, is a twelfth-order waterway).
stream order categorical measurement datum
OD reading or cfu's or cells per millilitre
An environmental datum which describes the number of bacteria in a sample.
Restriction enzyme for first characterization
primary enzyme (LMAAI)
PFGE test specification
First PFGE pattern from given diagnostic restriction enzyme
PFGE primary test
Restriction enzyme for second characterization
secondary enzyme (LMACI)
Second PFGE pattern from given diagnostic restriction enzyme
PFGE secondary test
inferred from BCCDC interviews and Bionumerics
Multilocus sequence typing (MLST) is a technique in molecular biology for the typing of multiple loci. The procedure characterizes isolates of microbial species using the DNA sequences of internal fragments of multiple housekeeping genes. Sequence types are grouped into clonal complexes by their similarity to a central allelic profile (genotype). As such, clonal complexes represent sequence types that share a number of identical alleles e.g. 5/7
URI: http://en.wikipedia.org/wiki/Multilocus_sequence_typing ; http://eburst.mlst.net/3.asp
Multilocus sequence typing (MLST) is a technique in molecular biology for the typing of multiple loci. The procedure characterizes isolates of microbial species using the DNA sequences of internal fragments of multiple housekeeping genes. For each housekeeping gene, the different sequences present within a bacterial species are assigned as distinct alleles and, for each isolate, the alleles at each of the loci define the allelic profile or sequence type (ST).
The process of fingerprinting the core genome of a bacteria.
Add under upcomming OBI "DNA fingerprinting assay".
Some bacteria like E coli have a highly variable genome, and so to type them methods must focus on typing the core genome that is common to all strains.
16S ribosomal RNA sequencing is a sequencing method used to identify and compare bacteria present within a given sample. 16S rRNA gene sequencing is a well-established method for studying phylogeny and taxonomy of samples from complex microbiomes or environments that are difficult or impossible to study.
URI: http://www.illumina.com/applications/microbiology/microbial-sequencing-methods/16S-rrna-sequencing.html
A pathogenic shiga toxin produced by STEC E. coli.
Stx toxin type datum
Stx toxin subtype datum
A qPCR measurement result of Stx1 gene amplification.
A measurement datum which describes the level of Stx1 toxin derived tissue culture toxicity.
A qPCR measurement result of Stx2 gene amplification.
A measurement datum which describes the level of Stx2 toxin derived tissue culture toxicity.
An AccuProbe assay that uses a luminometer and DNA probe designed to identify a specific bacteria or fungus species within a culture.
Nucleic acid hybridization tests are based on the ability of complementary nucleic acid strands to specifically align and associate to form stable double-stranded complexes (6). The ACCUPROBE method uses a single-stranded DNA probe with a chemiluminescent label that is complementary to the ribosomal RNA of the target organism. After the ribosomal RNA is released from the target organism, the labeled DNA probe combines with the target organism’s ribosomal RNA to form a stable DNA:RNA hybrid. The Selection Reagent allows for the differentiation of non-hybridized and hybridized probes.The light signal emitted by the DNA:RNA hybrids is measured by a GEN-PROBE luminometer. A positive result is a luminometer reading equal to or greater than the cut-off. A value below this cut-off is the negative result.
AccuProbe culture identification assay
An AccuProbe reagent kit for identifying Listeria monocytogenes.
URI: http://www.hologic.com/sites/default/files/package%20inserts/103051F-EN-RevC.pdf
AccuProbe Listeria monocytogenes culture identification reagent kit
A categorical diagnostic result of an AccuProbe test.
Ribotyping involves the fingerprinting of genomic DNA restriction fragments that contain all or part of the genes coding for the 16S and 23S rRNA. By digesting the genes with a specific restriction enzyme, fragments of different lengths are generated. By performing a Gel electrophoresis with the digested samples, the fragments can be visualised as lines on the gel, where larger fragments are close to the start of the gel, and smaller fragments further down. After blotting onto a matrix and probing, these lines form a unique pattern for each species and can be used to identify the origin of the DNA, almost like a barcode can identify a product.
This method is based on restriction endonuclease digestion of bacterial chromosomal DNA, followed by Southern hybridization to probes for sequences in the regions of bacterial DNA coding for the 5S-16S-23S (the Escherichia coli rrnB rRNA operon) rRNA operon. The probes have been developed that are directed to highly conserved regions of the rRNA operon present in all eubacteria and can therefore be used for ribotyping most bacteria
A device that generates an automated genetic fingerprint of a bacterium from a bacterial suspension.
an automated system that takes a purified bacterial suspension, lyses the cells, extracts the DNA, restriction endonuclease digests the DNA, separates the digest on a gel, transfers the DNA bands to a membrane, probes the bands with non-radioisotope-labeled, 5S-16S-23S rRNA-specific probes (Southern hybridization), photographs the membrane, and finally compares the bar code-like pattern to databases in order to identify the genus and species.
Qualicon (DuPont) RiboPrinter Microbial Characterization System
A dataset which is a library of RiboPrinter recognised patterns.
DuPont identification number from the DuPont identification library
The identification of an isolate was determined when the corresponding patterns matched one of the patterns of the DuPont Identification library of the RiboPrinter1 with a similarity of >0.85. The similarity threshold for an isolate joining a ribogroup is an adaptive value between 0.90 and 0.96, depending on the size of the ribogroup.
Similarity of pattern to one of the patterns of the DuPont Identification library of the RiboPrinter
Date the sequencing run was performed
sequencing run date
A laboratory sequencing datum which describes the location the sequencing run was performed.
Illumina (MiSeq, HiSeq), PacBio, Ion Torrent, (Roche 454), SOLiD ABI
A sequencing plaform (brand) is a name of a company that produces sequencer equipment.
sequencing platform (brand)
A lab sequencing datum which describes a pre-defined sequence of steps to run the automated sequencing pipeline.
sequencing application
the sequencing conditions and the analyte being measured
obsolete: sequencing assay
A laboratory sequencing datum which describes the method and chemistry used to determine the order of nucleotides in a DNA molecule.
sequencing chemistry
A datum of the number of base pairs per read.
A GSCID/BRC data item is a field in one of the GSCID/BRC Project and Sample Application Standard subsets.
obsolete: GSCID-BRC data item
Molecular barcodes, called Multiplex Identifiers (MIDs), that are used to specifically tag unique samples in a sequencing run. Sequence should be reported in uppercase letters
sequencing run multiplex identifiers
Derived from Illumina Sample Sheet specification: http://support.illumina.com/content/dam/illumina-support/documents/documentation/system_documentation/miseq/miseq-sample-sheet-quick-ref-guide-15028392-j.pdf
1,2,3, AX234, etc.
A sequencing run sample identifier is an alphanumeric identifier for a sample. In bioinformatics processing this identifier is assigned to a sample in order to track it through the process of sequencing and analysis.
PulseNet: SubmittedNumber
sample name
sample title
sequencing run sample identifier
Number of sequencing chemistry cycles
sequencing count of chemistry cycles
Pre-filled, ready-to-use reagent cartridges. Used to produce improved chemistry, cluster density and read length as well as improve quality (Q) scores. Reagent components are encoded to interact with the sequencing system to validate compatibility with user-defined applications.
sequencing kit
A string datum which is the version/configuration of the reagent cartidge.
Adapters provide priming sequences for both amplification and sequencing of the sample-library fragments. Both adapters should be reported; in uppercase letters
adapter sequence
The removal of adapter sequences from demultiplexed data reads
read adapter trimming
Illumina metagenomic protocol (part 15044223), with Nextera
Packaged kits (containing adapters, indexes, enzymes, buffers etc), tailored for specific sequencing workflows, which allow the simplified preparation of sequencing-ready libraries for small genomes, amplicons, and plasmids.
GROUP: IRIDA Ontology (Emma) and http://applications.illumina.com/applications/sequencing/ngs-library-prep.html
The estimated size of the genome prior to sequencing. Of particular importance in the sequencing of (eukaryotic) genome which could remain in draft form for a long or unspecified period.
number of expected base pairs per genome
Raw data are filtered to remove any reads that do not meet the overall quality as measured by a chastity filter. The chastity of a base call is calculated as the ratio of the brightest intensity divided by the sum of the brightest and second brightest intensities. Clusters passing filter are represented by PF in analysis reports. Clusters pass filter if no more than one base call in the first 25 cycles has a chastity of < 0.6.
URI: http://support.illumina.com/sequencing/sequencing_instruments/miseq/questions.html
Cluster Generation is a process by which libraries amplified into clonal clusters on a flow cell. The density of those clusters in the lane, is the cluster density.
URI: https://www.broadinstitute.org/files/shared/illuminavids/clusterGenSlides.pdf
An assembly quality control datum that describes the quality of the identification of nucleobases generated in sequencing, where the score is logarithimically related to the probability of an error in base calling.
URI: http://en.wikipedia.org/wiki/Phred_quality_score
the GROUP: MIxS term encompasses assembly method; estimated error rate; method of calculation
Assembly method refers to how the reads were assembled into contigs for which either a de novo or mapping (reference based) strategy is used.
from within "Finishing strategy" in GROUP: MIxS
An assembly quality control datum that describes the status of the assembly which is categorised from draft to finished.
CITATION: Chain, P.S., Grafham, D.V., Fulton, R.S., Fitzgerald, M.G., Hostetler, J., Muzny, D., Ali, J., Birren, B., Bruce, D.C., Buhay, C., et al. (2009). Genomics. Genome project standards in a new era of sequencing. Science 326, 236-237.
"Attempting to convey the relative integrity and reliability of the data, six levels or terms have been proposed and applied to describe genome sequences." See subclass choices.
assembly status
Coverage (read depth or depth) is the average number of reads representing a given nucleotide in the reconstructed sequence.
URI: http://en.wikipedia.org/wiki/Shotgun_sequencing
Damion Dooley's note: Wikipedia defines calculation with: "the length of the original genome (G), the number of reads(N), and the average read length(L) as N * L/G"
A contig count is the count of contigs that belong to a sequence assembly.
contig count
Name/version of the assembly provided by the submitter that is used in the genome browsers and in the community
assembly name (identifier)
For cases where annotation was provided by a community jamboree or model organism database rather than by a specific submitter
obsolete: NCBI BioSample data item
An IRIDA case ID is a tracking identifier for a case used in the IRIDA.ca software system. It is used to cross-reference anonymized IDs.
An NCBI BioProject data item is a datum within the NCBI BioProject standard collection
obsolete: NCBI BioProject data item
The INDISC consortium "Minimum data for Matching" standard aims to define a format to capture reads and minimum metadata. It is developed by the "Repository and storage of sequence and meta-data" workgroup 2. It is used in the Global Microbial Identifier platform.
obsolete: INSDC MDM standard
A MixS data item is a term or field defined in the Genomic Standards Consortium MIxS standard.
obsolete: MIxS data item
The 'draft data standard' class contains draft representations of formal or defacto third party standards and related components. These representations may have been crafted without any involvement of related standards issuers and so no guarantee can be provided about their currency, accuracy or veracity.
draft data standard
obsolete: HIPPA PHI data item
obsolete: PulseNet data item
The I2B2 Workbench Data Protection role standard is a standard which names and lists data protection roles between a user and a given dataset that define the level of detail a user has access to.
Derived from the Data Protection Track of the I2B2 Workbench software specification: https://www.i2b2.org/software/files/PDF/current/IM_Architecture.pdf
I2B2 Data Protection role standard
order: NCIT:C115935 # healthy NCIT:C25610 # pathologic / diseased NCIT:C28554 # deceased
A description of whether a given subject organism appeared healthy, sick or deceased at the time of specimen extraction. If sick or deceased, additional details should be provided in project-specific fields.
subject health status (GSCID-BRC)
The GSCID-BRC Core Sample Standard is an extension of the GMI MDM data standard
GSCID-BRC Core Sample standard
A Core Project item is a field in the GSCID/BRC Project and Sample Application Core Project Standard.
GSCID-BRC Core Project standard
Specimen category is a categorical variable that broadly indicates the source of a specimen in order for data processing systems like NCBI's biosample submission portal to anticipate other fields related to the source. Currently this distinguishes between "clinical or host associated" specimens and "environmental/food or other pathogen" specimens.
specimen category
Age unit of the age measurement of a subject (individual organism).
Damion Dooley Feb 20, 2017: GSCID-BRC calls for an explicit field here whereas NCBI Biosample and MIxS don't.
subject age - unit
The National Center for Biotechnology Information offers standards for submitting genomic project data to their BioProject and BioSample databases.
National Center for Biotechnology Information standard
NCBI standard
A datum containing the city or region or more precise geographical location identifier for the site of a specimen collection event.
Adapted from NIAID GSCID-BRC metadata working group
Note that this is expressed in a particular format in some standards.
specimen collection location - city or region
The country of the site of a given specimen collection event.
specimen collection location - country
The Darwin Core is body of standards. It includes a glossary of terms (in other contexts these might be called properties, elements, fields, columns, attributes, or concepts) intended to facilitate the sharing of information about biological diversity by providing reference definitions, examples, and commentaries.
Darwin Core Terms
A datetime measurement related to a person's travel with respect to potential epidemilogical implications.
travel history item
The date of a person's departure from their primary residence (at that time) on a journey to one or more other locations.
travel start date
The date of a person's return to some residence from a journey originating at that residence.
travel end date
Infection aquired during travel is a boolean datum indicating a diagnosis of a traveller's infection during a given trip.
infection aquired during travel
This is a model of the datums involved in an epidemiology investigation.
draft pathogenic epidemiology case investigation record
The draft epi case exposure model describes datums related to the possible transmission of a pathogen between a case person and other people, places, animals etc.
draft pathogenic epi case exposure record
A description of a food item that a case patient has come in contact with.
draft pathogenic epi case food record
food brought back from travel
An epidemiology contact network model is a definition of the information necessary to connect pathogen transmission patterns between individuals or animals in connection with an outbreak investigation.
epidemiology contact network model
An epi contact network - human is contact information about a person who may be involved in transmitting a pathogen.
epi contact network model - human
This is a model that provides location and transportation information about an animal that may be involved in transmitting a pathogen to a human or other animal.
epi contact network model - animal
A note is text that provides human-readable information on one or more subjects.
note
An epi case general info model contains datum specifications about an epidemiology investigation case including the person involved, contact information and their demographics.
draft pathogenic epi case general information record
A record of the details around how, when, and from what an isolate was extracted.
draft pathogenic epi case isolate detail record
A specimen source substance is an organism substance or food product or environmental substance from which the specimen was extracted.
specimen source substance
An isolate sequence filename is the file name (http://edamontology.org/data_1050) of the contig assembly file created by a bioinformatics assembly process.
isolate sequence filename
A cluster identifier is an identifier that locates a genomic variant of an organism within a community of past or present genetically related organisms.
cluster identifier
A laboratory test performed on a specimen from a patient with regard to potential pathogenic disease.
draft pathogenic epi case test record
A lab test requestor is the individual or agency requesting that one or more tests be performed on a specimen.
contact specification - lab test requester
A food cultural origin datum indicates the cultural origin of a food product.
food cultural origin
A record of a patient's recent travel - departure and return, mode of travel and locations visited - as it may pertain to an outbreak pathogen transmission event.
draft pathogenic epi case travel record
Region (England) (entry subject to GAZ replacement)
An epi network contact is a person who may have recieved or transmitted an infectious disease related to an outbreak investigation.
contact specification - epi network contact
This model contains data type specifications for whole genome sequencing and epidemiology investigation contextual data.
public health lab epidemiology contextual data standard
This is a set of datums involved in laboratory processing of whole-genome-sequenced isolates.
draft whole genome sequencing lab test record
A data specification which records the bioinformatics process of a draft whole genome sequencing product.
draft WGS lab bioinformatics process record
A data specification which records the sequencing datum of a draft whole genome sequencing product.
draft WGS lab sequencing record
An NCBI SRA meta information item is a field specification for a NCBI Sequence Read Archive record.
NCBI SRA meta information standard
An isolate raw read filename is the file name (http://edamontology.org/data_1050) of the raw read file created by a genomic sequencing assay.
isolate raw read filename
The version identifier of a packaged kit tailored for specific sequencing workflows.
library preparation kit version
The name and version of software used in a bioinformatics workflow to improve the quality of sequencing reads.
read trimming and filtering software
A laboratory sequencing datum which describes the name of the bioinformatics pipeline used.
bioinformatics pipeline name
A laboratory sequencing datum which describes the version of the bioinformatics pipeline used.
bioinformatics pipeline version
A laboratory sequencing datum which describes the protocol for the bioinformatics pipeline.
bioinformatics pipeline protocol
A data specification which records the sequencing quality datum of a draft whole genome sequencing product.
draft WGS lab sequencing quality metrics record
A data specification which records the assembly quality datum of a draft whole genome sequencing product.
draft WGS lab assembly quality metrics record
A general label indicating the primary study goal. These are only relevant for Primary submission projects (not Umbrella projects).
Damion Dooley's note: According to http://trace.ddbj.nig.ac.jp/news/2014-11-12_e.html, "A BioProject record can have multiple project data types"
project data type
Genome assembly project utilizing already existing sequence data including data that was submitted by a different group
assembly project
A sequencing project involving clone-ends
clone ends project
A sequencing project involving DNA methylation, histone modification, and/or chromatin accessibility datasets
epigenomics project
Exome resequencing project
exome resequencing project
A whole, or partial, genome sequencing project (with or without a genome assembly)
genome sequencing project
The Relational Sequencing TB Data Platform (ReSeqTB) catalogs a vast amount of genotypic, phenotypic and related metadata from Mycobacterium tuberculosis (Mtb) strains to enable the development of clinically useful, WHO-endorsed in vitro diagnostic assays for rapid drug susceptibility testing of Mtb.
draft ReSeq Tuberculosis data platform standard
In expressions like: "<= 8mg/L"
The measurement comparator is a sign indicating that a measurement is above, equal to, or below a given threshold.
test threshold measurement comparator
The "less than" comparator indicates that a given substance was present at less than a given quantity or concentration.
less than
The "less than or equal to" comparator indicates that a given substance was present at less than or equal to a given quantity or concentration.
less than or equal to
The "equal to" comparator indicates that a given substance was present at the given quantity or concentration.
equal to
The "greater than or equal to" comparator indicates that a given substance was present at greater than or equal to a given quantity or concentration.
greater than or equal to
The "greater than" comparator indicates that a given substance was present at greater than a given quantity or concentration.
greater than
order: OBI:0001616 # specimen identifier OBI:0001614 # GenBank ID GENEPIO:0001100 # antibiogram drug test model GENEPIO:0002062 # amr testing reference standard GENEPIO:0002045 # amr resistance testing method GENEPIO:0002047 # ... version or reagent GENEPIO:0002049 # amr testing platform GENEPIO:0002056 # ... vendor
The NCBI antibiogram standard details the reporting specifications for antimicrobial susceptibility and resistance data derived from drug resistant pathogens. This information is submitted as an antibiogram table on BioSample records.
NCBI Antibiogram standard
obsolete: NCBI isolate AMR testing model
A restaurant or an eatery, is a business which prepares and serves food and drinks to customers in exchange for money.
obsolete: restaurant
iPHIS standard
The Canadian Integrated Public Health Information System (iPHIS) System provides a standard for holding reportable disease cases from participating jurisdictions.
Canadian Integrated Public Health Information System (iPHIS) Standard
The MIRU24 - international standard is a mycobacterial interspersed repetitive units (MIRU) typing method that classifies Mycobacterium tuberculosis complex (MBTC) bacteria according to a multiple locus VNTR [variable number of tandem repeats] analysis (MLVA) typing scheme of counts of repeats at 24 sequence loci.
The ordering of loci is as follows: MIRU 04, MIRU 26, MIRU 40, MIRU 10, MIRU 16, MIRU 31, 424 577, 2165, 401, 3690, 4156, 2163, 1955, 4052, MIRU 02, MIRU 23, MIRU 39, MIRU 20, MIRU 24, MIRU 27, 2347, 2461, 3171
MIRU24 - international standard
The MIRU24 - Canadian standard is a Mycobacterium tuberculosis typing method exactly like MIRU24 - international standard except that the report of the ordering of the matching loci is different.
The ordering of loci is as follows: MIRU 02, MIRU 04, MIRU 10, MIRU 16, MIRU 20, MIRU 23, MIRU 24, MIRU 26, MIRU 27, MIRU 31, MIRU 39, MIRU 40, 424, 577, 1955, 2163, 2165, 2347, 2401, 2461, 3171, 3690, 4052, 4156
MIRU24 - Canadian standard
spray-wading water
pool water
obsolete: hot tub
A cafeteria is a type of food service location in which there is little or no waiting staff table service, whether a restaurant or within an institution such as a large office building or school.
obsolete: cafeteria
obsolete: bakery
A delicatessen or deli is a retail establishment that sells a selection of unusual or foreign prepared foods.
obsolete: delicatessen
A food kiosk is a kiosk (a booth with an open window on one side) that sells food.
obsolete: food kiosk
A grocery store is a retail store that primarily sells food.
obsolete: grocery store
A specialty/ethnic food store is a store specializing in a particular variety of food or food of cultural / regional origin.
obsolete: specialty/ethnic store
A market, or marketplace, is a location where people regularly gather for the purchase and sale of provisions, livestock, and other goods
obsolete: market
A time measurement datum that pertains to a patient's medical treatment.
treatment history datum
A restaurant providing prepared meals or other food items that the purchaser intends to eat elsewhere
obsolete: take out restaurant
A treatment start date is a date/time datum which indicates the start of a particular medical treatment for a patient.
treatment start date
canoeing / kayaking / boating
hiking
camping
obsolete: social gathering
obsolete: party
obsolete: wedding
obsolete: baby shower
obsolete: potluck
obsolete: community event
A long term care facility provides a type of residential care. It is a place of residence for people who require continual nursing care and have significant difficulty coping with the required activities of daily living.
obsolete: long term care facility
A treatment end date is a date/time datum which indicates the end of a particular medical treatment for a patient.
treatment end date
food related exposure event
Some bacteria are associated with particular foods. Need relationship
infection-specific food detail
A tuberculosis treatment antibiotic is an antibiotic used in the treatment of tuberculosis.
tuberculosis treatment drug
“Treatment of Tuberculosis Guidelines”, WHO, Geneva, 2010, 30 www.who.int/tb/ - See more at: http://www.tbfacts.org/tb-drugs/#sthash.nibuzCLV.dpuf
vegetarian
A time measurement datum that pertains to an organism's physical location.
organism location history datum
This will take on a sub-herarchy of food types.
food avoidance
special diet
water related exposure event
municipal water
A time measurement datum indicating the year a person immigrated to a given country.
immigration year of arrival
bottled water
An event where one or more hosts are exposed to an infectious pathogen
infectious disease exposure event
human related exposure event
animal related exposure event
Identification or description of the specific individual from which this sample was obtained
NCBI BioSample isolate (human name or description)
obsolete: petting zoo
agricultural fair
An isolate passage history is a record of the cyclic growth process that led to it, including number of times its was put through the process, and the method used.
isolate passage history datum
For Eschericia coli: STEC, UPEC
A pathotype is a common name for a group of organisms (of the same species) that have the same pathogenicity on a specified host
NCBI pathotype
Duplicate term, replaced by more appropriate FOODON term FOODON:00003357 'pet treat'.
obsolete: pet treat
Duplicate term, replaced by more appropriate FOODON term, FOODON:00003356
obsolete: pet food (raw)
An epidemiology travel datum is a datum regarding a particular human's travel trip destination, mode, and motivation, with respect to an epidemiology investigation.
human exposure event - travel datum
boat / cruise travel
train travel
bus travel
car travel
airline travel
A travel mode is a type of transportation which a given human has used while travelling on a particular trip.
travel mode
A travel reason is a motivation for traveling on a particular trip expressed by the traveller.
travel reason
travel for pleasure
business activity
religious missionairy activity
rural backpacking activity
visiting relative/friends
travel tour
unsure of travel reason
The tuberculosis draft standard is a GenEpiO set of draft genomic and clinical data items related to Mycobacterium tuberculosis that various agencies are using in their own reporting.
draft tuberculosis - specimen contextual data standard
behavioural risk factor
obsolete: E. coli serotype part
O antigen
H antigen
homeless status
A serotype or serovar is a distinct variation within a species of bacteria or virus or among immune cells of different individuals. These microorganisms, viruses, or cells are classified together based on their cell surface antigens, allowing the epidemiologic classification of organisms to the sub-species level
serovar/serotype common name
Salmonella serovar
Salmonella serovar name
Salmonella antigenic formula
drug use status
incarceration status
HIV status
HIV risk status
A.I.D.S status
drug abuse status
injection drug use status
recreational drug use status
methadone use status
substantial alcohol use/abuse status
smoking status
A country of birth is the country that a given person (or animal) was born in.
country of birth
Tb_1 (with respect to an Illumina SampleSheet.csv spreadsheet) 13 (with respect to a ReSeqTB SNP pipeline sample report)
A sequence number is a numeric identifier of a sequence with respect to a particular data table or dataset.
sequence number
The 'date last seen alive' is the date that a subject (patient) was last known (seen, heard, messaged) to be alive.
date last seen alive
second line or reserve tuberculosis drug
tuberculosis infection anatomical site
obsolete: NCBI Antibiogram model
order: GENEPIO:0001187 # antimicrobial resistance test drug GENEPIO:0002112 # drug MIC GENEPIO:0002080 # drug minimum inhibitory concentration unit GENEPIO:0001001 # measurement comparator NCIT:C85539 # antimicrobial resistance phenotype GENEPIO:0002181 # antimicrobial resistance phenotype - ECOFF
This is the minimal set of parameters for drug test results for a particular antimicrobial agent.
draft antibiogram drug test model
A date-time datum that marks the predicted start of possible human or animal exposure to a pathogen agent, directly or indirectly, based on a suspected pathogen and first symptom date-time.
predicted exposure start
A date-time datum that marks the predicted end of possible human or animal exposure to a pathogen agent, directly or indirectly, based on a suspected pathogen and first symptom date-time.
predicted exposure end
Map: - project that results in non-sequence map data such as genetic map, radiation hybrid map, cytogenetic map, optical map, and etc.
map project
Metagenome: sequence analysis of environmental samples
metagenome project
Metagenome assembly: a genome assembly generated from sequenced environmental samples
metagenome assembly project
Other: a free text description is provided to indicate Other data type
other project data type
Phenotype or Genotype: project correlating phenotype and genotype
phenotype or genotype project
Proteome: large scale proteomics experiment including mass spec. analysis
proteome project
Random Survey: sequence generated from a random sampling of the collected sample; not intended to be comprehensive sampling of the material.
random survey project
Targeted locus (loci): project to sequence specific loci, such as a 16S rRNA sequencing
targeted locus (loci) project
Transcriptome or Gene expression: large scale RNA sequencing or expression analysis. Includes cDNA, EST, RNA_seq, and microarray.
transcriptome or gene expression
A sequencing project with a primary goal of identifying large or small sequence variation across populations.
variation project
(Afghanistan|Albania|Algeria|American Samoa|Andorra|Angola|Anguilla|Antarctica|Antigua and Barbuda|Arctic Ocean|Argentina|Armenia|Aruba|Ashmore and Cartier Islands|Atlantic Ocean|Australia|Austria|Azerbaijan|Bahamas|Bahrain|Baltic Sea|Baker Island|Bangladesh|Barbados|Bassas da India|Belarus|Belgium|Belize|Benin|Bermuda|Bhutan|Bolivia|Borneo|Bosnia and Herzegovina|Botswana|Bouvet Island|Brazil|British Virgin Islands|Brunei|Bulgaria|Burkina Faso|Burundi|Cambodia|Cameroon|Canada|Cape Verde|Cayman Islands|Central African Republic|Chad|Chile|China|Christmas Island|Clipperton Island|Cocos Islands|Colombia|Comoros|Cook Islands|Coral Sea Islands|Costa Rica|Cote d'Ivoire|Croatia|Cuba|Curacao|Cyprus|Czech Republic|Democratic Republic of the Congo|Denmark|Djibouti|Dominica|Dominican Republic|East Timor|Ecuador|Egypt|El Salvador|Equatorial Guinea|Eritrea|Estonia|Ethiopia|Europa Island|Falkland Islands (Islas Malvinas)|Faroe Islands|Fiji|Finland|France|French Guiana|French Polynesia|French Southern and Antarctic Lands|Gabon|Gambia|Gaza Strip|Georgia|Germany|Ghana|Gibraltar|Glorioso Islands|Greece|Greenland|Grenada|Guadeloupe|Guam|Guatemala|Guernsey|Guinea|Guinea-Bissau|Guyana|Haiti|Heard Island and McDonald Islands|Honduras|Hong Kong|Howland Island|Hungary|Iceland|India|Indian Ocean|Indonesia|Iran|Iraq|Ireland|Isle of Man|Israel|Italy|Jamaica|Jan Mayen|Japan|Jarvis Island|Jersey|Johnston Atoll|Jordan|Juan de Nova Island|Kazakhstan|Kenya|Kerguelen Archipelago|Kingman Reef|Kiribati|Kosovo|Kuwait|Kyrgyzstan|Laos|Latvia|Lebanon|Lesotho|Liberia|Libya|Liechtenstein|Line Islands|Lithuania|Luxembourg|Macau|Macedonia|Madagascar|Malawi|Malaysia|Maldives|Mali|Malta|Marshall Islands|Martinique|Mauritania|Mauritius|Mayotte|Mediterranean Sea|Mexico|Micronesia|Midway Islands|Moldova|Monaco|Mongolia|Montenegro|Montserrat|Morocco|Mozambique|Myanmar|Namibia|Nauru|Navassa Island|Nepal|Netherlands|New Caledonia|New Zealand|Nicaragua|Niger|Nigeria|Niue|Norfolk Island|North Korea|North Sea|Northern Mariana Islands|Norway|Oman|Pacific Ocean|Pakistan|Palau|Palmyra Atoll|Panama|Papua New Guinea|Paracel Islands|Paraguay|Peru|Philippines|Pitcairn Islands|Poland|Portugal|Puerto Rico|Qatar|Republic of the Congo|Reunion|Romania|Ross Sea|Russia|Rwanda|Saint Helena|Saint Kitts and Nevis|Saint Lucia|Saint Pierre and Miquelon|Saint Vincent and the Grenadines|Samoa|San Marino|Sao Tome and Principe|Saudi Arabia|Senegal|Serbia|Seychelles|Sierra Leone|Singapore|Sint Maarten|Slovakia|Slovenia|Solomon Islands|Somalia|South Africa|South Georgia and the South Sandwich Islands|South Korea|South Sudan|Southern Ocean|Spain|Spratly Islands|Sri Lanka|State of Palestine|Sudan|Suriname|Svalbard|Swaziland|Sweden|Switzerland|Syria|Taiwan|Tajikistan|Tanzania|Tasman Sea|Thailand|Togo|Tokelau|Tonga|Trinidad and Tobago|Tromelin Island|Tunisia|Turkey|Turkmenistan|Turks and Caicos Islands|Tuvalu|USA|Uganda|Ukraine|United Arab Emirates|United Kingdom|Uruguay|Uzbekistan|Vanuatu|Venezuela|Viet Nam|Virgin Islands|Wake Island|Wallis and Futuna|West Bank|Western Sahara|Yemen|Zambia|Zimbabwe|Historical Country Names|Belgian Congo|British Guiana|Burma|Czechoslovakia|Former Yugoslav Republic of Macedonia|Korea|Netherlands Antilles|Serbia and Montenegro|Siam|USSR|Yugoslavia|Zaire)(:[a-zA-Z0-9 ]+)?
help: Consult the http://www.insdc.org/country.html country list for valid options.
The INSDC country qualifier is a textual controlled vocabulary used to indicate the country of origin of a DNA sample. It can also have the following format: country:sub_region, such as: "Canada:Vancouver".
INSDC country qualifier
phenotype
Phenotype: phenotypic measurements for submission to dbGaP
phenotype project objective
genome material
genome material from specimen
TB lineage 7 - Ethiopia
An object aggregate which has as members whole organs or parts of organs, possibly from different organisms.
organs or organ parts
A travel destination which a given human has travelled to on a particular trip and is outside Canada.
travel outside Canada
A travel destination which a given human has travelled to on a particular trip and is outside a given province/territory of interest.
travel outside province/territory
A data specification established for use by The Canadian COVID-19 Genomics Network (CanCOGeN) project for SARS-CoV-2 contextual data (metadata) harmonization and curation across data providers.
The Canadian COVID-19 Genomics Network SARS-CoV-2 specification
The Canadian COVID-19 Genomics Network severe acute respiratory syndrome coronavirus 2 specification
The Canadian coronavirus 2019 Genomics Network severe acute respiratory syndrome coronavirus 2 specification
CanCOGeN SARS-CoV-2 specification
An instance of a "data field category" that contains the "bioproject accession field", "biosample accession field", and "GISAID accession field".
A data field category which receives a range of one or more data fields.
data field category
An instance of the "database identifiers field category" that contains the "bioproject accession field".
A data field category which refers to database identifier fields.
database identifiers
database identifiers slot category
database identifiers field category
An identifier data field which describes the user-defined name for the sample.
sample collector sample identifier
sample_collector_sample_ID
specimen collector sample ID
sample collector sample identifier field
sample collector sample identifier slot
specimen collector sample ID slot
Example Guidance: Every Sample ID from a single submitter must be unique. It can have any format, but we suggest that you make it concise, unique and consistent within your lab, and as informative as possible.
specimen collector sample ID field
A livespan history item is a date-associated event pertaining to the life of a subject.
lifespan history item
A data field which describes the primary identifer of a related specimen previously submitted to the repository.
related specimen primary ID
related specimen primary identifier
related specimen primary ID slot
related specimen primary identifier field
related specimen primary identifier slot
Example Guidance: Store the primary ID of the related specimen previously submitted to the National Microbiology Laboratory so that the samples can be linked and tracked through the system.
related specimen primary ID field
A data field which describes the identifer assigned to a sequenced isolate in Integrated Rapid Infectious Disease Analysis (IRIDA) bioinformatics platform.
IRIDA sample identifier
IRIDA sample name
IRIDA sample ID slot
IRIDA sample identifier slot
IRIDA sample name slot
Integrated Rapid Infectious Disease Analysis sample ID field
Integrated Rapid Infectious Disease Analysis sample ID slot
Integrated Rapid Infectious Disease Analysis sample identifier field
Integrated Rapid Infectious Disease Analysis sample identifier slot
Integrated Rapid Infectious Disease Analysis sample name field
Integrated Rapid Infectious Disease Analysis sample name slot
Example Guidance: Store the IRIDA sample name. The IRIDA sample name will be created by the individual entering data into the IRIDA platform. IRIDA samples may be linked to metadata and sequence data, or just metadata alone. It is recommended that the IRIDA sample name be the same as, or contain, the specimen collector sample ID for better traceability. It is also recommended that the IRIDA sample name mirror the GISAID accession. IRIDA sample names cannot contain slashes. Slashes should be replaced by underscores. See IRIDA documentation for more information regarding special characters (https://irida.corefacility.ca/documentation/user/user/samples/#adding-a-new-sample).
IRIDA sample name field
An identifier data field which describes the International Nucleotide Sequence Database Collaboration (INSDC) umbrella accession number of the BioProject to which the BioSample belongs.
umbrella bioproject accession
umbrella bioproject accession slot
Example Guidance: Required if submission is linked to an umbrella BioProject. An umbrella BioProject links together related BioProjects. A valid BioProject umbrella accession has prefix PRJN, PRJE or PRJD. Your laboratory can have one or many BioProjects.
umbrella bioproject accession field
An identifier data field which describes the International Nucleotide Sequence Database Collaboration (INSDC) accession number of the BioProject(s) to which the BioSample belongs.
bioproject accession
bioproject_accession
bioproject accession slot
Example Guidance: Required if submission is linked to a BioProject. BioProjects are an organizing tool that links together raw sequence data, assemblies, and their associated metadata. A valid BioProject accession has prefix PRJN, PRJE or PRJD, e.g., PRJNA12345 and is created once at the beginning of a new sequencing project. Your laboratory can have one or many BioProjects.
bioproject accession field
A data field which describes the identifier assigned to a BioSample in International Nucleotide Sequence Database Collaboration (INSDC) archives.
biosample accession
biosample_accession
biosample accession slot
Example Guidance: Store the accession returned from the BioSample submission. NCBI BioSamples will have the prefix SAMN, while ENA BioSamples will have the prefix SAMEA.
biosample accession field
A data field which describes the Sequence Read Archive (SRA), European Nucleotide Archive (ENA) or DDBJ Sequence Read Archive (DRA) identifier linking raw read data, methodological metadata and quality control metrics submitted to the International Nucleotide Sequence Database Collaboration (INSDC).
SRA accession
SRA_accession
SRA accession slot
Sequence Read Archive accession field
Sequence Read Archive accession slot
DDBJ = DNA DataBank of Japan Example Guidance: Store the accession assigned to the submitted .run.. NCBI-SRA accessions start with SRR, EBI-ENA runs start with ERR and DRA accessions start with DRR.
SRA accession field
A data field which describes the GenBank/ENA/DDBJ identifier assigned to the sequence in the International Nucleotide Sequence Database Collaboration (INSDC) archives.
GenBank accession
GenBank/ENA/DDBJ accession
GenBank_accession
GenBank accession slot
GenBank/ENA/DDBJ accession field
GenBank/ENA/DDBJ accession slot
National Genetic Sequence Data Base accession field
National Genetic Sequence Data Base accession slot
GenBank = National Genetic Sequence Data Base; ENA = European Nucleotide Archive; DDBJ = DNA DataBank of Japan Example Guidance: Store the accession returned from a GenBank/ENA/DDBJ submission (viral genome assembly).
GenBank accession field
An identifier data field which describes the Global Initiative on Sharing Avian Influenza Data (GISAID) accession number assigned to the sequence.
GISAID accession
GISAID accession slot
Global Initiative on Sharing Avian Influenza Data accession field
Global Initiative on Sharing Avian Influenza Data accession slot
Example Guidance: Store the accession returned from the GISAID submission.
GISAID accession field
A data field which describes the identifier assigned to a sample by a third party service provider.
third party lab sample ID
third party lab sample identifier
third party lab sample ID slot
third party lab sample identifier field
third party lab sample identifier slot
Example Guidance: Store the sample identifier supplied by the third party services provider.
third party lab sample ID field
An instance of the "sample collection and processing field category" that contains the "sample collection date field".
A data field category which refers to sample collection and processing information fields.
sample collection and processing
sample collection and processing slot category
sample collection and processing field category
untreated water
A data field which describes the name of the organization with which the sample collector is affiliated.
sample collected by
sample_collected_by
sample collected by slot
Example Guidance: The name of the agency should be written out in full, (with minor exceptions) and be consistent across multiple submissions.
sample collected by field
treated water - ambient temperature
A data field which describes the email address of the contact responsible for follow-up regarding the sample.
sample collector contact email
sample_collector_contact_email
sample collector contact email slot
Example Guidance: The email address can represent a specific individual or laboratory.
sample collector contact email field
655 Lab St, Vancouver, British Columbia, V5N 2A2, Canada
A data field which describes the mailing address of the agency submitting the sample.
sample collector contact address
sample collector contact address slot
Example Guidance: The mailing address should be in the format: Street number and name, City, State/Province/Region, Country, Postal Code/Zip Code
sample collector contact address field
Centers for Disease Control and Prevention
A data field which describes the name of the agency that submitted the sequence to a database.
Not to be confused with 'sequenced by' http://purl.obolibrary.org/obo/GENEPIO_0100416
sequence submitted by
sequence_submitted_by
sequence submitted by slot
sequence submitted by field
epidemiology investigation data item
Unclear semantics and origin
obsolete distribution event
obsolete supply point / event
A data field which describes the email address of the agency responsible for submission of the sequence.
Not to be confused with 'sequenced by contact email' http://purl.obolibrary.org/obo/GENEPIO_0100422
sequence submitter contact email
sequence submitter contact email slot
sequence submitter contact email field
123 Sunnybrooke St, Toronto, Ontario, M4P 1L6, Canada
A data field which describes the mailing address of the agency responsible for submission of the sequence.
Not to be confused with 'sequenced by contact address' http://purl.obolibrary.org/obo/GENEPIO_0100423
sequence submitter contact address
sequence submitter contact address slot
sequence submitter contact address field
well water - treated
organism datum
A role which inheres in an organism and is realized by the process of being alive.
organism role
isolate organism role
A data field which describes the date on which the sample was collected.
sample collection date
sample_collection_date
sample collection date slot
Example Guidance: Record the collection date accurately in the template. Required granularity includes year, month and day. Before sharing this data, ensure this date is not considered identifiable information. If this date is considered identifiable, it is acceptable to add .jitter. to the collection date by adding or subtracting calendar days. Do not change the collection date in your original records. Alternatively, ”received date” may be used as a substitute in the data you share. The date should be provided in ISO 8601 standard format .YYYY-MM-DD..
sample collection date field
animal role
A data field which describes the precision to which the "sample collection date" was provided.
sample collection date precision
sample collection date precision slot
Used to further describe the .sample collection date field. [GENEPIO:0001174]. Example Guidance: Provide the precision of granularity to the .day., .month., or .year. for the date provided in the .sample collection date. field. The .sample collection date. will be truncated to the precision specified upon export; .day. for .YYYY-MM-DD., .month. for .YYYY-MM., or .year. for .YYYY..
sample collection date precision field
A data field which describes the date on which the sample was received.
sample received date
sample_received_date
sample received date slot
Example Guidance: The date the sample was received by a lab that was not the point of collection. ISO 8601 standard .YYYY-MM-DD..
sample received date field
A data field which describes the country of origin of the sample.
geo_loc name (country)
geographical location country name
geo_loc name (country) slot
geographical location country name field
geographical location country name slot
Example Guidance: Provide the country name from the pick list in the template
geo_loc name (country) field
taxonomic datum
A data field which describes the state, province, or territory of origin of the sample.
geo_loc name (state/province/territory)
geographical location state or province or territory name
geo_loc name (state/province/territory) slot
geographical location state or province or territory name field
geographical location state or province or territory name slot
Example Guidance: Provide the state/province/territory name from the GAZ geography ontology. Search for geography terms here: https://www.ebi.ac.uk/ols/ontologies/gaz
geo_loc name (state/province/territory) field
A course of treatment designed to resolve an infectious disease
infectious disease treatment
This is a collection of drugs used to test antimicrobial resistance.
This is a class of chemicals by use. They are organized more indirectly in CHEBI via 'has role' some 'antimicrobial agent'. Note: NCBI provides special requirements for antibiotic test-selection for BETA-LACTAMASE, see https://www.ncbi.nlm.nih.gov/biosample/docs/beta-lactamase/ Damion Dooley note: Used http://cts.fiehnlab.ucdavis.edu/conversion/batchConvert to convert antibiotic name to CHEBI entries. 60% match, some matches off, had to curate hits manually. Note that this is a longer list of antibiotics that we will need to incorporate, perhaps through ARO: https://www.ncbi.nlm.nih.gov/biosample/docs/antibiogram/?format=txt
antimicrobial resistance test drug
A data field which describes the city of origin of the sample.
geo_loc name (city)
geographical location city name
geo_loc name (city) slot
geographical location city name field
geographical location city name slot
Example Guidance: Provide the city name from the GAZ geography ontology. Search for geography terms here: https://www.ebi.ac.uk/ols/ontologies/gaz
geo_loc name (city) field
Severe acute respiratory syndrome coronavirus 2 [NCBITaxon:2697049]
A data field which describes the taxonomic name of the organism.
organism
organism slot
Example Guidance: Put the genus and species (and subspecies if applicable) of the bacteria, if known. The standardized term can be sourced from this look-up service: https://www.ebi.ac.uk/ols/ontologies/ncbitaxon.
organism field
Judgements here are marked down after an agent's (doctor/veterenary) analysis of symptoms.
analytic datum
obsolete: type of illness
A specimen which has been confirmed by laboratory test(s) to contain a disease-causing agent such as a pathogen
specimen with confirmed presence of disease agent
A data field which describes the reason that the sample was collected.
purpose of sampling
purpose_of_sampling
purpose of sampling slot
Example Guidance: Select a value from the pick list in the template.
purpose of sampling field
Screening of bat specimens in museum collections.
A data field which describes additional information pertaining to the reason the sample was collected.
purpose of sampling details
purpose of sampling details slot
Example Guidance: Provide a free text description of the sampling strategy or samples collected.
purpose of sampling details field
A data field which describes the name of the third party company or laboratory that provided services.
third party lab service provider name
third party lab service provider name slot
Example Guidance: Provide the full, unabbreviated name of the company or laboratory.
third party lab service provider name field
A data field which describes the type of specimen submitted to the National Microbiology Laboratory (NML) for testing.
NML submitted specimen type
National Microbiology Laboratory submitted specimen type
NML submitted specimen type slot
National Microbiology Laboratory submitted specimen type field
National Microbiology Laboratory submitted specimen type slot
Example Guidance: This information is required for upload through the CNPHI LaSER system. Select the specimen type from the pick list provided. If sequence data is being submitted rather than a specimen for testing, select “Not Applicable”.
NML submitted specimen type field
dietary restriction
A person which has a patient care role.
patient type
obsolete: mother
A data field which describes the relationship of the current specimen to the specimen/sample previously submitted to the repository.
Related specimen relationship type
Related specimen relationship type slot
Example Guidance: Provide the tag that describes how the previous sample is related to the current sample being submitted from the pick list provided, so that the samples can be linked and tracked in the system.
Related specimen relationship type field
A data field which describes the substance obtained from an anatomical part of an organism.
anatomical material
anatomical_material
anatomical material slot
Example Guidance: Provide a descriptor if an anatomical material was sampled. Use the pick list provided in the template. If a desired term is missing from the pick list, use this look-up service to identify a standardized term: https://www.ebi.ac.uk/ols/ontologies/uberon. If not applicable, leave blank.
anatomical material field
A subject disease outcome is an assessment of the persistence of a given disease course in a subject (patient)
Note that this is closely related to OGMS_0000063 "disease course" that lists chronic, progressive, transient and accute processes.
subject disease outcome
A data field which describes the anatomical part of an organism.
anatomical part
anatomical_part
anatomical part slot
Example Guidance: Provide a descriptor if an anatomical part was sampled. Use the pick list provided in the template. If a desired term is missing from the pick list, use this look-up service to identify a standardized term: https://www.ebi.ac.uk/ols/ontologies/uberon. If not applicable, leave blank.
anatomical part field
A data field which describes the substance excreted/secreted from an organism.
body product
body_product
body product slot
Example Guidance: Provide a descriptor if a body product was sampled. Use the pick list provided in the template. If a desired term is missing from the pick list, use this look-up service to identify a standardized term: https://www.ebi.ac.uk/ols/ontologies/uberon. If not applicable, leave blank.
body product field
treated water - warm/hot
jacuzzi water
whirlpool water
A host datum is a datum that pertains to infection-related information about an organism (animal or human) who is likely bearing a pathogen
patient as host datum
Soil, water, sewage, door handle, bed handrail, face mask, etc. Example input: Face mask [OBI:0002787]
A data field which describes the substance obtained from the natural or man-made environment.
environmental material
environmental_material
environmental material slot
Example Guidance: Provide a descriptor if an environmental material was sampled. Use the pick list provided in the template. If a desired term is missing from the pick list, use this look-up service to identify a standardized term: https://www.ebi.ac.uk/ols/ontologies/envo. If not applicable, leave blank.
environmental material field
pregnancy history item
date of conception
lifespan history record
obsolete: food cooking method
obsolete: food preservation method
infectious disease case datum
laboratory data
Hospital, wet market, bat cave, etc. Example input: Hospital [ENVO:00002173]
A data field which describes an environmental location as a site in the natural or built environment.
environmental site
environmental_site
environmental site slot
Example Guidance: Provide a descriptor if an environmental site was sampled. Use the pick list provided in the template. If a desired term is missing from the pick list, use this look-up service to identify a standardized term: https://www.ebi.ac.uk/ols/ontologies/envo. If not applicable, leave blank.
environmental site field
A data field which describes the instrument or container used to collect the sample.
collection device
collection_device
collection device slot
Example Guidance: Provide a descriptor if a collection device was used for sampling. Use the pick list provided in the template. If a desired term is missing from the pick list, use this look-up service to identify a standardized term: https://www.ebi.ac.uk/ols/ontologies/obi. If not applicable, leave blank.
collection device field
specimen record
The type of material from which the specimen was obtained. Specimens are usually categorized as food, body products or tissues, or environmental material.
specimen type (host or environmental context)
specimen source material category
Organism has a symbiotic relationship with host
symbiotic role
obsolete: NCBI BioSample attribute package
obsolete: host sample material
Bronchoalveolar lavage (BAL) [GENEPIO:0100032]
A data field which describes the process used to collect the sample.
collection method
collection_method
collection method slot
Example Guidance: Provide a descriptor if a collection method was used for sampling. Use the pick list provided in the template. If a desired term is missing from the pick list, use this look-up service to identify a standardized term: https://www.ebi.ac.uk/ols/ontologies/obi. If not applicable, leave blank.
collection method field
A data field which describes the name and version of a particular protocol used for sampling.
collection protocol
collection protocol slot
Example Guidance: Provide the name and version of the protocol used to collect the samples.
collection protocol field
food specimen detail
patient specimen
environmental
NCBI Biosample: environmental (swab or sampling)
environmental specimen
A specimen extracted from an animal
animal specimen
built environment specimen
food specimen
natural environment specimen
The type of person a patient had epidemiological (i.e. close proximity) contact with.
exposure event person
A data field which describes any processing applied to the sample during or after receiving the sample.
specimen processing
specimen processing slot
Example Guidance: Critical for interpreting data. Select all the applicable processes from the pick list. If virus was passaged, include information in .lab host., .passage number., and .passage method. fields. If none of the processes in the pick list apply, put .not applicable..
specimen processing field
A data field which describes the name and description of the laboratory host used to propagate the source organism or material from which the sample was obtained.
lab host
lab host slot
Example Guidance: Type of cell line used for propagation. Select a value form the pick list. If not passaged, put .not applicable..
lab host field
An exposure group statistics record is a sumary of disease outbreak statistics on a certain date of a group of humans or animals potentially exposed to a pathogen.
exposure group statistics record
symptom history item
health state record
obsolete: swab
A data field which describes the number of passages.
passage number
passage number slot
Example Guidance: Provide number of known passages. If not passaged, put .not applicable.
passage number field
[WHICH DEFINITION?] See http://medical-dictionary.thefreedictionary.com/aspirate
obsolete: fluid - aspirate
AVL buffer+30%EtOH lysate received from Respiratory Lab. P3 passage in Vero-1 via bioreactor large-scale batch passage. P3 batch derived from the SP-2/reference lab strain.
A data field which describes how the organism was passaged.
passage method
passage method slot
Example Guidance: Free text. Provide a short description. If not passaged, put .not applicable..
passage method field
A data field which describes the biomaterial extracted from samples for the purpose of sequencing.
biomaterial extracted
biomaterial extracted slot
Example Guidance: Provide the biomaterial extracted from the pick list in the template.
biomaterial extracted field
Plant rinse is a rinse derived from plant material from one or more plants.
plant rinse
An instance of the "host information field category" that contains the "host (scientific name) field".
A data field category which refers to host information fields.
host information
host information slot category
host information field category
outbreak animal exposure event location
animal exposure process
animal exposure event by material
exposure by human contact
unnecessary distinction
obsolete: human exposure activity type
outbreak human exposure event location
A process in which one or more humans may be exposed to one or more contagious human infectious disease carriers.
human to human exposure process
water exposure by source
human water activity
This list would be customized to include organizations local to an application's software installation. It is an example of a set of ontology terms that would best be organized by a central authority if federated installations need to share investigator contact info for example.
health authority
order: HP:0000118 # symptom FLU:0000976 # onset GENEPIO:0001789 # cessation GENEPIO:0001784 # duration
symptom record
A visual pattern caused by DNA fragments concentrated in stratefied bands in a Pulsed-field gel electrophoresis (PFGE) gel plate.
PFGE pattern
phage type salmonella (DT)
phage type e-coli 0157 (PT)
sequence record
A type of built structure that is suspected to be related to an outbreak investigation.
outbreak exposure event location
lab test history record
obsolete: earth surface
A data specification is a specification of a data structure that can hold a categorical, textual or numeric variable, or that has such variables or other data structures as component parts.
A data standard, may be defined as a data specification, but a data specification isn't necessarily a formal or de-facto data standard - it would have to be sanctioned by a community of users and developers to take on that status.
data specification
A specimen history item is a time-related datum about a particular specimen
specimen history item
A host field which describes the commonly used name of the host.
host (common name)
host (common name) slot
Example Guidance: Common name or scientific name are required if there was a host. Common name examples e.g. human, bat. Select a value from the pick list. If the sample was environmental, put .not applicable..
host (common name) field
A host field which describes the taxonomic or scientific name of the host.
host (scientific name)
host (scientific name) slot
Example Guidance: Common name or scientific name are required if there was a host. Scientific name examples e.g. Homo sapiens. Select a value from the pick list. If the sample was environmental, put .not applicable..
host (scientific name) field
A host field which describes the health status of the host at the time of sample collection.
host health state
host health state slot
Example Guidance: If known, select a value from the pick list.
host health state field
A host data field which describes additional information pertaining to the health or disease status of the host at time of collection.
host health status details
host health status details slot
host health status details field
A host data field which describes the disease outcome in the host.
host health outcome
host health outcome slot
host health outcome field
A host data field which describes the name of the disease experienced by the host.
host disease
host_disease
host disease slot
Example Guidance: This field is only required if there was a host. If the host was a human select COVID-19 from the pick list. If the host was asymptomatic, this can be recorded under “host health state details”. .COVID-19. should still be provided if patient is asymptomatic. If the host is not human, and the disease state is not known or the host appears healthy, put “not applicable”.
host disease field
A host data field which describes the age of the host at the time of sampling.
host age
host age slot
Example Guidance: If known, provide age. Age-binning is also acceptable.
host age field
A host data field which describes the units used to measure the host's age.
host age unit
host age unit slot
Example Guidance: If known, provide the age units used to measure the host's age from the pick list.
host age unit field
A host data field which describes the age category of the host at the time of sampling.
host age bin
host age bin slot
Example Guidance: Age bins in 10 year intervals have been provided. If a host's age cannot be specified due to provacy concerns, an age bin can be used as an alternative.
host age bin field
A host data field which describes the gender of the host at the time of sample collection.
host gender
host gender slot
host gender field
A host geographical location field which describes the country where the host resides.
host residence geo_loc name (country)
host residence geo_loc name (country) slot
host residence geographical location country name field
host residence geographical location country name slot
host residence geo_loc name (country) field
A host geographical location field which describes the state or province or territory of residence of the host.
host residence geo_loc name (state/province/territory)
host residence geo_loc name (state/province/territory) slot
host residence geographical location state or province or territory name field
host residence geographical location state or province or territory name slot
Example Guidance: Select the province/territory name from pick list provided in the template.
host residence geo_loc name (state/province/territory) field
A host data field which describes the unique identifier by which each host can be referred to.
host subject ID
host subject identifier
host subject ID slot
host subject identifier field
host subject identifier slot
Example Guidance: Should be a unique, user-defined identifier. This ID can help link laboratory data with epidemiological data, however, is likely sensitive information. Consult the data steward.
host subject ID field
A data field which describes the date on which the symptoms began or were first noted.
symptom onset date slot
Example Guidance: If known, provide the symptom onset date in ISO 8601 standard format .YYYY-MM-DD..
symptom onset date field
A data field which describes the perceived change in function or sensation (loss, disturbance or appearance) indicative of a disease, reported by a patient.
Generally, "symptoms" are subjective and reported by the patient, while "signs" are observed and reported by a clinician. However, data collected using case report forms are usually relayed by the patient and thus both are deamed "reported by a patient" in this definition.
signs and symptoms
signs and symptoms slot
Example Guidance: Select all of the symptoms experienced by the host from the pick list.
signs and symptoms field
A data field which describes a medical condition that existed prior to the current infection (pre-existing condition) or a variable associated with an increased risk of disease or infection (risk factor).
pre-existing conditions and risk factors
pre-existing conditions and risk factors slot
Example Guidance: Select all of the pre-existing conditions and risk factors experienced by the host from the pick list. If the desired term is missing, contact the curation team.
pre-existing conditions and risk factors field
Acute respiratory failure [MONDO:0001208]
A data field which describes medical complications that are believed to have occurred as a result of host disease.
complications
complications slot
Example Guidance: Select all of the complications experienced by the host from the pick list.
complications field
An instance of the "host vaccination information field category" that contains the "host vaccination status field".
A data field category which refers to host vaccination information fields.
host vaccination information
host vaccination information slot category
host vaccination information field category
A data field which describes the vaccination status of the host.
host vaccination status
host vaccination status slot
Statuses associated with this field: fully vaccinated, partially vaccinated, or not vaccinated. Example Guidance: Select the vaccination status of the host from the pick list.
host vaccination status field
A data field which describes the number of doses of the vaccine received by the host.
number of vaccine doses received
number of vaccine doses received slot
Example Guidance: Record how many doses of the vaccine the host has received.
number of vaccine doses received field
An instance of the "host exposure information field category" that contains the "exposure event field".
A data field category which refers to host exposure information fields.
host exposure information
host exposure information slot category
host exposure information field category
A geographical data field which describes the country where the host was likely exposed to the causative agent of the illness.
location of exposure geo_loc name (country)
location of exposure geo_loc name (country) slot
location of exposure geographical location country name field
location of exposure geographical location country name slot
Example Guidance: This location pertains to the country the host was believed to be exposed, and may not be the same as the host's country of residence. If known, provide the country name from the pick list.
location of exposure geo_loc name (country) field
A geographical data field which describes the name of the city that was the destination of most recent travel.
destination of most recent travel (city)
destination city of most recent travel field
destination city of most recent travel slot
destination of most recent travel (city) slot
Example Guidance: Provide the name of the city that the host travelled to. Use this look-up service to identify the standardized term: https://www.ebi.ac.uk/ols/ontologies/gaz
destination of most recent travel (city) field
A geographical data field which describes the name of the province that was the destination of most recent travel.
destination of most recent travel (state/province/territory)
destination of most recent travel (state/province/territory) slot
destination state or province or territory of most recent travel field
destination state or province or territory of most recent travel slot
Example Guidance: Provide the name of the state/province/territory that the host travelled to. Use this look-up service to identify the standardized term: https://www.ebi.ac.uk/ols/ontologies/gaz
destination of most recent travel (state/province/territory) field
A geographical data field which describes the name of the country that was the destination of most recent travel.
destination of most recent travel (country)
destination of most recent travel (country) slot
Example Guidance: Provide the name of the country that the host travelled to. Use this look-up service to identify the standardized term: https://www.ebi.ac.uk/ols/ontologies/gaz
destination of most recent travel (country) field
A date field which describes the date of an individual's most recent departure from their primary residence (at time of data collection) on a journey to one or more other locations.
most recent travel departure date
most recent travel departure date slot
Example Guidance: Provide the travel departure date in ISO 8601 standard format .YYYY-MM-DD..
most recent travel departure date field
A date field which describes the date of an individual's most recent return to some residence from a journey originating at that residence.
most recent travel return date
most recent travel return date slot
Example Guidance: Provide the travel return date in ISO 8601 standard format .YYYY-MM-DD..
most recent travel return date field
Canada, Vancouver; USA, Seattle; Italy, Milan
A data field which describes an individuals travel history in last six months.
travel history
travel history slot
Example Guidance: Specify the countries (and more granular locations if known) travelled in the last six months; can include multiple travels. Separate multiple travel events with a semicolon. Provide as free text.
travel history field
A data field which describes an event leading to exposure.
exposure event
exposure event slot
Example Guidance: If known, select the exposure event from the pick list.
exposure event field
Direct (human-to-human contact) [TRANS:0000001]
A data field which describes the exposure transmission contact type.
exposure contact level
exposure contact level slot
Example Guidance: Select direct or indirect exposure from the pick list.
exposure contact level field
A data field which describes the role of the host in relation to the exposure setting.
host role
host role slot
Example Guidance: Select the host's personal role(s) from the pick list provided in the template. If the desired term is missing, contact the curation team.
host role field
diagnostic test
obsolete: sample datum
A laboratory sequencing datum is a datum related to the sequencing assay process applied to an isolate.
obsolete: laboratory sequencing datum
genomic sequencing annotation datum
ISSUE: lab test results are appropriate to lab test types. Logic around that?
lab test record
sequencing assembly datum
A container id is an identifier that refers to a container object about a patient specimen. Container ids are referenced in clinical patient records reported to be suspect, or lab test results.
container record
identifier of a person with the context of a health care system
health care personal identifier
A data field which describes the setting leading to exposure.
exposure setting
exposure setting slot
Example Guidance: Select the host exposure setting(s) from the pick list provided in the template. If a desired term is missing, contact the curation team.
exposure setting field
A strain identifier is the unique microbial or eukaryotic strain name from a reference database that a sample has been matched to.
strain identifier
A line list is a collection of suspected or known disease outbreak cases. It may also include details about healthy patients associated with an exposure event (picnic, concert etc.) who have been interviewed in order to compare food intake, assess risk factors, etc. Note that the health status of people associated with an exposure event can change from healthy or unknown status, to ill patient.
line list object
A data field which describes additional host exposure information.
exposure details
exposure details slot
Example Guidance: Free text description of the exposure.
exposure details field
This class is a temporary holding bin for items that need a class hierarchy home, definition, and/or subclass items. Some classes have subclasses that are currently disjoint in other ontologies like ENVO, so awaiting resolution on such issues.
awaiting ontology review
The IRIDA user ID is a user account identifier provided by the IRIDA.ca system.
An instance of the "host reinfection information field category" that contains the "prior infection isolate field".
A data field category which refers to host reinfection information fields.
host reinfection information
host reinfection information slot category
host reinfection information field category
A data field which describes whether there was prior Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection.
prior SARS-CoV-2 infection
prior SARS-CoV-2 infection slot
Example Guidance: If known, provide infromation about whether the individual had a previous SARS-CoV-2 infection. Select a value from the pick list.
prior SARS-CoV-2 infection field
A data field which describes the identifier of the isolate found in the prior Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection.
prior SARS-CoV-2 infection isolate
prior SARS-CoV-2 infection isolate ID slot
prior SARS-CoV-2 infection isolate identifier field
prior SARS-CoV-2 infection isolate identifier slot
Example Guidance: Provide the isolate name of the most recent prior infection. Structure the .isolate. name to be ICTV/INSDC compliant in the following format: .SARS-CoV-2/host/country/sampleID/date..
prior SARS-CoV-2 infection isolate ID field
A data field which describes the date of diagnosis of the prior Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection.
prior SARS-CoV-2 infection date
prior SARS-CoV-2 infection date slot
Example Guidance: Provide the date that the most recent prior infection was diagnosed. Provide the prior SARS-CoV-2 infection date in ISO 8601 standard format .YYYY-MM-DD..
prior SARS-CoV-2 infection date field
Prior antiviral treatment [GENEPIO:0100037]
A data field which describes whether there was prior Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) treatment with an antiviral agent.
prior SARS-CoV-2 antiviral treatment
prior SARS-CoV-2 antiviral treatment slot
Example Guidance: If known, provide infromation about whether the individual had a previous SARS-CoV-2 antiviral treatment. Select a value from the pick list.
prior SARS-CoV-2 antiviral treatment field
A data field which describes the name of the antiviral treatment agent administered during the prior Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection.
prior SARS-CoV-2 antiviral treatment agent
prior SARS-CoV-2 antiviral treatment agent slot
Example Guidance: Provide the name of the antiviral treatment agent administered during the most recent prior infection. If no treatment was administered, put .No treatment.. If multiple antiviral agents were administered, list them all separated by commas.
prior SARS-CoV-2 antiviral treatment agent field
A data field which describeds the date treatment was first administered during the prior Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection.
prior SARS-CoV-2 antiviral treatment date
prior SARS-CoV-2 antiviral treatment date slot
Example Guidance: Provide the date that the antiviral treatment agent was first administered during the most recenrt prior infection. Provide the prior SARS-CoV-2 treatment date in ISO 8601 standard format .YYYY-MM-DD..
prior SARS-CoV-2 antiviral treatment date field
An instance of the "sequencing field category" that contains the "sequencing date field".
A data field category which refers to sequencing information fields.
sequencing, sequencing information
sequencing information slot category
sequencing slot category
sequencing field category
The count of healthy individuals or animals on a certain date/time from a group that was likely exposed to a pathogen
exposure group healthy count
The count of ill individuals or animals on a certain date/time from a group that was likely exposed to a pathogen
exposure group ill count
human general activity
Baseline surveillance (random sampling) [GENEPIO:0100005]
A data field which describes the reason that the sample was sequenced.
purpose of sequencing
purpose_of_sequencing
purpose of sequencing slot
Example Guidance: The reason why a sample was originally collected may differ from the reason why it was selected for sequencing. The reason a sample was sequenced may provide information about potential biases in sequencing strategy. Provide the purpose of sequencing from the picklist in the template. The reason for sample collection should be indicated in the .purpose of sampling. field.
purpose of sequencing field
Screened for S gene target failure (S dropout)
A data field which describes the description of why the sample was sequenced providing specific details.
purpose of sequencing details
purpose of sequencing details slot
Example Guidance: Provide an expanded description of why the sample was sequenced using pick list. The description may include the importance of the sequences for a particular public health investigation/surveillance activity/research question. Suggested standardized descriptions include: Screened for S gene target failure (S dropout), Screened for mink variants, Screened for B.1.1.7 variant, Screened for B.1.135 variant, Screened for P.1 variant, Screened due to travel history, Screened due to close contact with infected individual, Assessing public health control measures, Determining early introductions and spread, Investigating airline-related exposures, Investigating temporary foreign worker, Investigating remote regions, Investigating health care workers, Investigating schools/universities, Investigating reinfection.
purpose of sequencing details field
A date field which describes the date the sample was sequenced.
sequencing date
sequencing date slot
Example Guidance: Provide the sequencing date in ISO 8601 standard format .YYYY-MM-DD..
sequencing date field
A data field which describes user-specified identifier for the library prepared for sequencing.
library ID
library identifier
library_ID
library ID slot
library identifier field
library identifier slot
Example Guidance: The library name should be unique, and can be an autogenerated ID from your LIMS, or modification of the isolate ID.
library ID field
A data field which describes the length of the amplicon generated by polymerase chain reaction (PCR) amplification.
amplicon size
amplicon size slot
Example Guidance: Provide the amplicon size, including the units.
amplicon size field
A data field which describes the name of the library preparation kit used to generate the library being sequenced.
Some specification definitions may be more specific on the type of library preparation kit used (e.g. DNA).
library preparation kit
library_preparation_kit
library preparation kit slot
Example Guidance: Provide the name of the library preparation kit used.
library preparation kit field
A data field which describes the barcode of the flow cell used for sequencing.
flow cell barcode
flow cell barcode slot
Example Guidance: Provide the barcode of the flow cell used for sequencing the sample.
flow cell barcode field
Oxford Nanopore MinION [GENEPIO:0100142]
A data field which describes the model of the sequencing instrument used.
sequencing instrument
sequencing_instrument
sequencing instrument slot
Example Guidance: Select the sequencing instrument from the pick list.
sequencing instrument field
1D_DNA_MinION, ARTIC Network Protocol V3
A data field which describes the name and version number of the sequencing protocol used.
sequencing protocol name
sequencing protocol name slot
Example Guidance: Provide the name and version of the sequencing protocol.
sequencing protocol name field
Genomes were generated through amplicon sequencing of 1200 bp amplicons with Freed schema primers. Libraries were created using Illumina DNA Prep kits, and sequence data was produced using Miseq Micro v2 (500 cycles) sequencing kits.
A data field which describes the protocol used to generate the sequence.
sequencing protocol
sequencing_protocol
sequencing protocol slot
Example Guidance: Provide a free text description of the methods and materials used to generate the sequence. Suggested text, fill in information where indicated.: .Viral sequencing was performed following a tiling amplicon strategy using the <fill in> primer scheme. Sequencing was performed using a <fill in> sequencing instrument. Libraries were prepared using <fill in> library kit. .
sequencing protocol field
A data field which describes the manufacturer's kit number.
sequencing kit number
sequencing kit number slot
Example Guidance: Alphanumeric value.
sequencing kit number field
A data field which describes the specifications of the primers (primer sequences, binding positions, fragment size generated, etc.) used to generate the amplicons to be sequenced.
amplicon pcr primer scheme
amplicon pcr primer scheme slot
amplicon polymerase chain reaction primer scheme field
amplicon polymerase chain reaction primer scheme slot
Example Guidance: Provide the name and version of the primer scheme used to generate the amplicons for sequencing.
amplicon pcr primer scheme field
An instance of the "bioinformatics and QC metrics field category" that contains the "dehosting method field".
A data field category which refers to bioinformatics and quality control (QC) metrics fields.
bioinformatics and QC metrics
bioinformatics and QC metrics slot category
bioinformatics and Quality Control metrics field category
bioinformatics and Quality Control metrics slot category
bioinformatics and QC metrics field category
A data field which describes the method used for raw data processing such as removing barcodes, adapter trimming, filtering etc.
raw sequence data processing method
raw sequence data processing method slot
Example Guidance: Provide the name and version numbers of the software used to process the raw data.
raw sequence data processing method field
A data field which describes the method used to remove host reads from the pathogen sequence.
dehosting method
dehosting method slot
Example Guidance: Provide the name and version number of the software used to remove host reads.
dehosting method field
A data field which describes the name of the consensus sequence.
consensus sequence name
consensus sequence name slot
Example Guidance: Provide the name and version number of the consensus sequence.
consensus sequence name field
A data field which describes the user-defined filename of the FASTA file.
assembly filename
consensus sequence filename
consensus sequence filename slot
Example Guidance: Provide the name and version number of the consensus sequence FASTA file.
consensus sequence filename field
A data field which describes the filepath of the consensus sequence file.
consensus sequence filepath
consensus sequence filepath slot
Example Guidance: Provide the filepath of the consensus sequence FASTA file.
consensus sequence filepath field
A data field which describes the name of the software used to generate the consensus sequence.
consensus sequence software name
consensus sequence software name slot
Example Guidance: Provide the name of the software used to generate the consensus sequence.
consensus sequence software name field
An exposure can be narrowed down to a single date, or can be reasoned to exist with a lower and/or upper bound date. A single date exposure has lower and upper bound dates set as the same value.
exposure history record
isolate history record
An outbreak date may have an official start, but because it might be ongoing, it may not have an end (yet).
outbreak history record
Needs to cover the various pregnancy events
pregnancy history record
Issue: a diagnosis is a set of diseases, each of which can be marked primary or secondary "Illness causality" with respect to a particular case? Requires a relation annotation.
diagnosis record
A data field which describes the version of the software used to generate the consensus sequence.
consensus sequence software version
consensus sequence software version slot
Example Guidance: Provide the version of the software used to generate the consensus sequence.
consensus sequence software version field
exposure event record
hospitalization event record
A data field which describes the percentage of the reference genome covered by the sequenced data, to a prescribed depth.
breadth of coverage value
breadth of coverage value slot
Example Guidance: Provide value as a percent.
breadth of coverage value field
exposure history item
A data field which describes the average number of reads representing a given nucleotide in the reconstructed sequence.
depth of coverage value
depth of coverage value slot
Example Guidance: Provide value as a fold of coverage.
depth of coverage value field
A data field which describes the threshold used as a cut-off for the depth of coverage.
depth of coverage threshold
depth of coverage threshold slot
Example Guidance: Provide the threshold fold coverage.
depth of coverage threshold field
A data field which describes the user-specified filename of the read 1 (r1) FASTQ file.
r1 fastq filename
r1_fastq_filename
r1 fastq filename slot
Example Guidance: Provide the r1 FASTQ filename.
r1 fastq filename field
A data field which describes the user-specified filename of the read 2 (r2) FASTQ file.
r2 fastq filename
r2_fastq_filename
r2 fastq filename slot
Example Guidance: Provide the r2 FASTQ filename.
r2 fastq filename field
A data field which describes the filepath of the read 1 (r1) FASTQ file.
r1 fastq filepath
r1 fastq filepath slot
Example Guidance: Provide the filepath of the r1 FASTQ file.
r1 fastq filepath field
A data field which describes the filepath of the read 2 (r2) FASTQ file.
r2 fastq filepath
r2 fastq filepath slot
Example Guidance: Provide the filepath of the r2 FASTQ file.
r2 fastq filepath field
A data field which describes the user-specified filename of the FAST5 file.
fast5 filename
fast5_filename
fast5 filename slot
Example Guidance: Provide the FAST5 filename.
fast5 filename field
A data field which describes the filepath of the FAST5 file.
fast5 filepath
fast5 filepath slot
Example Guidance: Provide the filepath of the FAST5 file.
fast5 filepath field
A data field which describes the number of total base pairs generated by the sequencing process.
number of base pairs sequenced
number of base pairs sequenced slot
Example Guidance: Provide a numerical value (no need to include units).
number of base pairs sequenced field
A data field which describes the file size of the assembled genome described as the number of base pairs.
consensus genome length
consensus genome length slot
consensus genome length field
A data field which describes the number of N (unidentified nucleotide) symbols present in the consensus fasta sequence, per 100kbp of sequence.
Ns per 100 kbp
Ns per 100 kilobase pairs
Ns per 100 kbp slot
Ns per 100 kilobase pairs field
Ns per 100 kilobase pairs slot
unidentified nucleotides per 100 kbp field
unidentified nucleotides per 100 kbp slot
Ns per 100 kbp field
A data field which describes the persistent, unique identifier of a genome database entry.
reference genome accession
reference genome accession slot
Example Guidance: Provide the accession number of the reference genome.
reference genome accession field
hospital admission date
A date-time datum that marks the end of possible human or animal exposure to a pathogen agent, directly or indirectly.
exposure event end
A date-time datum that marks the start of a human or animal exposure event to a suspected pathogen agent, directly or indirectly.
This datum is NOT predicted as a function of pathogen and first symptom date.
exposure event start
A data field which describes the name and version number of the bioinformatics protocol used.
bioinformatics protocol
bioinformatics protocol slot
Example Guidance: Further details regarding the methods used to process raw data, and/or generate assemblies, and/or generate consensus sequences can be provided in an SOP or protocol. Provide the name and version number of the protocol, or a link if deposited in a protocol repository.
bioinformatics protocol field
hospitalization history item
isolate history item
outbreak history item
hospital discharge date
A notification date is the date that an outbreak is suspected by a laboratory or other agency and is reported per outbreak detection guidelines.
notification date
An outbreak date is on which disease onset appears to have occured
outbreak date
An outbreak over date is the date on which a disease outbreak appears to have abated
outbreak over
test history item
An instance of the "lineage and variant information field category" that contains the "lineage/clade name field".
A data field category which refers to lineage and variant information fields.
lineage and variant information
lineage and variant information slot category
lineage and variant information field category
lab test result date
A data field which describes the name of the lineage or clade.
lineage/clade name
lineage or clade name field
lineage or clade name slot
lineage/clade name slot
Example Guidance: Provide the Pangolin or Nextstrain lineage/clade name.
lineage/clade name field
A data field which describe the name of the software used to determine the lineage/clade.
lineage/clade analysis software name
lineage or clade analysis software name field
lineage or clade analysis software name slot
lineage/clade analysis software name slot
Example Guidance: Provide the name of the software used to determine the lineage/clade.
lineage/clade analysis software name field
A data field which describes the version of the software used to determine the lineage/clade.
lineage/clade analysis software version
lineage or clade analysis software version field
lineage or clade analysis software version slot
lineage/clade analysis software version slot
Example Guidance: Provide the version of the software used ot determine the lineage/clade.
lineage/clade analysis software version field
Variant of Concern (VOC) [GENEPIO:0100083]
A data field which describes the variant classification of the lineage/clade.
variant designation
variant designation slot
Example Guidance: If the lineage/clade is considered a Variant of Concern, select Variant of Concern from the pick list. If the lineage/clade contains mutations of concern (mutations that increase transmission, clincal severity, or other epidemiological fa ctors) but it not a global Variant of Concern, select Variant. If the lineage/clade does not contain mutations of concern, leave blank.
variant designation field
RT-qPCR TaqPath assay: S gene target failure
A data field which describes the evidence used to make the variant determination.
variant evidence
variant evidence details
variant evidence details slot
variant evidence slot
Example Guidance: List the set of lineage-defining mutations used to make the variant determination. If there are mutations of interest/concern observed in addition to lineage-defining mutations, describe those here.
Example Guidance: Select whether the sample was screened using RT-qPCR or by sequencing from the pick list.
variant evidence details field
variant evidence field
An instance of the "pathogen diagnostic testing field category" that contains the "diagnostic pcr protocol field".
A data field category which refers to pathogen diagnostic testing information fields.
pathogen diagnostic testing
pathogen diagnostic testing slot category
pathogen diagnostic testing field category
An instance of the "contributor acknowledgement field category" that contains the "authors field".
A data field category which refers to contributor acknowledgement information fields.
contributor acknowledgement
contributor acknowledgement slot category
contributor acknowledgement field category
A data field which describes the names of individuals contributing to the processes of sample collection, sequence generation, analysis, and data submission.
authors
data authors slot
data contributors fields
data contributors slot
Example Guidance: Include the first and last names of all individuals that should be attributed, separated by a comma.
data authors field
A data field which describes the DataHarmonizer software and template version provenance.
DataHarmonizer provenance
DataHarmonizer provenance slot
Example Guidance: The current software and template version information will be automatically generated in this field after the user utilizes the .validate. function. This information will be generated regardless as to whether the row is valid of not.
DataHarmonizer provenance field
A data item that is a set of entities, referenced by mention, that don't necessarily have something in common.
While "enumeration" is a "data item" not everything referenced within an enumeration qualifies as a "data item". Not to be confused with "data set" which describes "data item"s of the same type that have something in common.
data enumeration
An analytic datum which describes the observed or detectable signs, and experienced symptomps of an illness, injury, or condition.
signs & symptoms
A particular attribute (feature, quality or process history) of a food sample.
The underlying facets will be supplied from the FoodOn food ontology.
food specimen datum
order: FOODON:03411564 # food source FOODON:00002381 # food product by organism FOODON:03311737 # processed food product NCIT:C71898 # brand name
A food specimen type is a categorization of a food specimen, by the organism it is or came from, or by a class of food products.
food specimen specification
An agency that has reported a disease cluster.
disease cluster notification agency
This is a subset of OBI investigation identifier. It pertains only to NCBI Biosample projects
obsolete: NCBI BioProject ID
The count of individuals or animals for which no health status is available on a certain date/time from a group that was likely exposed to a pathogen.
exposure group unknown health status count
A role which inheres in a person and is realized by the process of being in the context of civilization
person role
An exposed person role is the role a person takes on who has been exposed to a pathogen. In serious situations this may call for special treatment, e.g. quarantine.
exposed person role
Redundant with "term replaced by" entity.
obsolete: parent-guardian role
parent-guardian role
illness causality
pre-existing condition
To restore to the normal state after some pathologic process.
Dorland's Illustrated Medical Dictionary, 30th ed.
improving
recovering
resolving health trend
close interpersonal relationship exposure
Found to be redudant with another term, deprecrated in favor of said term.
exposure to individual with diarrhea
other human exposure
sexual contact exposure
exposure via diaper changing (human fecal)
container identifier
outbreak identifier
reference genome size
The assembly genome size is the sum of all lengths of a sequence assembly's contigs.
As noted in Quast documentation: " The total assembly size may increase (and in some cases exceeds the genome size) due to contaminants (see Chitsaz et al. (2011)), misassembled contigs, repeats, and hubs that contribute to multiple contigs. "
assembly genome size
Identifier for a reference genome (used to build or compare an assembly) that is used in the genome browsers and in the community
reference genome identifier
Assembly QC
The 'genome size delta ratio' is a ratio of the difference between a sample's genome assembly size and the size of a given reference genome, over the reference genome size. The formula: | (reference_genome_size - assembly_genome_size) | / reference_genome_size This yeilds a decimal / percentage ranging from 0 = exact length, to say .1 which is equivalent to a 10% variance. If the ratio is too far from a quality control ratio that depends on the species in question, this indicates a bad assembly or a mis-identified sample.
genome size delta ratio
This is the upper acceptable limit of the 'genome size delta ratio' with respect to a particular species. For Salmonella a 0.10 variance in length between an assembly size and a reference genome size may be acceptable. For E-coli a more generous 0.30 or .40 variance should be allowed, given the pathogenic subspecies’ highly dynamic genome.
genome size delta ratio QC threshold
The contig N50 length QC threshold is a minimum length threshold that a contig N50 length datum should be above for good QC. A lower length is indicative of assembly problems (insufficient read depth) or a mismatched reference genome.
contig N50 length QC threshold
The contig N99 length QC threshold is the minimum length that a contig N99 or NG99 length datum can be for satisfactory QC. This threshold avoids having too many gene coding regions prematurely clipped inside short contigs. An assembly having 1% or more of its content in less than 2Kbp chunks is cause for concern. Bacterial genes are generally about 1Kbp in length.
contig N99 length QC threshold
Homo sapiens
The species of the host organism from which a specimen (pathogen) organism was obtained. Use the full taxonomic name, eg, "Homo sapiens".
subject organism (host) taxonomic species
A single datum having to do with a metric for genomic sequence assembly quality control. A "quality control measurement" can be defined as a measurement that has some norm within a definable context, e.g. for a certain subspecies. It may be a calculated quantity. A "quality control metric" is an upper or lower bound threshold that a measurement is compared to. Surpassing the threshold may indicate an error situation. A "measure" can indicate an amount of activity, consumption, transformation, etc. but doesn't itself convey an over-stepping of bounds in the way that a metric does.
assembly quality control datum
GSCID-BRC:Clinical/host-associated pathogen
clinical or host-associated pathogen
Clinical/host-associated pathogen
Pathogen.cl
The N99 length definition is identical to the N50 definition except that the threshold for determining the contigs is 1% of the nucleotides. This contig basepair length can be compared to a minimum threshold to determine if gene annotation (where contigs greater than say 2000bp are necessary) would generally succeed.
contig N99
The upper threshold of contig counts that are acceptable in a genome assembly. This may vary based on the overall genome length and depth of coverage. A large contig count may indicate insufficient read coverage.
contig count QC threshold
Indicates how the knowledge derived from the project can be applied, and to what field(s).
Damion Dooley's note: NAIAD GRCID-BRC has Project Relevance map to OBO Foundry Study Design (http://purl.obolibrary.org/obo/OBI_0500000) but this is a bit of a stretch.
project relevance
agricultural project relevance
medical knowledge relevance
industrial processing relevance
evolution modelling relevance
environmental project relevance
model organism relevance
The NCBI BioProject model includes all datums associated with the current NCBI BioProject specification.
obsolete: NCBI BioProject model
obsolete: NCBI SRA model
Damion Dooley notes: NCBI doesn't quite make the distinction but it may be helpful to distinguish sample submission facilitator vs submitter/repository organization contact? So should we have a BioSample_submission_facilitator field and a BioSample_contact_information field?
Damion's note: There are a few different kinds of biosample, and required fields depend on the type selected.
draft NCBI BioSample model - mixed clinical and environmental/food/other
monoisolate
A monoisolate sample scope involves specimens from a single animal, cultured cell-line, inbred population, or possibly a heterogeneous population when a single genome assembly is generated from a pooled sample because multiple individuals are needed to collect enough material and an inbred line is not available; however, this situation is not preferred.
monoisolate sample scope
multiisolate
A multiisolate sample scope contains multiple individuals that represent distinct specimen collections, a population (representative of a species).
This is often used for variation or phenotype and genotype studies. This should not be used when multiple genomes will be annotated. Eventually, multiple locus_tag prefixes will be able to be assigned to a single multiisolate genome sequencing project, but currently only a single prefix can be registered per project. Therefore, individual monoisolate projects need to be registered when more than one genome will be annotated.
multiisolate sample scope
multispecies
A multi-species sample scope involves a sample representing multiple species.
multispecies sample scope
environment
An environment sample scope indicates that the species content of the sample is not known. Generally, nucleic acid is directly isolated from an environmental sample for analysis. This is used for metagenome studies.
environment sample scope
A synthetic sample scope involves a sample synthesized in a laboratory.
synthetic sample scope
single cell
Other project objective: specify an objective not listed above
other project objective
environmental, food or other pathogen
environmental/food/other
Pathogen.env
Whole: the project makes use of the whole sample material (most common case). Use this for whole genome sequencing studies, transcriptome studies that are not targeting specific loci, epigenetic studies of a genome, and metagenomes or unbiased transcriptome studies of metagenomes.
whole genomic data capture
raw sequence reads
A raw sequence reads project objective has the goal of submission of raw reads to SRA or Trace repositories
raw sequence read objective
sequence
A sequence project objective has a goal of submission of sequence data to standard archival sequence databases (yielding accession.version identifiers; e.g., whole genome shotgun, cDNA sequences, transcript shotgun assemblies)
sequence project objective
analysis
An "analysis project objective" indicates there was an other analysis not otherwise indicated, includes submission of BAM files.
This defn. could be a negation of the "not otherwise indicated".
analysis objective
assembly
Submission of genome assembly (AGP data)
assembly objective
annotation
Sequence annotation data
sequence annotation objective
sequence variation
Variation: identification of sequence variation data for submission to dbSNP or dbVAR
sequence variation project objective
epigenetic markers
DNA methylation, histone modification, chromatin accessibility datasets
epigenetic markers objective
expression
Expression: assays of transcript or protein existence or abundance
transcript or protein expression objective
maps
Maps: non-sequence based map data; e.g., genetic, radiation hybrid, cytogenetic, etc.
mapping objective
Phenotypic descriptive data.
phenotypic observation data from specimen
select sequence if any sequence data is generated from this project.
sequencing
sequencing project method
array
Select Array if that is the primary method and no sequence data is submitted
array project method
mass spectrometry
Select Mass Spectrometry if that is the primary method
mass spectrometry project method
order: NCIT:C40974 # first name NCIT:C40975 # last name NCIT:C42775 # email address GENEPIO:0001756 # phone
contact specification - person
A categorical investigation datum is a datum pertaining to some entity examined for scientific research or diagnostic purposes and which has a scope that is broader than one of the clinical, environmental or epidemiological domains.
investigation datum
An organism and its host share physical space but no evidence exists to determine if one benefits from this arrangement.
commensal role
draft isolate details model
An age measurement datum which is the age since birth of a given organism that is involved in an investigation or study at a given time.
subject age
draft NCBI component model
draft IRIDA BioSample model
draft GenEpiO epidemiology case record
A subject description is a field containing additional information about an organism (related to an investigation, study and/or specimen) that is not included in other defined vocabulary fields.
subject description
host description
NCBI BioSample
The host profile or identifiers text is the "identification or description of the specific individual from which this sample was obtained".
host profile or identifers
A subject identifier is an identifier of a subject organism within the context of a particular investigation, study, or specimen extraction event.
This varies in its type (numeric or string) and its central repository depending on its context (use in a particular application/instance). Note: GSCID-BRC specification states " 'Host' is not the preferred term since some specimens may lack any detectable pathogen". In other words, a person would technically (logically) only have a host identifier AFTER they have been diagnosed as having a pathogen. A health care personal identifier, or a case identifier would be better than a more ephemeral "host id"
subject identifier
A name of disease in a subject that is related to a given investigation, study and/or specimen.
Controlled vocabulary. Human specimen source: https://bioportal.bioontology.org/ontologies/DOID or https://www.ncbi.nlm.nih.gov/mesh/1000067
subject disease
INSDC term (top level)
A categorical choice recorded when a measurement value was known to be recorded in the past but the observed value cannot be located or retrieved for some reason.
NCBI Biosample: missing
missing
'not applicable' is an appropriate value for the measure of femur length for a patient with a missing limb
A categorical choice recorded when a measurable datum does not apply to a given context.
not applicable
A categorical choice recorded when a datum was not measured with respect to some entity during some process.
NCBI Biosample: not collected
not collected
draft isolate identifier model
draft GenEpiO isolate testing model
draft NCBI isolate source location model
draft GenEpiO isolate environment model
A subject disease stage is a measure of the acuteness of a subject organism's diagnosed disease, if any, at a given time in an investigation, study or specimen extraction event.
subject disease stage
environmental datum
temperature of sample
de-novo assembly
obsolete: sample body source
contig pre-analysis minimum length QC threshold
A 'contig length QC threshold' is an integer setting which can be applied by an algorithm to an array of assembly and annotation contig lengths to remove (filter out) all items less than the threshold value. The reduced array is used for calculation of statistics.
QUAST specifies which of its report stats are affected by the "--min-contig" minimum contig length parameter.
contig length QC threshold
The NG50 length is the same as the N50 length except that the length of the reference genome is used in the calculation rather than the assembly genome size.
"Note that N50 is calculated in the context of the assembly size rather than the genome size. Therefore, comparisons of N50 values derived from assemblies of significantly different lengths are usually not informative, even if for the same genome. To address this, the authors of the Assemblathon competition derived a new measure called NG50. The NG50 statistic is the same as N50 except that it is 50% of the known or estimated genome size that must be of the NG50 length or longer. This allows for meaningful comparisons between different assemblies. In the typical case that the assembly size is not more than the genome size, the NG50 statistic will not be more than the N50 statistic." - wikipedia
contig NG50
A contig length is the count of base pairs in a given sequence assembly contig.
contig length
An assembly quality control datum which is defined as number of contigs equal to or longer than the contig N50, when the assembly itself is factored into the calculation.
QUAST manual
contig L50
The LG99 count is like the L99 count except that the length of the reference genome is used in the calculation rather than the sum of assembly contig lengths.
contig LG99
An organism isolate datum is any datum pertaining to an isolate organism
obsolete: specimen from subject datum
A product of an animal, as in blood, feces, sputum, etc. that has no particular anatomical site
animal body product
This is the scientific role or category that the subject organism or material has with respect to an investigation.
obsolete: specimen source material category
draft GenEpiO general information record
An antigenic formula is a string composed of codes representing categorized results of tests performed on various viral, bacterial or immune cell surface antigens.
antigenic formula
This is the taxonomic species descriptor of a specimen isolate (an organism found within a specimen.)
specimen organism taxonomy (species)
An identifier moe3l indicates an identifier, the organization it has been issued by, and the status of the identifier - whether it is a primary one, active or archaic.
identifier model
help:This should be populated with a selection from INSDC.org controlled vocabulary for providers: ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/coll_dump.txt
The curator organization name is the name of an organization that manages a given repository of entities (samples, isolates, sequences ...)
curator organization name
An isolate identifier is an identifier assigned to a given isolate by a particular agency that is handling or storing it.
isolate identifier
An identifier status describes the principle role of an identifier assigned to an entity by its curator or handler. An entity may have a number of identifiers assigned to it over time. An identifier may be phased-out as can happen when its content is transferred to another curator.
identifier status
A data protection role is a role (or user permission) that a user has with respect to particular data.
A data server may be able to provide a protected(modified) dataset with metadata indicating what parts have a protection role with respect to the user requesting this information. A data protection role would be inherited from a user's relation to an entitiy to the entity's components or subclasses.
data protection role
An identifier used in the initial submission of content to a repository.
original submission
This was created to help define a contributing organization to a repository. However this still needs organizing. The "collected_by" field is free text but contact name AND organization could be associated with this in controlled vocabulary.
NCBI Contributing organization / project
food - liquid
draft NCBI BioSample identifier model
An INSDC institution code is an identifier of an organization from a list of sequence repository organizations managed by INSDC.
INSDC institution code
draft IRIDA epidemiological case model
An identifier that had been used previously but is no longer promoted.
previous (archaic) identifier
A geographical location datum is a datum that refers to a real, hypothesized or fanciful spatial location
geographic location datum
A categorical tree specification datum is a categorical value specification which takes its value from the ontology URI identifier of any one of its subclass items; these may be organized in a hierarchy.
A categorical tree specification datum may have its own URI identifier as its value. This could be interpreted to mean that the datum was recorded but that no particular categorical subclass distinction was observed. This in effect makes the datum act as a boolean variable.
obsolete: categorical tree specification
A geographic coordinate entity composed of both latitude and longitude components.
latitude and longitude coordinate (ISO 6709)
order: NCIT:C25464 # country ENVO:00000005 # state / province etc.
Geographical origin of the sample; use the appropriate name from this list http://www.insdc.org/documents/country-qualifier-vocabulary. Use a colon to separate the country or ocean from more detailed information about the location, eg "Canada: Vancouver" or "Germany: halfway down Zugspitze, Alps"
draft NCBI BioSample geo_loc_name model
draft GenEpiO isolate sequencing model
A case ID is a unique identifier associated with a particular episode of care for an individual or animal.
case identifier
An animal that has had a substantial part of its reproductive organs removed surgically.
Not a PATO phenotypic sex catigorical value.
neuter
A phenotypic sex quality 'pooled male and female' is a categorical value used when the male and female categories or levels of a factor are combined. If used to describe a single organism, then the organism will be one or the other.
NCBI BioSample: 'pooled male and female'
pooled male and female
A categorical choice recorded while the data for a given measurable datum has not finished being collected, is awaiting a conclusion, or has not yet been communicated.
undetermined
in process
swimming / wading
NECESSARY? : What details are categorical and what are freehand? This item was originally too broad; moved sub-items to Treatment.
infection detail datum
This is problematic - its not clear if this is reporting that antibiotics were administered, or whether they are recommended as a result of diagnosis.
antibiotics required
The International Nucleotide Sequence Database Collaboration (INSDC) is a long-standing foundational initiative that operates between DDBJ, EMBL-EBI and NCBI. INSDC covers the spectrum of data raw reads, though alignments and assemblies to functional annotation, enriched with contextual information relating to samples and experimental configurations.
International Nucleotide Database Collaboration standard
INSDC standard
outcome of pregnancy associated with illness
A categorical choice indicating that information of an expected format was not given a value may be given at the later stage.
not provided
stable health status
induced abortion
live birth
obsolete: gestation duration (weeks)
date of pregnancy outcome
contact specification - physician
obsolete: matrix - solid
contact specification - parent/guardian
contact specification - patient
draft GenEpiO case epidemiology record
order: NCIT:C25464 # Country ENVO:00000005 # major administrative subdivision aka state/province/territory/region (via GenEpiO -> GAZ ) NCIT:C80234 # Municipality (via GenEpiO -> GAZ cities) NCIT:C25690 # Street Address NCIT:C25621 # postal code
The address component of a contact specification.
contact specification - address
obsolete: draft IRIDA model
A datum related to the sequencing assay process applied to an isolate.
laboratory sequencing datum
host illness associated with
draft subject demographic specification
E. coli K antigen specification
other antigen specification
E. coli serotype specification
Damion's note: This will be converted to a categorical tree specification list of serovars by name or id asap.
Salmonella serovar specification
A lab test specification indicates the inputs and outputs (results / conclusions) of a test.
test specification
listeria antigen
obsolete: matrix - fluid
listeria serotype 1/2a
listeria serotype 1/2b
listeria serotype 1/2c
listeria serotype 1/2
listeria serotype 3a
listeria serotype 3b
listeria serotype 4a
listeria serotype 4b
listeria serotype 4c
listeria serotype 4d
listeria serotype 4e
non-monocytogenes listeria antigen
listeria serotype 3c
textual test result
This is an organizational category for grouping parameters relevant to biomedical research projects.
obsolete: draft GenEpiO BioProject standard
NCBI BioSample collection code
draft NCBI BioSample host model
food - solid
lab test datum
Xbal
Ascl
Smal
Blnl
Apal
Kpnl
Taxonomy below subspecies; sometimes used in viruses to denote subgroups taken from a single isolate.
NCBI Biosample
subgroup
help:This is an optional additional subtype classification as per organism convention
A viral subtype is a classification name for a virus according to some protocol.
viral subtype
serotype specification
IRIDA
An integer and character referring to a pattern of opaque or confluent lysis caused by a panel of bacteriophage infections e.g. 14a.
SNOMED: http://www.snomedbrowser.com/Codes/Details/272405002
phage type specification
obsolete: swab - food contact surface
An NCBI culture collection is a composite identifier containing “institution code:collection code”.
Annotation with a culture_collection qualifier implies that the sequence was obtained from a sample retrieved (by the submitter or a collaborator) from the indicated culture collection, or that the sequence was obtained from a sample that was deposited (by the submitter or a collaborator) in the indicated culture collection. See the description for the proper format and list of allowed institutes, http://www.insdc.org/controlled-vocabulary-culturecollection-qualifier.
NCBI culture collection
The NCBI specimen voucher is an identifier composed of “institution code:collection code:specimen id” parts. In addition to a specimen identifier, it includes an institution-code (and optional collection-code) taken from a controlled vocabulary maintained by the INSDC that denotes the museum or herbarium collection where the specimen resides.
NCBI specimen voucher
culture identifier
human; dog; horse
The natural language (non-taxonomic) name of the type of organism (human or animal) that is the subject of a given investigation, study and/or specimen.
Damion Dooley's note: as of 2017 this is a problematic field for NCBI Biosample because it is slotted into "host" field, yet field is listed as "host common name" which does not fit with requirement that scientific name be provided.
subject organism common name
temperature of air - average daily
obsolete: swab - inanimate object surface
obsolete: swab - meat
obsolete: swab - rectal swab
obsolete: swab - tissue
unknown source
patient sample
human clinical specimen
"environment (swab or sampling)" is a specific response for NCBI BioSample that could be mapped or unified with "environment sample" used elsewhere in GenEpiO
obsolete: environmental (swab or sampling)
avian - wild
avian - domesticated
human clinical specimen - invasive
In chemistry, pH is a numeric scale used to specify the acidity or basicity(alkalinity) of an aqueous solution
Wikipedia
Normally falls within the bounds of 0 - 14
pH measurement
precipitation
The assembly and annotation objective is the set of objectives that assembly and annotation techniques (including instruments and software platforms) applied to a sample are meant to satisfy. This impacts on the quality control thresholds applied to the sequencing project.
assembly and annotation project objective
line list row record
This class contains components under development for fulfilling GenEpiO and other standard data specifications. Components are relevant to epidemiological, laboratory, clinical or environmental pathogen sample data collection and analysis.
draft GenEpiO component record
region
A subnational region is a type of subnational entity similar to a nation's state, province, or territory.
subnational region
A data standard related to public health research and service delivery.
public health data standard
0D space
Reagent: material studied was obtained by chemical reaction, precipitation.
reagent derived material from specimen
transcriptome
Transcriptome: transcript and/or expression data.
transcriptome data from specimen
Proteome material is protein or peptide sequences.
proteome data derived from specimen
Purified chromosome: one or more chromosomes or replicons were experimentally purified.
purified chromosome from specimen
targeted locus/loci
TargetedLocusLoci: capturing specific loci (gene, genomic region, bar code standard).
Targeted Locus Loci data capture
clone ends
CloneEnds: capturing clone end data.
clone end data capture
exome
Exome: capturing exon-specific data.
exome specific data capture
random survey
Sequences generated from a random sampling of the collected sample; not intended to be comprehensive sampling of the material
Is this with respect to an isolate or a specimen derived culture?
random survey data capture
This is a collection of various human (and animal contact location) contact information specifications used in data standards.
contact specification
order: NCIT:C40978 # phone GENEPIO:0001896 # phone type
contact specification - phone
millimetres per day
obsolete: millisiemens
millisiemens per centimetre
cubic metre per second
micromole per kilogram
micromole per litre
quality control record
Standard draft: describing the minimum information needed for submission to a public database.
1 - standard draft
High quality draft: describing sequences with little to no manual review.
2 - high quality draft
Improved high quality draft: in which data is either reviewed by people or machines to some extent to indicate that most of the genetic data is assembled correctly, but some errors may still be present.
3 - improved high quality draft
Annotation-directed improvement: in which genetic information in various gene regions is represented as accurately as possible.
4 - annotation-directed improvement
Non-contiguous finished: which includes sequences that have been reviewed by both people and machines and would be considered complete except for “recalcitrant regions” that are proving problematic for genome closure.
5 - non-contiguous finished
Finished: which describes un-gapped complete sequences that have minimal errors, if any. The biology of the microbe will determine whether this finished genome consists of more than one chromosome.
6 - finished
The NG99 length is the same as the N99 length except that the length of the reference genome is used in the calculation rather than the sum of assembly contig lengths.
contig NG99
An assembly quality control datum which is defined as number of contigs equal to or longer than the contig N50, when the genome size is factored into the calculation.
contig LG50
Contig L99 is the number of contigs equal to or longer than contig N99. The length of the assembly itself is used in the calculation.
contig L99
A subject age at time of specimen extraction is the age (since birth) of the organism at the time a given specimen was extracted.
subject age at time of specimen collection
A public health related data standard involving a particular species of pathogen.
pathogen specific data standard
The draft tuberculosis contextual data standard is a data standard for the collection of contextual information of a given tuberculosis case that pertain to typing, clinical treatment, and potential research questions.
draft tuberculosis contextual data standard
The PulseNet Canada Salmonella submission standard details the fields required in a PuseNet Canada pathogen submission report for Salmonella in spreadsheet format
draft PulseNet Canada Salmonella submission standard
A PFGE pattern resulting from DNA fragmentation induced by the Xbal enzyme.
PFGE Xbal pattern
A PFGE pattern resulting from DNA fragmentation induced by the Blnl enzyme.
PFGE Blnl pattern
NLEP ID
An NLEP ID is a unique identifier code for a sample registered with the Canadian "National Laboratory for Enteric Pathogens" (NLEP)
Pulsenet Canada spreadsheet.
National Laboratory for Enteric Pathogens Identifier
Date an uploaded sample was re-uploaded or had its metadata modified.
upload modified date
A travel destination is a destination city (or populated place of some scale) which a given human has travelled to on a particular trip.
travel destination
A symptom duration is a date-time entity which is the duration (in hours or days or weeks etc.) that one or more symptoms persist for in a particular human or animal
This may be a calculated field if symptoms are reported to cease on a particular date. Often however symptom duration is reported more generally as a date or time range since cesation date is less certain.
symptom duration
The city where a specimen was collected (taken) from a subject or environment
specimen collection location - city
obsolete: sample city
This is the genus-level taxonomic name of an organism playing a pathogen role
genus of pathogen
This is the species-level taxonomic name of an organism playing a pathogen role
species of pathogen
A symptom cessation date is a date-time entity that marks the end of one or more reported symptoms pertaining to an episode of human or animal illness
symptom cessation date
This is a catch-all category for listing specimen related terms
specimen datum
isolate identifier specification
The 'data obfuscated' role between a user and given data entails that the user is authorized to see particular fields that have been transformed consistently such that statistics performed on those fields would yeild the same results as statistics applied to the un-obfuscated data. The purpose of obfuscation is to prevent related individuals or organizations from being identified.
data obfuscated
The 'data aggregated' role between a user and given data entails that the user is authorized to see aggregated results (like the patient count) via preset reports, queries or views. The results are not obfuscated.
data aggregated
A 'limited data set' role between a user and given data entails that a user is authorized to see some of the fields but the remainder are withheld (or encrypted).
limited data set
help:In this dataset, selected data have been de-identified (anonymized) for access by dataset users.
A 'de-identified data' role between a user and given data entails that the user is authorized to see only those fields (including those that are encrypted) which do not contain information that could be use to identify particular individuals (whether patients or medical practitioners) or potentially organizations in the case where an investigation may implicate them.
Damion Dooley's note: There is a case in the "draft tuberculosis contextual data standard" that has this be a boolean selection. If a categorical field is linked directly, and it has no underlings, this indicates that it is being treated as a boolean feature.
Generally de-identified data should include HIPAA patient privacy fields as indicated in https://www.hipaa.com/hipaa-protected-health-information-what-does-phi-include/
de-identified data
A 'data protected' role between a user and given data entails that a user must be authorized in order to view that data.
data protected
A datum containing the name of persons or institute who collected a given specimen.
specimen collector
NCBI BioSample culture identifier
A user identifier is an identifier provided as part of an authentication process of a client (user) to a service (server). User identifiers normally persist over time, in contrast to session identifiers which are temporary.
user identifier
sequence identifier
metagenomic species identification
Note: REPLACE WITH Citation: SIO_000174 ????
document citation identifier
organization identifier
collection identifier
variant calling / pathogen identification and clustering
isolate (pathogen) identification
obsolete: NCBI BioSample ID -
1) Escherichia coli O104:H4 str. C227-11 clinical isolate 2010_333_NC-6 2) CD8+ T cells from female TSG6-knockout BALB/c mouse 3) Human metagenome isolated from urine of healthy female
A specimen (or sample) title should be short and informative. Each specimen title must be unique in a submission.
NCBI BioSample record documentation refers to a "BioSample title", stating that it is "auto-generated if one is not supplied by the submitter." This is distinct from any assigned BioSession accession, or other "external sample identifier" that may have been issued by the source database or repository.
specimen title
draft GenEpiO isolate source context
A categorical choice recorded when the data for a given measurable datum is available but not shared publicly because of information privacy concerns.
restricted access
State (United States of America)
A health status trend is a short-term prognosis about whether health is improving, worsening or unchanging
health status trend datum
The Integrated Taxonomic Information System (ITIS) contains authoritative taxonomic information on plants, animals, fungi, and microbes of North America and the world.
Integrated Taxonomic Information System
ITIS
MeSH is the National Library of Medicine's controlled vocabulary thesaurus. It consists of sets of terms naming descriptors in a hierarchical structure that permits searching at various levels of specificity.
Medical Subject Headings
MESH
The National Cancer Institute Thesaurus (NCIt) provides reference terminology for many NCI and other systems. It covers vocabulary for clinical care, translational and basic research, and public information and administrative activities.
National Cancer Institude Thesaurus
NCIT
The NIFSTD ontology of the Neuroscience Information Framework is composed of a collection of OWL modules with separate modules covering major domains of neuroscience: anatomy, cell, subcellular, molecule, organism, function and dysfunction.
NIFSTD
SNOMED CT is a large clinical health terminology product owned and distributed by SNOMED International.
SNOMEDCT
ASFIS is a database curated by the United Nations Food And Agriculture Organization (FAO) Fisheries and Aquaculture Statistics and Information Branch (FIPS). It contains over 12,700 species items selected according to their interest or relation to fisheries and aquaculture.
UN FAO Fisheries and Aquaculture Statistics and Information Branch database
ASFIS
FTT
TGN
Wikipedia is a free online encyclopedia that aims to allow anyone to edit articles.
SWEETRealm
The GeoNames geographical database covers all countries and contains over eleven million placenames that are available for download free of charge.
Geonames
EcoLexicon is a terminological resource developed by the LexiCon Research Group at the University of Granada.
EcoLexicon
A standard established for use by the Integrated Rapid Infectious Disease Analysis (IRIDA) project, which is a Canadian-led initiative to build an open source, end-to-end platform for infectious disease genomic epidemiology.
draft IRIDA standard
ISO 3166-1 is part of the ISO 3166 standard published by the International Organization for Standardization (ISO), and defines codes for the names of countries, dependent territories, and special areas of geographical interest.
ISO 3166-2 is part of the ISO 3166 standard published by the International Organization for Standardization (ISO), and defines codes for identifying the principal subdivisions (e.g., provinces or states) of all countries coded in ISO 3166-1.
Information Technology – Codes For The Identification Of The States And Equivalent Areas Within The United States, Puerto Rico, And The Insular Areas
American National Standards Institute
ANSI INCITS 38
The Geographic Names Information System (GNIS), developed by the U.S. Geological Survey in cooperation with the U.S. Board on Geographic Names, contains information about physical and cultural geographic features in the United States and associated areas, both current and historical.
GNISID
LTER
order: OBI:0001628 # investigation identifier OBI:0001616 # specimen identifier GENEPIO:0001808 # specimen title GENEPIO:0000113 # specimen category sep:00196 # specimen description OBI:0001479 # specimen from organism GENEPIO:0001640 # specimen organism taxonomy (species) GENEPIO:0000027 # specimen source context GENEPIO:0001722 # NCBI specimen voucher GENEPIO:0001429 # strain identifier GENEPIO:0001798 # NCBI BioSample culture identifier GENEPIO:0001717 # viral subtype OMP:0000207 # serotype phenotype SO:0001027 # genotype GENEPIO:0001079 # serovar GENEPIO:0001716 # subgroup GENEPIO:0001055 # NCBI pathotype GENEPIO:0001054 # isolate passage history GENEPIO:0001656 # latitude and longitude coordinate GENEPIO:0001657 # NCBI BioSample geo_loc_name model GENEPIO:0001051 # NCBI BioSample isolate (human name or description) GENEPIO:0001648 # NCBI Contributing organization / project GENEPIO:0001797 # specimen collector OBI:0001619 # specimen collection date OBI:0001888 # sequencing facility contact person GENEPIO:0001651 # INSDC institution code GENEPIO:0001721 # NCBI culture collection GENEPIO:0001567 # subject (host) taxonomic species GENEPIO:0001724 # subject organism common name GENEPIO:0001775 # subject age at time of specimen collection GENEPIO:0000026 # subject health status at time of specimen extraction GENEPIO:0000031 # subject sex GENEPIO:0001614 # subject description GENEPIO:0001617 # subject disease GENEPIO:0001625 # subject disease stage GENEPIO:0001212 # subject disease outcome
A National Center for Biotechnology Information BioSample specification defines fields and terms that provide "descriptions of biological source materials used in experimental assays".
NCBI BioSample Pathogen.cl standard
The National Center for Biotechnology Information BioProject standard is a collection of datums that describe biological data related to a single initiative, originating from a single organization or from a consortium. A BioProject record provides users a single place to find links to the diverse data types generated for that project.
NCBI lists project data type and other controlled vocabulary fields at : https://www.ncbi.nlm.nih.gov/books/NBK54364/
NCBI BioProject standard
Objective
The format of the BioProject Accession is five alpha-letters followed by one to six numbers. For example PRJNA43021
Project Accession
Methodology
The American Hospital Association has issued HIPAA Updated Guidelines for Releasing Information on the Condition of Patients
American Hospital Association HIPAA Standard
AHA HIPPA standard
PubMed comprises more than 26 million citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites.
NCBI PubMed
PubMed
PulseNet, a national and international surveillance system used to identify and respond to foodborne disease outbreaks, has a standardized laboratory method and data submission standard for pathogen isolate typing test results and related isolate contextual data. From this information clusters of disease can be identified that might represent unrecognized outbreaks.
Pulse Net International BioSample Metadata
PulseNet submission standard
AHA HIPPA: http://www.aha.org/content/00-10/overview0302.pdf
Good - Vital signs are stable and within normal limits. Patient is conscious and comfortable. Indicators are excellent.
AHA Hippa: Good
good health status
Good
satisfactory
Fair - Vital signs are stable and within normal limits. Patient is conscious, but may be uncomfortable. Indicators are favorable.
fair health status
fair
Stable
Serious - Vital signs may be unstable and not within normal limits. Patient is acutely ill. Indicators are questionable.
serious health status
Serious
A health status history datum is a record of the longer-term pattern or presence of a given patient's health status.
health status history datum
(0,0) is the origin of the cartesian coordinate system.
A point in zero-dimensional (0D) space in which the origin is a fixed point of reference for the geometry of the surrounding space.
"In mathematics, the origin of a Euclidean space is a special point, usually denoted by the letter O, used as a fixed point of reference for the geometry of the surrounding space. In physical problems, the choice of origin is often arbitrary, meaning any choice of origin will ultimately give the same answer. This allows one to pick an origin point that makes the mathematics as simple as possible, often by taking advantage of some kind of geometric symmetry."
origin
United Kingdom National Health Service trusts, boards, etc. have some terminology in common for public disclosure of patient health conditions.
National Health Service terminology
NHS standard
Damion Dooley's note: This is a contentious term. AHA calls for it never to be used, since the common phrase "critical but stable" is misleading by the very nature of "critical". The NHS however has it as one of its central terms. The use of "stable" also points to a health trend, rather than a state. A separate "health status trend datum" has been set up to capture this.
critical but stable health status
critical but stable
NHS Terms: https://en.wikipedia.org/wiki/Medical_state
comfortable health status
Comfortable
progressing well health status
progressing well
Damion Dooley note: This term (weakly) implies that the patient is recovered enough to be released from hospital. Technically this isn't a health status though, it is a patient medical service state.
discharged from hospital
discharged
A data item which is about the collection state of a datum at some point in time.
Damion Dooley note: We'll need to incorporate NIAID GSCID-BRC Sample data standards mention: Unknown/Not Applicable/Censored Allowed Unknown/not applicable/not available/ available upon request
A given datum's datum status value is metadata, i.e. a statement about a particular datum, often when no actual data entry or categorical choice for that datum has been made.
datum status
INSDC missing value reporting terms: http://www.ebi.ac.uk/ena/about/missing-values-reporting
A categorical choice indicating that a datum is available for retrieval.
In theory any datum that has a recorded value has 'recorded' for its datum status.
recorded
Patient is awaiting physician and/or assessment.
Very similar to 'datum status' 'in process' status.
undetermined health status - awaiting assessment
deteriorating
worsening health trend
An N-dimensional space consists of n dimensions, each with an origin. It can be translated via various coordinate systems, and can be populated with N and lesser dimensional vectors.
n-dimensional space
A distance metric exists between any two members of a one-dimensional set. Should have vector as subclass?
1D space
This data type is for an item that can map to a point, line, set or area on a surface (2 dimensional space) or to the surface itself. It can be a slice of a higher dimensional space. It can be defined by a cartesian or radial coordinate system.
2D space
3D space
n-dimensional coordinate
This covers the description of data and abstract structure in n-dimensional space. Within space there are coordinate systems, coordinates, and entities made up of coordinates.
n-dimensional concept
This should cover all interval data
1D coordinate
2D coordinate
A decimal latitude measurement in degrees in conformance with the ISO 6709 standard.
This is failing Hermit reasoner since it rejects totalDigits, and fractionDigits: 'has primitive data type' exactly 1 xsd:decimal[>= -90.0 , <= 90.0 , totalDigits 8 , fractionDigits 6]'
latitude specification (ISO 6709)
A decimal longitude measurement in degrees in conformance with the ISO 6709 standard.
longitude specification (ISO 6709)
1D coordinate system
A 2D coordinate system is a coordinate system in 2 dimensional space. Each coordinate is composed of an offset from the origin of each dimension
2D coordinate system
3D coordinate system
A coordinate system composed of a radius from the origin of one dimension combined with angular offsets from the origins of the remaining dimensions.
radial coordinate system
Damion Dooley's note: IAO lat/long can't be made a subclass of "angular coordinate" or disjoint contradiction arises with "immaterial entity"
angular coordinate
A coordinate composed of a given dimension and the offset from the origin of the dimension to some point
linear coordinate
An area calculation datum is a functional mapping of a two dimensional surface area (can be anything from an abstract polygon, to a postal code or country) to a 1 dimensional scalar. The original surface area may be curved, e.g. spheroid. The surface area can also be described using only one input - for example the radius scalar of a polar coordinate plane described by pi*r^2.
area calculation
geographic coordinate
removed date
A datetime range intermediate datum is a datetime item grouped under a process, and occuring after some process start and before some process end.
datetime range intermediate
updated date
This seems to be covered by 'datetime range intermediate'
datetime range member - UNUSED?
datetime range item
The ending date of a process
datetime range end
The starting date of a process
datetime range start
Wikipedia: "The significant figures of a number are digits that carry meaning contributing to its measurement resolution."
significant digits
As mentioned here: http://www.datypic.com/sc/xsd11/t-xsd_dateTimeStamp.html , we could change this to dateTimeStamp if we need to enforce a time zone?
Some dates don't belong to a range other than the overall timeline. Other dates associated with a process fall within a range that has a start and end bound.
datetime linear coordinate
A datetime set item is a datetime that has been grouped semantically under a given type of process
The instant is subject to the level of granularity of the observed time. Year / Month / Day / Hour / Minute / Second
datetime set item
created date
entity history item
n-dimensional entity
Generic term allowing for different geometries. Can encompass the infinite surface area of a plane, or some portion bounded by a circumference or polygon for example.
surface area
A designated area on earth is one or more areas defined by one or more boundaries. A boundary can be defined by a polygon perimeter, a lat/long and radius, or a fiat-boundary geographic featureset like a named river channel or mountain ridge; it may have one or more names associated with it. Note that areas associated with a name may change their boundary definitions over time.
designated area on Earth
landmark
/^((:<FSA>[ABCEGHJKLMNPRSTVXY][0-9][ABCEGHJKLMNPRSTVWXYZ])) ?(:<LDU>[0-9][ABCEGHJKLMNPRSTVWXYZ][0-9])$/i, $FSA $LDU
A Canadian postal code is a postal code that pertains to a geographic region of Canada.
Note that a Canadian postal code can cover multiple communities. Secondly, postal codes can be retired, and then reintroduced elsewhere. Historical data associations may need to take the date of postal code mapping into account.
Canada postal code
/^((:<FSA>[ABCEGHJKLMNPRSTVXY][0-9][ABCEGHJKLMNPRSTVWXYZ]))$/i, $FSA
The "Canadia postal code FSA" is the leading FSA (Forward Sortation Area) 3 character portion of a full 6 character Canadian postal code. It can be used to reduce the geographic granularity of a postal code for data generalization or obfuscation.
Canada postal code FSA
A "USA zip code" is a five digit (Zone Improvement Plan) or 9 digit postal code pertaining to a region of the United States of America. The optional trailing 4 digits of a 9 digit zip code provide greater granularity of delivery target.
obsolete: US postal code
alphanumeric phrase
entity history record
generic range history record
lingual set
non-lingual set
phone type
mobile
phone type - mobile
work
phone type - work
A set does not have a direct distance metric between its members.
set
This data type is for items that have a unique order or rank with respect to each other in a set BUT NO meaningful DISTANCE metric exists between items aside from their position in the full set. "Favorite soft drinks" or "Favorite colours" or "Closest friends" are examples. Letters of the alphabet cannot be interpreted as ordinal with respect to their use in words, since no uniform rules exist about their placement in words. But they can be ordinal insofar as they are stated in a particular order in listing off the alphabet. A distance metric becomes possible if the items have units, e.g. 5cm or 10degrees celcius. The set's elements can then be mapped to one dimension.
ordered set
An unordered set is a set of elements which have no intrinsic (semantic) order with respect to each other. The set of all living people is not intrinsically ordered; an ordering can only be provided by looking at some partiular feature of the given set elements.
The set can have a very large or infinite (open-ended) number of values. Because the elements are essentially open-ended, we can only offer a lookup-as-you-type function for selecting past-used items. Use "Categorical" for unordered sets where items are finite, pre-defined and not too numerous. Strings are only indirectly ordered insofar as strings can be sorted by character - but this requires picking apar the name strings, an examination which has no inherent semantic relation to the things being named. That one email address or name comes before another is arbitrary. Only numbers are directly ordered.
unordered set
Subclasses here are types of string that have a particular syntactic structure or constraint to them that should be expressable using regular expressions.
set of unordered strings
phone number (North America)
A set of points that exist in a 2-dimensional plane. (This plane may be a cross-section of points defined in n > 2 dimensions).
points in 2 dimensions
In Euclidean space, quadrics have dimension D = 2, and are known as quadric surfaces.
quadratic surface
A spheroid, or ellipsoid of revolution, is a quadric surface obtained by rotating an ellipse about one of its principal axes; in other words, an ellipsoid with two equal semi-diameters.
spheroid
In mathematics, a plane is a flat, two-dimensional surface. A plane is the two-dimensional analogue of a point (zero dimensions), a line (one dimension) and three-dimensional space. Planes can arise as subspaces of some higher-dimensional space, as with the walls of a room, or they may enjoy an independent existence in their own right, as in the setting of Euclidean geometry." "When working exclusively in two-dimensional Euclidean space, the definite article is used, so, the plane refers to the whole space.
plane
Issue: this implicitly affects 'significant digits' datum.
quantity unit
decimal
integer
ones
tens
hundreds
thousands
tenths
hundredths
millions
Number types can have min / max limits for validation. Regular expressions would be used mostly for data entry transformation and display.
number
A product name and model number of a manufacturer's genomic (dna) sequencer.
sequencing instrument model
A circle is a simple closed shape in Euclidean geometry. It is the set of all points in a plane that are at a given distance from a given point, the centre; equivalently it is the curve traced out by a point that moves so that its distance from a given point is constant.
circle
Illumina platform
Damion Dooley's note: This platform is in-house and not a product per se. Complete Genomics states: "Complete Genomics’ sequencing platform employs high-density DNA nanoarrays that are populated with DNA nanoballs (DNBs™). Base identification is performed using an unchained ligation-based read technology known as combinatorial probe-anchor ligation (cPAL™). The sequencing instrumentation is custom-developed to support this process. Details are described in our Science publication (Drmanac et al., 2010)."
Complete Genomics platform
earth area boundary census
Roche LS454 platform
PacBio platform
SOLiD 4hq System
SOLiD 5500
SOLiD 5500xl
SOLiD PI System
SOLiD System 2.0
SOLiD System 3.0
A two dimensional entity is an entity composed of one or more points on a two dimensional surface.
2D entity
obsolete: Ion Torrent PGM
454 Genome Sequencer FLX Titanium
454 Genome Sequencer
454 Genome Sequencer Junior
obsolete: Illumina HiSeq Sequencer
Whether any method was used to select for or against, enrich, or screen the material being sequenced.
library selection
Selection of methylated DNA fragments using an antibody raised against 5-methylcytosine or 5-methylcytidine (m5C).
5-methylcytidine antibody method
Cap-analysis gene expression.
CAGE method
Cot-filtered highly repetitive genomic DNA
CF-H method
Cot-filtered moderately repetitive genomic DNA
CF-M method
Cot-filtered single/low-copy genomic DNA
CF-S method
Cot-filtered theoretical single-copy genomic DNA
CF-T method
Chromatin immunoprecipitation
ChIP method
Deoxyribonuclease (MNase) digestion
DNAse method
Hypo-methylated partial restriction digest
HMPR method
Selection by hybridization in array or solution.
Hybrid Selection method
Enrichment by methyl-CpG binding domain.
NCBI SRA: MBD2 protein methyl-CpG binding domain
MBD2 protein methyl-CpG binding domain method
Methyl Filtrated
MF method
Micrococcal Nuclease (MNase) digestion
MNase method
Methylation Spanning Linking Library
MSLL method
Source material was selected by designed primers.
PCR method
Rapid Amplification of cDNA Ends.
RACE method
Source material was selected by randomly generated primers.
RANDOM PCR method
Random selection by shearing or other method.
RANDOM method
Source material was selected by reverse transcription PCR
RT-PCR method
Reproducible genomic subsets, often generated by restriction fragment size selection, containing a manageable number of loci to facilitate re-sampling.
Reduced Representation method
DNA fractionation using restriction enzymes.
Restriction Digest method
PolyA selection or enrichment for messenger RNA (mRNA). complementary DNA.
cDNA method
Physical selection of size appropriate targets.
size fractionation method
Other library enrichment, screening, or selection process.
other library method
The library source specifies the type of source material that is being sequenced.
library source
Genomic DNA (includes PCR products from genomic DNA).
genomic source
Mixed material from metagenome.
metagenomic source
Transcription products from community targets
metatranscriptomic source
Other, unspecified, or unknown library source material.
other library source
Synthetic DNA.
synthetic source
Transcription products or non genomic DNA (EST, cDNA, RT-PCR, screened libraries).
transcriptomic source
Viral RNA.
viral RNA source
Sequencing technique intended for this library.
library strategy
Sequencing of overlapping or distinct PCR or RT-PCR products. For example, metagenomic community profiling using SSU rRNA
amplicon strategy
MethylC-seq. Sequencing following treatment of DNA with bisulfite to convert cytosine residues to uracil depending on methylation status.
Bisulfite-Seq strategy
Clone end (5', 3', or both) sequencing.
clone end strategy
Genomic clone based (hierarchical) sequencing.
clone strategy
Concatenated Tag Sequencing
CTS strategy
Direct sequencing of chromatin immunoprecipitates.
ChIP-Seq strategy
Sequencing of hypersensitive sites, or segments of open chromatin that are more readily cleaved by DNaseI.
DNase-Hypersensitivity strategy
Single pass sequencing of cDNA templates
EST strategy
Sequencing intended to finish (close) gaps in existing coverage.
finishing strategy
Full-length sequencing of cDNA templates
FL-cDNA strategy
Direct sequencing of methylated fractions sequencing strategy.
MBD-Seq strategy
Direct sequencing following MNase digestion.
MNase-Seq strategy
Methylation-Sensitive Restriction Enzyme Sequencing strategy.
MRE-Seq strategy
Methylated DNA Immunoprecipitation Sequencing strategy.
MeDIP-Seq strategy
Library strategy not listed.
other library strategy
Shotgun of pooled clones (usually BACs and Fosmids).
pool clone strategy
Random sequencing of whole transcriptome.
RNA-Seq strategy
Random sequencing of a whole chromosome or other replicon isolated from a genome.
WCS strategy
Random sequencing of the whole genome.
WGS strategy
Random sequencing of exonic regions selected from the genome.
WXS strategy
Free form text describing the protocol by which the sequencing library was constructed.
library construction protocol
The submitter's name for this library.
NCBI SRA: LIBRARY_NAME
library name
A two dimensional boundary is a continuous path (loop) defined on a two dimensional surface.
2D boundary
cfu/100mL
A colony forming unit count which is a count of viable bacterial numbers in 100 milliliters of liquid.
Should this be deprecated? Need to find working examples that actually use / 100mL.
colony forming unit per 100 milliliter
A multiplier in the decimal number system that has been applied to an accompanying number or set of numbers often to simplfy their appearance. Numbers described by multipliers may have lost significant digits through rounding or trimming.
decimal quantity unit
draft tuberculosis - dataset features and provenance
draft tuberculosis - case specimen characteristics
draft tuberculosis - case subject characteristics
draft tuberculosis - case risk factors
draft tuberculosis - case clinical presentation
draft tuberculosis - case laboratory testing
draft tuberculosis - case medication
draft isolate whole genome sequencing model
draft tuberculosis - case model
A Mycobacterium tuberculosis lineage is a named family of strains of tuberculosis, named usually with reference to their shared geographic origin.
Mycobacterium tuberculosis lineage
A TB-Lineage identification tool using spoligotypes and MIRU data: http://tbinsight.cs.rpi.edu/run_tb_lineage.html
Out-of-Africa migration and Neolithic coexpansion of Mycobacterium tuberculosis with modern humans http://www.nature.com/ng/journal/v45/n10/full/ng.2744.html
TB lineage 2 - East-Asian, includes Bejing
TB lineage 3 - East-African Indian, includes CAS/Delhi
TB lineage 4 - Euro-American, includes Haarlem, LAM3, X, T, F11, H37Rv
TB lineage 1 - Indo-Oceanic
TB lineage 5 - West African 1
TB lineage 6 - West African 2
An isolate preparation facility is a type of organization that provides the service of isolating organisms of interest from provided specimens.
isolate preparation facility
plant product
geospatial name
A personal health datum is a datum that pertains to the health situation or history of an individual.
Personal health datum covers the following information 'has member' some 'analytic datum' 'has member' some 'behavioural risk factor' 'has member' some 'country of birth' 'has member' some 'dietary restrictions' 'has member' some 'Disease Attributes' 'has member' some 'health status history datum' 'has member' some 'health status trend datum' 'has member' some 'host hospital service status' 'has member' some 'subject disease stage' 'has member' some 'subject health status' 'has member' some 'subject health status (AHA)' 'has member' some 'subject health status (GSCID-BRC)' 'has member' some 'subject health status (NCIT)' 'has member' some 'subject health status (UK NHS)' 'has member' some 'subject health status at time of specimen extraction' 'has member' some 'tuberculosis disease anatomical site' 'has member' some comorbidity 'has member' some disease 'has member' some symptom
personal health datum
A host hospital service status indicates the state of a host's interaction with hospital medical services.
host hospital service status
admitted to hospital
Received treatment but not admitted.
treated and released (not admitted to hospital)
Treated and Released
Received treatment. Transferred to a different facility.
treated and transferred
Treated and Transferred
satisfactory health status
subject health status (UK NHS)
subject health status (AHA)
stable health trend
An ordinal variable is a categorical variable whose values have sequential order, but no distance metric between them.
obsolete: ordinal variable
mapping (reference based)
data protection item
subject provided consent
An ordinal tree specification is a value specification entity whose subclasses each represent a possible value selection, and which have a linear order with respect to their siblings.
ordinal value specification
consent datum
agency provided consent
draft ISO sequence repository field
Centre of circle, ellipse or parabola; centre of mass.
A centre point is a point used in the description of an n-dimentional entity from which other (given) aspects of the entity are most efficienty described. A point of symmetry. The entity must have only one such point.
Probably a better formal math defn?
centre point
This covers the following entities: 'has member' some 'antimicrobial phenotype' 'has member' some 'antimicrobial resistance test drug' 'has member' some 'antimicrobial resistance test platform' 'has member' some 'antimicrobial resistance testing method' 'has member' some 'antimicrobial resistance testing method version or reagent' 'has member' some 'antimicrobial resistance testing reference standard' 'has member' some 'antimicrobial resistance testing reference standard version' 'has member' some 'antimicrobial resistance tissue specificity' 'has member' some 'antimicrobial resistant plasmid type' 'has member' some 'automated testing platform vendor' 'has member' some 'draft antibiogram drug test model' 'has member' some 'in-vitro microbial susceptibility test' 'has member' some 'measurement comparator' 'has member' some 'MIC unit' 'has member' some 'MIC value' 'has member' some 'Minimum Inhibitory Concentration Test' 'has member' some 'test drug maximum concentration' 'has member' some 'test drug minimum concentration' 'has member' some 'tuberculosis treatment drug'
This is a collection of antibiotic resistance process parameters and outputs
phenotypic antimicrobial drug susceptibility test datum
The resistance phenotype of an isolate represents the interpretation of an MIC value with regard to some breakpoint threshold e.g. resistant (R), sensitive (S), intermediate (I), wild type (WT), or non-wild type (NWT)
obsolete: antimicrobial resistance phenotype
Intermediate resistance indicates that an isolate is observed to offer an intermediate level of resistance to a given antibiotic.
obsolete: antibiotic intermediate resistance (I)
Non-susceptible indicates that an isolate is observed to offer complete resistance to a given antibiotic.
obsolete: antibiotic nonsensitive (high resistance)
A not defined resistance indicates that an isolate was not tested against a given antibiotic, or the result of the test was inconclusive.
Damion Dooley note: Is this the same as "indeterminate"?
antibiotic resistance not defined
Resistant indicates that an isolate is observed to offer a greater than intermediate level of resistance to a given antibiotic.
obsolete: antibiotic resistant (R)
Susceptible indicates that an isolate is observed to offer a detectable but less than intermediate level of resistance to a given antibiotic.
obsolete: antibiotic sensitive (S)
Susceptible - dose dependent indicates that an isolate is observed to offer resistance to a given antibiotic when a sufficient dose is given.
obsolete: sensitive - dose dependent
A MIC test measurement resulting from a laboratory dilution method.
Damion Dooley's note: is this still useful? Currently "MIC dilution measurement specification' refers directly via 'is about' to "broth dilution method" but that may be too specific.
MIC dilution measurement datum
The type of assay used to determine the minimum inhibitory concentration.
obsolete: antimicrobial resistance testing method
obsolete: agar dilution evidence
The commercial kit or product used to determine the MIC e.g. E-Test. If a commercial product was not used, include the type of media used.
antimicrobial resistance testing method device or reagent
antimicrobial resistant plasmid type
The instrumentation used to determine minimum inhibitory concentration values.
obsolete: antimicrobial resistance testing platform
obsolete: Microscan
obsolete: Phoenix
obsolete: Sensititre
obsolete: Vitek
obsolete: Trek
obsolete: manual - noncommercial
The manufacturer of an antibiotic resistance lab typing platform
obsolete: antimicrobial resistance testing platform vendor
obsolete: Siemens
obsolete: Biomérieux
obsolete: Becton Dickinson
A manual in vitro diagnostic device used by laboratories to determine the MIC (Minimum Inhibitory Concentration) and whether or not a specific strain of bacterium or fungus is susceptible to the action of a specific antimicrobial.
E-Test
Epsilometer test
Etest (device)
GM-NEG
The clinical and laboratory guidelines or standards that prescribe the threshold values for determining resistance phenotypes.
obsolete: antimicrobial resistance testing reference standard
BSAC is a British inter-professional organisation involved in antibiotic education, research and leadership
obsolete: British Society for Antimicrobial Chemotherapy (BSAC)
obsolete: Clinical and Laboratory Standards Institute (CLSI)
DIN is recognized by the Federal Government of Germany as the competent standards organization for Germany and as the national standards body representing Germany in non-governmental international standards organizations.
obsolete: Deutsches Institut für Normung
obsolete: German Institute for Standardization (DIN)
EUCAST is a standing committee jointly organized by ESCMID, ECDC and European national breakpoint committees; it deals with breakpoints and technical aspects of phenotypic in vitro antimicrobial susceptibility testing.
obsolete: European Committe on Antimicrobial Susceptibility Testing (EUCAST)
obsolete: National Committee on Clinical Laboratory Standards (NCCLS)
La SFM a vocation à rassembler les microbiologistes de France et des pays francophones, travaillant dans les différents domaines de la microbiologie médicale, industrielle, et environnementale, en physiologie, génétique, taxonomie, hygiène, agents antimicrobiens, ...concernant les bactéries, virus, champignons et parasites.
The French Society of Microbiology (SFM) is a non-profit association which aims to bring together microbiologists from French-speaking countries, working in the domains of bacteria, viruses, Fungi and parasites, and related medical, industrial and environmental microbiology, physiology, genetics, taxonomy, hygiene, and antimicrobial agents.
This isn't at moment considered a valid EBI antibiogram choice?
obsolete: Société Française de Microbiologie (SFM)
Replaced by domain appropriate term created in the Comprehensive Antibiotic Resistance Database (CARD).
obsolete: SIR
obsolete: WRG
first line tuberculosis drug
last resort antibiotic
NIAID standard
NIAID provides The GSCID/BRC Project and Sample Application Standard. It is designed to capture standardized human pathogen and vector sequencing metadata to support epidemiologic and genotype-phenotype association studies for human infectious diseases.
National Institute of Allergy and Infectious Disease standard
A RefSeq accession identifier is an accession identifier for selected NCBI-curated genomic, transcript and protein sequences. These identifiers are distinct from DDBJ/EMBL/GenBank identifiers.
RefSeq accession identifier
A Genomic Standards Consortium standard is an international, community-driven standard to facilitate genomic data integration, discovery and comparison.
Genomic Standards Consortium (GSC) standard
A landform, biome or built environment at site that a given specimen was collected from.
specimen collection site - geographic feature
A particular human patient, or a given animal or plant.
An investigative subject which is an organism.
subject organism
help=The number of passages should be expressed as a numerical value.
The number of serial iterations that an isolate is grown in one environment.
number of passages
help:The passage protocol should include, when applicable, inoculum size, media type, temperature and duration of incubation.
A passage protocol should detail the number of serial iterations that an isolate is grown in one environment, and the conditions of that environment.
passage protocol
The unit provided for an antibiotic drug test dosage.
obsolete: drug minimum inhibitory concentration unit
order: GENEPIO:0001237 # specimen type (host or environmental context) OBI:0001619 # specimen collection date OBI:0000659 # specimen collection process GENEPIO:0002094 # specimen collection device GENEPIO:00001600 # draft sequence repository data - geographic location ENVO:00010483 # environmental material ENVO:00002297 # environmental feature GENEPIO:0001567 # subject (host) taxonomic species GENEPIO:0000110 # subject health status GENEPIO:0001617 # subject disease GENEPIO:0000028 # subject body product GENEPIO:0000025 # specimen source anatomical site FOODON:03411564 # draft sequence repository data - food processing
draft sequence repository data - specimen collection
order: GENEPIO:0002105 # Specimen processing organization role NCIT:C93874 # organization name NCIT:C40974 # first name NCIT:C40975 # last name NCIT:C93582 # job title NCIT:C42775 # email address GENEPIO:0001756 # phone NCIT:C25464 # Country ENVO:00000005 # major administrative subdivision -> GAZ state/province/territory/region) NCIT:C80234 # Municipality” (via GenEpiO -> GAZ cities) NCIT:C25690 # Street Address
Contact information for an organization related to specimen collection, processing or storage.
contact specification - specimen related organization
order: GENEPIO:0002082 # specimen related organization GENEPIO:0002081 # specimen collection GENEPIO:0002086 # geographic location GENEPIO:0002084 # isolate GENEPIO:0002087 # isolate history GENEPIO:0002106 # food specimen GENEPIO:0002088 # antibiogram GENEPIO:0002085 # sequencing GENEPIO:0002090 # sequencing QC GENEPIO:0002089 # virulence GENEPIO:0002092 # submission to EBI GENEPIO:0002091 # submission to NCBI/DDBJ
This draft specification provides a collection of fields related to the contextual data of a specimen, its genomic sequencing, and its pathogenic epidemiology.
draft sequence repository contextual data standard
order: GENEPIO:0001640 # specimen taxonomy GENEPIO:0001429 # strain identifier GENEPIO:0001644 # isolate identifier OBI:0000079 # culture medium GENEPIO:0002107 # isolation medium
draft sequence repository data - isolate
order: GENEPIO:0000069 # sequencing date OBI:0000079 # culture medium” (via MicrO, yields a list of formulas). GENEPIO:0002093 # sequencing dna extraction method EFO:0000683 # replicate GENEPIO:0000085 # library preparation kit GENEPIO:0000149 # library preparation kit version GENEPIO:0000075 # sequencing chemistry GENEPIO:0001921 # sequencing instrument model GENEPIO:0000150 # read trimming and filtering software GENEPIO:0000084 # read adapter trimming software GENEPIO:0002095 # read paired-end merging software GENEPIO:0000090 # assembly method GENEPIO:0000151 # bioinformatics pipeline name GENEPIO:0000153 # bioinformatics pipeline protocol GENEPIO:0000152 # bioinformatics pipeline version GENEPIO:0000095 # genome annotation algorithm
draft sequence repository data - sequencing
order: GENEPIO_0001656 # latitude and longitude ISO 6709 GENEPIO:0000118 # specimen collection country GENEPIO:0002097 # specimen collection state/prov/ter/region GENEPIO:0001785 # specimen collection city
The geographical origin of the sample by city, region, country or latitude and logitude.
draft sequence repository data - geographic location
order: GENEPIO:0002078 # number of passages GENEPIO:0002079 # passage protocol
draft sequence repository data - isolate passage history
order: GENEPIO:0001100 # antimicrobial drug tests GENEPIO:0002101 # test drug minimum concentration GENEPIO:0002100 # test drug maximum concentration GENEPIO:0002045 # antimicrobial resistance testing method GENEPIO:0002047 # antimicrobial testing method version or reagent GENEPIO:0002062 # antimicrobial resistance testing reference standard GENEPIO:0002049 # antimicrobial resistance testing platform
A dataset of the minimal inhibitory concentrations (value, unit, sign (<,>, =)) and resistance phenotypes (resistant, sensitive or undetermined) of the sequenced isolate against different antibiotics tested.
draft sequence repository data - antibiogram
order: GENEPIO:0002130 # Virulence factor name GENEPIO:0002131 # Virulence testing protocol GENEPIO:0002132 # detection limit
The virulence factors determined to be present in the sequenced isolate by phenotypic or target amplification methods e.g. Shiga toxins, hemolysins.
draft sequence repository data - virulence
order: OBI:0001941 # N50 GENEPIO_0000092 # sequencing depth / read coverage
Measurements or calculated quantities used to assess the extent and success of the sequence assembly process. Metric thresholds are species-specific.
draft sequence repository data - sequencing quality control
order: OBI:0001616 # specimen identifier GENEPIO:0001644 # isolate identifier GENEPIO:0001429 # strain identifier GENEPIO:0001640 # specimen organism taxonomy GENEPIO:0000113 # specimen category OBI:0001619 # specimen collection date GENEPIO:0001797 # specimen collector GENEPIO:0001657 # geo_loc_name GENEPIO:0001656 # latitude and longitude coord GENEPIO:0000027 # specimen source context GENEPIO:0001567 # subject organism taxonomy GENEPIO:0001724 # subject organism common name GENEPIO:0001617 # subject disease
draft sequence repository data - submission to NCBI/DDBJ
order: GENEPIO:0001644 # isolate identifier GENEPIO:0001429 # strain identifier GENEPIO:0001640 # specimen organism taxonomy GENEPIO:0001079 # serovar GENEPIO:0002135 # EBI environmental feature GENEPIO:0000113 # specimen category OBI:0001619 # specimen collection date GENEPIO:0001797 # specimen collector GENEPIO:0002086 # geographic location GENEPIO:0000027 # specimen source context GENEPIO:0002076 # geographic feature GENEPIO:0001567 # subject taxonomy GENEPIO:0000110 # subject health status
draft sequence repository data - submission to EBI
The procedure used to obtain genomic DNA from a sample through chemical, physical or mechanical means.
sequencing dna extraction method datum
Moved term to OBI, deprecated in favour of the OBI version.
obsolete: specimen collection device
The name and version of the software used to merge paired-end reads before assembly.
read paired-end merging software
The name and version of the software product used for removal of adapter sequences from demultiplexed data reads
read adapter trimming software
An ontology identifier or textual name of the most precise geographical location available for the site of a specimen collection event.
specimen collection location - state/province/territory/region
A wild type (WT) resistance phenotype indicates a bacterial pathogen belongs to a "Naïve", susceptible wild-type population with respect to a given antimicrobial. No acquired or mutational resistance mechanisms are present to the antimicrobial in question.
obsolete: wild type (WT)
A non-wild type (WT) resistance phenotype indicates a bacterial pathogen has an acquired or mutational resistance mechanism present with respect to the antimicrobial in question. The bacteria has a reduced susceptibility to this agent.
obsolete: non-wild type (NWT)
This is the maximum concentration of a drug applied during an an assay.
test drug maximum concentration
A data item which describes the minimum concentration of a drug applied during an an assay
test drug minimum concentration
obsolete: antimicrobial resistance tissue specificity
order: NCIT:C115935 # healthy NCIT:C126054 # non-pathalogical NCIT:C25610 # pathologic NCIT:C82508 # life threatening NCIT:C28554 # deceased
subject health status (NCIT)
order: NCIT:C40974 # first name NCIT:C40975 # last name NCIT:C93582 # job title NCIT:C42775 # email address GENEPIO:0001756 # phone
contact specification - professional role
An organization related to the collection, isolate production, sequencing or storage of specimen material or data.
specimen processing organization type
order: GENEPIO:0001533 # food specimen type FOODON:03450002 # food cooking method FOODON:03440011 # extent of heat treatment FOODON:03430113 # physical state, shape or form FOODON:03470107 # food preservation method FOODON:03490100 # container or wrapping FOODON:03480020 # food packing medium FOODON:03500010 # food contact surface GENEPIO:0000139 # food cultural origin FOODON:03460111 # treatment applied to food
This specification offers food source, product type, packaging and processing attributes relevant to describing a food specimen.
draft sequence repository data - food specimen
An isolation medium is a culture medium which has the disposition to encourage growth of particular bacteria to the exclusion of others in the same growth environment.
Chris has proposed this term for OBI as "enrichment culture medium"
isolation medium
order: GENEPIO:0000121 # start date GENEPIO:0000122 # end date GENEPIO:0001783 # travel destination GENEPIO:0001064 # travel mode GENEPIO:0001065 # travel reason
This record details a person's travel movement and duration for epidemiological analysis.
draft travel log specification
order: OBI:0001616 # BioSample_ID GENEPIO:0001640 # Species GENEPIO:0001187 # Antibiotic_Name GENEPIO:0002062 # AST_Standard GENEPIO:0002111 # Breakpoint_version NCIT:C85540 # Laboratory_typing_method GENEPIO:0002112 # Measurement GENEPIO:0002080 # Measurement_units GENEPIO:0001001 # Measurement_sign NCIT:C85539 # Resistance_phenotype GENEPIO:0002181 # Resistance_phenotype - ECOFF GENEPIO:0002049 # Platform
A standard for European Bioinformatics Institute (EBI) antibiogram data submission
draft EBI antimicrobial susceptibility test V. 2017-08-30
A MIC test measurement resulting from a laboratory diffusion method.
Damion Dooley's note: is this still useful? Currently "MIC diffusion measurement specification' refers directly via 'is about' to "Disk Diffusion Method".
MIC diffusion measurement datum
The version of the antimicrobial reistance testing reference standard protocol used in assessing an isolate.
antimicrobial resistance testing reference standard version
This is a component of an antibiogram that enables a choice of MIC measurements based on either the diffusion or dilution method. These methods call for different numeric input ranges and units.
draft sequence repository data - antibiogram MIC measurement
time value specification
The process of collecting a portion of feces from an organism.
Emma Griffiths
stool collection
feces collection
The process of collecting a portion of urine from an organism.
sputum collection
The process of removal and collection of specimen material from the surface of an entity by washing, or a similar application of fluids.
rinsing for specimen collection
The process of collecting specimen material using a swab collection device.
swabbing for specimen collection
The process of collecting bodily fluids that have been discharged from blood vessels usually arising from inflammation or injury.
exudate collection
The removal or collection of specimen material through the use of suction.
vacuuming for specimen collection
A tube that contains media or preservative
NOTE: there are different types of tubes with coloured caps indicating different preservatives etc.
tube containing media or preservative
A tube that contains antimicrobials
tube containing antimicrobial
A sterilized sampling bag that is puncture proof tabs for protection from damage due to wire-end protrusion and leak-proof closures.
Whirlpak sampling bag
spoon
fork
A shovel-like utensil that has a deep curved dish and a short handle and is used for digging into a soft substance for lifting out a portion.
hand scoop
trier
A device which generates a vacuum to provide suction of material.
vaccum device
investigation identifier specification
order: GENEPIO:0001640 # taxonomy GENEPIO:0002086 # geographic location GENEPIO:0002076 # geographic feature GENEPIO:0002106 # food FOODON:03510136 # food consumer GENEPIO:0002094 # specimen collection device GENEPIO:0000025 # anatomical site GENEPIO:0000028 # body product GENEPIO:0001724 # host organism common name GENEPIO:0001567 # host taxonomy UBERON:0000105 # life cycle GENEPIO:0001639 # antigenic formula GENEPIO:0001718 # serotype specification GENEPIO:0000045 # PFGE test specification
This is a draft (under development) collection of fields for capturing the contextual data for Enterobase (https://enterobase.warwick.ac.uk/) records.
draft Enterobase contextual data standard
The name of the virulence factor molecule produced by a pathogen that specifically causes disease, or that influences the host's function to allow the pathogen to thrive.
virulence factor name
help:The protocol for determining virulence should include, when applicable, inoculum preparation, platforms and instrumentation, conditions, cell lines and animal models.
The laboratory protocol used to determine virulence phenotypes and markers.
virulence testing protocol name
help:Detection limits should include the numerical cut-off (threshold) value and units for determining positive results e.g. qPCR value, CFUs.
The detection limit denotes the smallest measure that can be detected with reasonable certainty for a given analytical procedure.
detection limit
A disease cluster is an unusually high incidence of a particular disease or disorder occurring in close proximity in terms of both time and geography.
disease cluster
A disease cluster in which two or more cases have been linked by an infectious disease transmission process.
infectious disease cluster
help:used only with the source feature key; source feature keys containing the /environmental_sample qualifier should also contain the /isolation_source qualifier. entries including /environmental_sample must not include the /strain qualifier
Identifies sequences derived by direct molecular isolation from a bulk environmental DNA sample (by PCR with or without subsequent cloning of the product, DGGE, or other anonymous methods) with no reliable identification of the source organism. Environmental samples include clinical samples, gut contents, and other sequences from anonymous organisms that may be associated with a particular host. They do not include endosymbionts that can be reliably recovered from a particular host, organisms from a readily identifiable but uncultured field sample (e.g., many cyanobacteria), or phytoplasmas that can be reliably recovered from diseased plants (even though these cannot be grown in axenic culture).
ENA Webin:environmental_feature
EBI ENA Webin environmental feature
The European Nucleotide Archive (ENA) provides a comprehensive record of the world's nucleotide sequencing information, covering raw sequencing data, sequence assembly information and functional annotation. Webin is an ENA interface and standard for sequence submissions.
EBI European Nucleotide Archive Webin
help:Breadth of coverage should be reported as a percentage value (e.g. 95%) to a fold of coverage (e.g. 10X).
Eighty percent of the reference genome was covered by sequence fragments with a coverage depth of 4X; therefore, the breadth of coverage was 80% (4:5).
A data item which is the amount of a reference sequence covered by a sequence of interest.
breadth of coverage
The mean contig length is the count of base pairs in the average size contig of the sequence assembly.
mean contig length
order: GENEPIO:0000084 # read adapter trimming (y/n) GENEPIO:0002096 # read adapter trimming software GENEPIO:0002095 # read paired-end merging software GENEPIO:0000150 # read trimming and filtering software
The procedures used to remove adapters from raw sequence reads, trim low quality bases and where applicable, merge paired-end reads.
raw sequence data processing datum
Name of strain from which sample was obtained OR name of isolate from which sample was obtained.
specimen strain or isolate identifier
The geographical coordinates of the location where the sample was collected. Specify as degrees latitude and longitude in format "d[d.dddd] N|S d[dd.dddd] W|E", eg, 38.98 N 77.11 W
latitude and longitude coordinate (NCBI BioSample format)
decimal value specification
floating point value specification
unsigned integer
A 32 bit number having a range 0 - 4294967295.
unsigned integer value specification
date value specification
A specification for the size of an assembled genome as measured in base pairs.
This is a decimal because the megabasepair unit may involve a fractional component.
assembly genome size specification
sequencing facility name specification
date (ISO 8601)
A date should be recorded as YYYY-MM-DD according to ISO 8601. HOWEVER ... OWL 2.0 does not include xsd:date as a permitted data type, so this value specification only accepts xsd:dateTime
date value specification (ISO 8601)
strain identifier specification
A value specification for a MIC test measurement resulting from a laboratory diffusion method.
MIC diffusion measurement specification
unsigned short
A 16 bit integer ranging from 0 - 65535
unsigned short integer value specification
genomic sequence length specification
A value specification for a MIC test measurement resulting from a laboratory dilution method.
MIC dilution measurement specification
The date on which a specimen was collected, in ISO 8601 format.
specimen collection date (ISO 8601)
date of diagnosis (ISO 8601)
A value specification which describes the age since birth of a given organism that is involved in an investigation or study at a given time.
subject age specification
subject age at time of specimen collection specification
boolean
A boolean value specification indicates a presence (true value) or absence (false value) of a given feature.
boolean value specification
specimen identifier specification
email address specification
region, province, state or territory specification
A specification for a geographic location that a specimen was collected at.
specimen collection site specification
subject organism common name specification
A subject identifier specification is a specification including datatype pertaining to a given standard's subject identifier field.
subject identifier specification
A value specification which describes the name of a disease in a subject that is related to a given investigation, study and/or specimen.
subject disease specification
unsigned long integer
A 64 bit integer ranging from 0 - 18446744073709551615
unsigned long integer value specification
The physical location that a specimen was collected at. The location may be described by geographic coordinates, city or other geopolitical entity, biome, etc.
specimen collection site
drug MIC unit specification
A datum specification for the maximum concentration of a drug applied during an an assay.
test drug maximum concentration specification
A value specification which describes the minimum concentration of a drug applied during an an assay.
test drug minimum concentration specification
listeria antigen specification
URL specification
A value specification which describes the travel destination a given human has travelled to on a particular trip.
travel destination specification
A data specification for a specimen source substance, which is an organism substance or food product or environmental substance from which the specimen was extracted.
specimen source substance specification
Damion Dooley note: OBI has a variety of subclasses like "blood specimen" and "colon specimen" etc. which we have not added here. The are mapped to UBERON terms indirectly through the logic "derives from some [uberon term]". GenEpiO takes a different approach in describing this class with lists for "subject anatomical site", "subject body product", and "plant anatomy".
specimen from organism specification
duration specification
obsolete: field specification
obsolete: antimicrobial resistance phenotype - epidemiological cut-off values
PulseNet Canada field
PulseNet Canada Salmonella field
specimen collection service
bioinformatics analysis service
An isolate preparation service prepares isolates for molecular sequencing.
isolate preparation service
order: GENEPIO:0002222 # specimen collection service GENEPIO:0002226 # specimen repository/biobank service GENEPIO:0002224 # isolate preparation service OBI:0001904 # sequencing service OBI:0000992 # DNA sequencing service GENEPIO:0002223 # bioinformatics analysis service
specimen related service
specimen repository/biobank service
An organism datum about subject health status in which vital signs are unstable and not within normal limits, patient may be unconscious and indicators are unfavorable.
grave
critical health status
critical
A datum indicating one of six defined subspecies of Salmonella.
Salmonella subspecies
A PFGE pattern resulting from DNA fragmentation induced by the Spel enzyme.
PFGE Spel pattern
A collection of organisms that is indicative of faecal contamination.
Fecal indicator organism collections include bacterial groups such as thermotolerant coliforms or E. coli. Hence, they only infer that pathogens may be present
fecal indicator
An isolate derived from a food sample.
food isolate
A method for typing The RNA component of the small (30S) subunit of prokaryotic ribosomes.
microbial 16S RNA typing
E. coli H antigen specification
E. coli O antigen specification
string
string value specification
A sequencing platform brand provided by Helicos corporation (now defunct).
Helicos platform
A sequencing platform provided by the Ion Torrent company.
Ion Torrent platform
A sequencing platform provided by Life Technologies Corporation
Sequencing by Oligonucleotide Ligation and Detection
SOLiD sequening platform
obsolete: drag swab
Rinse is the liquid output of rinsing plant, animal or other material with liquid with the objective of extracting specimen material from that liquid.
rinse
Animal rinse is a rinse derived from animal material of one or more animals.
animal rinse
obsolete: surface wipe
A low flat-bottomed laboratory container for growing a layer of organisms such as bacteria, molds, and cells on a thin layer of nutrient medium.
A fluid that is obtained from rinsing meat for the purpose of collecting materials and organisms that are on its surface.
A sequencing platform provided by the BGI Genomics company.
A sequencing platform provided by the MGI company.
A fecal specimen collection method in which feces is obtained by inserting the collection device into the anus of the host, or the feces is captured as it is excreted.
Emma J Griffiths
A DNA sequencer which is manufactured by the Illumina corporation using sequence-by-synthesis chemistry that fits on a benchtop and uses P1 and P2 flow cells.
Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term.
An adapter for MinION or GridION DNA sequencers manufactured by the Oxford Nanopore corporation that enables sequencing on smaller, single-use flow cells.
Undigested food material, microbiota, and other materials found in the stomach.
A mixture of feces obtained from multiple individuals.
Feces that was recently excreted.
Feces which is deposited in the environment.
A specimen collection device that is used to collect soft sediments in lakes or oceans.
A severe acute respiratory syndrome-related coronavirus which is 1) bat-derived, 2) sharing 93.3% nucleotide identity with SARS-CoV-2, and 3) contains an insertion at the S1/S2 cleavage site in the spike protein.
RmYN02
A sampling strategy in which individuals are chosen for investigation into a disease cluster or outbreak.
Cluster/Outbreak investigation
The terms cluster and outbreak both describe the occurrence of new disease cases within a particular location and time period. The number of cases within a cluster are not necessarily greater than what is expected, however in an outbreak the number of cases does exceed the usual norm. In an outbreak the cases are confirmed to be epidemiologically linked while in a cluster an epidemiological connection is only suspected. Not all clusters are outbreaks, however each cluster needs to be investigated. [Source: https://covid19evidencereviews.saskhealthauthority.ca/en/permalink/coviddoc153]
cluster/outbreak investigation sampling
A sampling strategy in which individuals are sampled in the context of diagnostic testing.
Diagnostic testing
diagnostic testing sampling
A sampling strategy in which individuals are sampled in order to perform research.
Research
research sampling
A sampling strategy in which individuals are sampled for surveillance investigations.
Surveillance
surveillance sampling
A surveillance sampling strategy in which baseline is established at the beginning of a study or project by the selection of sample units via random sampling.
Baseline surveillance (random sampling)
random sampling
Such that each possible unit has a fixed and known or equal probability of selection. [Source: "Random Sample" (p.238) in Porta, M. (2014). A Dictionary of Epidemiology (6th ed.). Oxford University Press, Incorporated.]
baseline surveillance strategy
A surveillance sampling strategy in which an aspired outcome is explicity stated.
Targeted surveillance (non-random sampling)
Target" (p.279) in Porta, M. (2014). A Dictionary of Epidemiology (6th ed.). Oxford University Press, Incorporated.
non-random sampling
targeted surveillance strategy
A targeted surveillance strategy which is considered important and/or urgent.
Priority surveillance project
priority surveillance project strategy
A targeted surveillance strategy in which the aim is early detection of variants of concern (VoC) in individuals.
Screening for Variants of Concern (VoC)
screening for VOC
screening for VoC
screening for Variants of Concern strategy
A priority surveillance strategy in which subsets of a defined population can be identified who are, have been, or in the future may be exposed or not exposed - or exposed in different degrees - to a disease of interest and are selected to under go repeat sampling over a defined period of time.
Longitudinal surveillance (repeat sampling of individuals)
Cohort Study" (p.50) in Porta, M. (2014). A Dictionary of Epidemiology (6th ed.). Oxford University Press, Incorporated.
repeat sampling of individuals
longitudinal surveillance strategy
A priority surveillance strategy in which a population that previously tested positive for a disease of interest, and since confirmed to have recovered via a negative test, are monitored for positive test indication of re-infection with the disease of interest within a defined period of time.
Re-infection surveillance
re-infection surveillance strategy
A priority surveillance strategy in which individuals are monitored for investigation into vaccine escape, i.e., identifying variants that contain mutations that counteracted the immunity provided by vaccine(s) of interest.
Vaccine escape surveillance
vaccine escape surveillance strategy
A priority surveillance strategy in which individuals are selected if they have a travel history outside of the reporting region within a specified number of days before onset of symptoms.
Travel-associated surveillance
travel-associated surveillance strategy
A travel-associated surveillance strategy in which individuals are selected if they have an intranational travel history within a specified number of days before onset of symptoms.
Domestic travel surveillance
domestic travel surveillance strategy
A travel-associated surveillance strategy in which individuals are selected if they have a travel history outside of the reporting country in a specified number of days before onset of symptoms.
International travel surveillance
international travel surveillance strategy
An international travel-associated surveillance strategy in which individuals are selected if they have a travel history of crossing an international border via air travel or ground transport.
Surveillance of international border crossing by air travel or ground transport
surveillance of international border crossing by air travel or ground transport strategy
An international travel-associated surveillance strategy in which individuals are selected if they have a travel history of crossing an international border via air travel.
Surveillance of international border crossing by air travel
surveillance of international border crossing by air travel strategy
An international travel-associated surveillance strategy in which individuals are selected if they have a travel history of crossing an international border via ground transport.
Surveillance of international border crossing by ground transport
surveillance of international border crossing by ground transport strategy
Surveillance from international worker testing
surveillance from international worker testing strategy
obsolete: cluster/outbreak investigation strategy
An outbreak investigation sampling strategy in which individuals are chosen for investigation into a disease outbreak that has connections to two or more jurisdictions.
Multi-jurisdictional outbreak investigation
multi-jurisdictional outbreak investigation strategy
An outbreak investigation sampling strategy in which individuals are chosen for investigation into a disease outbreak that only has connections within a single jurisdiction.
Intra-jurisdictional outbreak investigation
intra-jurisdictional outbreak investigation strategy
obsolete: research strategy
A research sampling strategy in which individuals are sampled in order to perform a viral passage experiment.
Viral passage experiment
viral passage experiment strategy
A research sampling strategy in which samples are collected in order to test a method or protocol.
Protocol testing
Protocol testing experiment
protocol testing sampling
A personal protective clothing item which is a gown worn in order to provide a barrier between a person and the external environment.
A device which is used to collect liquid samples.
collection cup
A device which is a soft, absorbent material mounted on one or both ends of a stick.
swab
An aspiration process which involves putting a needle through the skin just above the pubic bone into the bladder to take a urine sample.
suprapubic aspiration
An aspiration process which collects tracheal secretions.
tracheal aspiration
An aspiration process which uses a vacuum source to remove a sample.
vacuum aspiration
A filtration process which removes solid particulates from the air via an air filtration device.
air filtration
The collection of bronchoalveolar lavage fluid (BAL) from the lungs.
BAL
bronchoalveolar lavage
The administration and evacuation of small volumes of liquid through an orogastric tube to remove toxic substances within the stomach.
gastric lavage
A collecting specimen from organism process in which a salt water solution is taken into the oral cavity, rinsed around, and gargled before being deposited into an external collection device.
mouth rinse and gargle
saline gargle
A specimen collection process in which a sample is collected by scraping a surface with a sterile sampling device.
scraping
A collecting specimen from organism process in which a skin site free of surface arterial flow is pierced with a sterile lancet, after a capillary blood droplet is formed a sample is captured in a capillary tupe.
finger prick
Antiviral treatment administered prior to the current regimen or test.
prior antiviral treatment
A collecting specimen from organism process in which fluid is added to the eye prior to sample collection, effectively "washing out" ocular surface molecules.
washout tear collection
The process of growing a virus in serial iterations.
virus passage
A secondary RNA extraction after performing reverse transcription polymerase chain reaction (RT-PCR). The desired output is RNA.
RNA re-extraction (post reverse transcription-polymerase chain reaction)
RNA re-extraction (post RT-PCR)
293 cells stably expressing the SARS-CoV receptor protein, angiotensin-converting enzyme 2 (ACE2).
293/hACE2 cell line
293/ACE2 cell line
Eptesicus fucus (big brown bat) kidney 3B cells.
Efk-3B clone 3B cell
Efk3B cell
Eptesicus fucus kidney 3B cell
EFK3B cell line
Normal human primary renal cortical epithelial cells.
human renal cortical epithelial cell line
HRCE cell line
VeroE6 cells expressing the transmembrane serine protease TMPRSS2.
Vero E6/TMPRSS2 cell
Vero-E6/TMPRSS2 cell
VeroE6/TMPRSS2 cell line
The condition of being treated as a patient in a hospital without admission to an intensive care unit (ICU).
Hospitalized (Non-ICU)
Hospitalized (non-intensive care units)
hospitalized (non-ICU) datum
The condition of being treated as a patient in a hospital intensive care unit (ICU).
Hospitalized (ICU)
Hospitalized (intensive care units)
hospitalized (ICU) datum
Separation of people with a contagious disease from population to reduce the spread of the disease.
Mechanical Ventilation
medically isolated datum
Medical isolation in a negative pressure environment: 6 to 12 air exchanges per hour, and direct exhaust to the outside or through a high efficiency particulate air filter.
Medically Isolated
medically isolated (negative pressure) datum
An age group that stratifies the age of a case to be between 0 to 9 years old (inclusive).
subject age at time of specimen collection bin (0 - 9)
An age group that stratifies the age of a case to be between 10 to 19 years old (inclusive).
subject age at time of specimen collection bin (10 - 19)
An age group that stratifies the age of a case to be between 20 to 29 years old (inclusive).
subject age at time of specimen collection bin (20 - 29)
An age group that stratifies the age of a case to be between 30 to 39 years old (inclusive).
subject age at time of specimen collection bin (30 - 39)
An age group that stratifies the age of a case to be between 40 to 49 years old (inclusive).
subject age at time of specimen collection bin (40 - 49)
An age group that stratifies the age of a case to be between 50 to 59 years old (inclusive).
subject age at time of specimen collection bin (50 - 59)
An age group that stratifies the age of a case to be between 60 to 69 years old (inclusive).
subject age at time of specimen collection bin (60 - 69)
An age group that stratifies the age of a case to be between 70 to 79 years old (inclusive).
subject age at time of specimen collection bin (70 - 79)
An age group that stratifies the age of a case to be between 80 to 89 years old (inclusive).
subject age at time of specimen collection bin (80 - 89)
An age group that stratifies the age of a case to be between 90 to 99 years old (inclusive).
subject age at time of specimen collection bin (90 - 99)
An age group that stratifies the age of a case to be greater than or equal to 100 years old.
subject age at time of specimen collection bin (100+)
Age of host at the time of sampling, expressed as an age group in years.
subject age at time of specimen collection bin
Inability to arouse in response to one or more external stimuli.
Inability to arouse (inability to stay awake)
inability to stay awake
inability to arouse
Persistent blue discoloration of the lips.
Cyanotic face (bluish face)
bluish face
cyanotic face
Generalized bluish discoloration of the body and the visible mucous membranes, which occurs due to inadequate oxygenation secondary to conditions that lead to an increase in deoxygenated hemoglobin or presence of abnormal hemoglobin.
central cyanosis
Cyanotic lips (bluish lips)
bluish lips
cyanotic lips
Bluish discoloration of the distal extremities (hands, fingertips, toes), and can sometimes involve circumoral and periorbital areas. Mucous membranes are generally not involved.
peripheral cyanosis
Fever that exceeds 38 degrees centigrade.
fever (>=100.4°F)
fever (>=38°C)
Focal or diffuse areas of ill-defined, hazy, increased lung attenuation, which cause pulmonary vascular indistinctness, yet through which vessels can still be identified via high-resolution computed tomography or the conventional radiograph.
Ground Glass Opacities (GGO)
GGO
ground glass opacities
Abnormally low blood oxygen level without the presence of dyspnea/dyspnoea.
Silent hypoxemia
silent hypoxemia
Inflammation of infection of the ear.
Otitis
otitis
Fluid exuded from the pharynx posterior wall.
Pharyngeal exudate
pharyngeal exudate
Replaced with entity from an appropriate domain ontology.
obsolete: prostration
Inflammatory chilblain-like nodules on the hands and/or fingers.
Pseudo-chilblains on fingers (covid fingers)
covid fingers
pseudo-chilblains on fingers
Inflammatory chilblain-like nodules on the feet and/or toes.
Pseudo-chilblains on toes (covid toes)
covid toes
pseudo-chilblains on toes
Trauma to the cardiac muscle or valves.
cardiac injury
A reflex action of the respiratory tract that is used to clear the upper airways, lasting for more than 8 weeks
chronic cough
A persistent disease that affects the gastrointestinal tract.
chronic gastrointestinal disease
The period of time less than or equal to six weeks after labor and delivery.
postpartum (≤6 weeks)
The use of a drug for a reason other than which it was intended or in a manner or in quantities other than directed.
drug abuse
The use of an injection drug for a reason other than which it was intended or in a manner or in quantities other than directed.
injection drug abuse
An individual who is receiving or has received a transplant of a heart.
cardiac transplant
An individual who is receiving or has received a transplant of a liver.
liver transplant
A variant designation which is 1) a variant of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), 2) believed to have genetic mutations that increase binding affinity to human cells, 3) linked to rapid spread in human populations, and 4) is being monitored.
Variant of Concern (VOC)
VOC
VoC
PHA4GE Definition: A category used for indicating that a variant of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) containing genetic mutations believed to increase binding affinity to human cells and linked to rapid spread in human populations is being monitored.
variant of concern (SARS-CoV-2)
A variant designation which is 1) a variant of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), 2) demonstrated to have genetic mutations that increase binding affinity to human cells, 3) linked to rapid spread in human populations, and 4) is under surveillance.
Variant of Interest (VOI)
VOI
PHA4GE Definition: A category used for indicating that a variant of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) containing genetic mutations demonstrated to increase binding affinity to human cells and linked to rapid spread in human populations is under surveillance.
variant of interest (SARS-CoV-2)
A disorder characterized by an arrhythmia with an above normal rate.
tachyarrhythmia
A disease process that results in acute hypoxia secondary to a rapid deterioration in respiratory status.Increased capillary permeability and changes in pressure gradients within the pulmonary capillaries and vasculature are mechanisms for which noncardiogenic pulmonary edema occurs. To differentiate from cardiogenic pulmonary edema, pulmonary capillary wedge pressure is not elevated and remains less than 18 mmHg.
noncardiogenic pulmonary edema
A clinical syndrome characterized by the acute onset of pulmonary edema following a significant central nervous system (CNS) insult.
NPE
neurogenic pulmonary edema
obsolete: cardiac injury
An acute form of myocarditis, whose main characteristic is a rapidly progressive clinical course with the need for hemodynamic support.
fulminant myocarditis
A diagnosis of Kawasaki disease (KD) based on the fulfillment of a set of clinical signs including fever of five or more days' duration with at least four of the following five signs: (i) bilateral conjunctival injection, (ii) cervical lymphadenopathy, (iii) polymorphous skin rash, (iv) changes in the lips or oral mucosa, and (v) changes of the distal extremities.Usual laboratory findings in KD patients include elevated erythrocyte sedimentation rate and C-reactive protein, hypoalbuminemeia, elevated serum hepatic transaminases and leukocytosis with thrombocytosis noted later in the course of the illness.
complete Kawasaki syndrome
complete Kawasaki disease
A diagnosis of Kawasaki disease (KD) when patients fail to meet “classic” clinical features but have laboratory findings usually associated with KD and no reasonable alternate diagnosis, they are said to have incomplete or atypical KD.
incomplete Kawasaki syndrome
incomplete Kawasaki disease
A condition of liver damage that is characterized by coagulopathy with no signs of encephalopathy.
acute liver injury
A lung injury that results from mechanical stress and strain that occur during tidal ventilation in the susceptible lung.
VILI
ventilation induced lung injury
An injury in muscle tissue caused by bruising, spraining or laceration.
muscle injury
An organ dysfunction to such a degree that normal homeostasis cannot be maintained without external clinical intervention.
organ failure
A infection caused by staphylococcus bacteria, bearing the secondary infection role
If a secondary staphylococcus infection was identified during or after treatment of the primary infection.
secondary staph infection
A infection caused by streptococcal bacteria, bearing the secondary infection role
If a secondary streptococcal infection was identified during or after treatment of the primary infection.
secondary strep infection
A systemtic inflammatory response to infectious and/or non-fectious etiologies, resulting in life-threatening, generalized form of acute circulatory failure associated with inadequate oxygen utilization by the cells.
Descriptive of both infectious and non-infectious etiologies.
hyperinflammatory shock
A persistent form of cardiogenic shock that presents as persistent tissue hyoperfusion despite administration of adequote doses of vasoactive medications and treatmenft of the underlying aetiology.
refractory cardiogenic shock
A persistent form of cardiogenic shock that presents simultaneously with vasoplegic shock.
refractory cardiogenic plus vasoplegic shock
A vaccination status in which an individual has completed a full series of an authorized vaccine according to the regional health institutional guidance.
fully vaccinated
A vaccination status in which an individual has started but not yet fully completed a vaccine series authorized and administered according to the regional health institutional guidance.
In general, people are considered partially vaccinated 2 weeks after their first dose in a single-dose or multi-dose vaccine series.
partially vaccinated
A vaccination status in which an individual has not completed or initiated a vaccine series authorized and administered according to the regional health institutional guidance.
unvaccinated
In general, people are considered not vaccinated if they have not received a single dose or have not yet completed the 2 weeks after their first dose in a single-dose or multi-dose vaccine series.
not vaccinated
A manufactured product which separates solids from fluids by adding a medium through which only a fluid can pass.
filter
An extract which is the output of an extraction process in which messenger RNA molecules are isolated from a specimen.
mRNA (messenger RNA)
messenger RNA extract
mRNA extract
A DNA sequencer manufactured by the Illumina corporation.
Illumina sequencing instrument model
A DNA sequencer manufactured by Solexa as one of its first sequencer lines, launched in 2006, and capable of sequencing 1 gigabase (Gb) of data in a single run.
Illumina Genome Analyzer
obsolete: Illumina Genome Analyzer II
obsolete: Illumina Genome Analyzer IIx
A DNA sequencer manufactured by the Illumina corporation using sequence-by-synthesis chemistry, and contains a HiScan Reader for sequencing and microarray-based analyses as well as an "SQ Module" to support microfluidics.
Illumina HiScanSQ
A DNA sequencer manufactured by the Illumina corporation using sequence-by-synthesis chemistry, enabling deep sequencing and high yield.
Illumina HiSeq
A DNA sequencer manufactured by the Illumina corporation using sequence-by-synthesis chemistry that oenabled sufficent depth and coverage to produce the first 30x human genome for $1000.
Illumina HiSeq X
A DNA sequencer manufactured by the Illumina corporation using sequence-by-synthesis chemistry that consists of a set of 5 HiSeq X Sequencing Systems.
Illumina HiSeq X 5
Illumina HiSeq X Five
A DNA sequencer that consists of a set of 10 HiSeq X Sequencing Systems.
Illumina HiSeq X 10
Illumina HiSeq X Ten
obsolete: Illumina HiSeq 1000
A DNA sequencer which is manufactured by the Illumina corporation, with a single flow cell and a throughput of up to 35-50 Gb per day.
Illumina HiSeq 1500
obsolete: Illumina HiSeq 2000
obsolete: Illumina HiSeq 2500
obsolete: Illumina HiSeq 3000
obsolete: Illumina HiSeq 4000
A DNA sequencer manufactured by the Illumina corporation using sequence-by-synthesis chemistry that is lightweight.
Illumina iSeq
A DNA sequencer manufactured by the Illumina corporation using sequence-by-synthesis chemistry that is lightweight and has an output capacity between 144MB-1.2GB.
Illumina iSeq 100
A DNA sequencer manufactured by the Illunina corporation using sequence-by-synthesis chemistry that has an output capacirty of 6 Tb and 20 billion reads in dual flow cell mode.
Illumina NovaSeq
A DNA sequencer which is manufactured by the Illumina corporation, with two flow cells and an output of up to 6000 Gb (32-40 B reads per run). The sequencer utilizes synthesis technology and patterned flow cells to optimize throughput and even spacing of sequencing clusters.
Illumina NovaSeq 6000
A DNA sequencer which is manufactured by the Illumina corporation using sequence-by-synthesis chemistry that fits on a benchtop and has an output capacity of 1.65-7.5 Gb.
Illumina MiniSeq
obsolete: Illumina MiSeq
Illumina NextSeq
obsolete: Illumina NextSeq 500
A DNA sequencer which is a desktop sequencer ideal for smaller-scale studies manufactured by the Illumina corporation. It supports sequencing of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology. The 550 is an upgrade on the 500 model.
Illumina NextSeq 550
A DNA sequencer which is manufactured by the Illumina corporation using sequence-by-synthesis chemistry that fits on a benchtop and has an output capacity of 30-360 Gb.
Illumina NextSeq 2000
A DNA sequencer manufactured by the Pacific Biosciences corporation.
Pacific Biosciences sequencing instrument model
A DNA sequencer manufactured by the Pacific Biosciences corporation which utilizes “SMRT Cells” for single-molecule real-time sequencing. The RS was the first model made by the company.
PacBio RS
obsolete: PacBio RS II
A DNA sequencer built upon single molecule real-time sequencing technology, optimized for generation with long reads and high consensus accuracy, and manufactured by the Pacific Biosciences corporation
PacBio Sequel
A DNA sequencer built upon single molecule real-time sequencing technology, optimized for generation of highly accurate ("HiFi") long reads, and which is manufactured by the Pacific Biosciences corporation.
PacBio Sequel II
A DNA sequencer manufactured by the Ion Torrent corporation.
Ion Torrent sequencing instrument model
A DNA sequencer manufactured by the Ion Torrent corporation which utilizes Ion semiconductor sequencing and has an output capacity of 300 MB - 1GB.
Ion Torrent PGM
A DNA sequencer manufactured by the Ion Torrent corporation which utilizes Ion semiconductor sequencing and has an output capacity of up to 15 Gb.
Ion Torrent Proton
A DNA sequencer manufactured by the Ion Torrent corporation which utilizes Ion semiconductor sequencing and requires only a small amount of input material while producing data faster than the S5 model.
Ion Torrent S5 XL
A DNA sequencer manufactured by the Ion Torrent corporation which utilizes Ion semiconductor sequencing and requires only a small amount of input material.
Ion Torrent S5
A DNA sequencer manufactured by the Oxford Nanopore corporation.
Oxford Nanopore sequencing instrument model
A DNA sequencer that is manufactured by the Oxford Nanopore Technologies corporation, that can run and analyze up to five individual flow cells producing up to 150 Gb of data per run. The sequencer produces real-time results and utilizes nanopore technology with the option of running the flow cells concurrently or individual
Oxford Nanopore GridION
A portable DNA sequencer which is manufactured by the Oxford Nanopore Technologies corporation, that uses consumable flow cells producing up to 30 Gb of DNA sequence data per flow cell. The sequencer produces real-time results and utilizes nanopore technology with up to 512 nanopore channels in the sensor array.
Oxford Nanopore MinION
A DNA sequencer that is manufactured by the Oxford Nanopore Technologies corporation, capable of running up to 48 flow cells and producing up to 7.6 Tb of data per run. The sequencer produces real-time results and utilizes Nanopore technology, with each flow cell allowing up to 3,000 nanopores to be sequencing simultaneously.
Oxford Nanopore PromethION
A DNA sequencer manufactured by the BGI Genomics corporation.
BGI Genomics sequencing instrument model
A DNA sequencer manufactured by the BGI Genomics corporation that utilizes Probe-Anchor Synthesis (cPAS) chemistry and "DNA Nanoballs".
BGI Genomics BGISEQ-500
A DNA sequencer manufactured by the MGI corporation.
MGI sequencing instrument model
A high throughput DNA sequencer manufactured by the MGI corporation with an output capacity of 1~6TB of data per day.
MGI DNBSEQ-T7
A DNA sequencer manufactured by the MGI corporation with an output capacity of 55GB~1440GB per run.
MGI DNBSEQ-G400
A DNA sequencer manufactured by the MGI corporation with an outout capacity of 55GB~330GB per run, which enables faster sequencing than the DNBSEQ-G400.
MGI DNBSEQ-G400RS FAST
A DNA sequencer manufactured by the MGI corporation with an output capacity of 10～150 GB per run and enables different read lengths.
MGI DNBSEQ-G50
A gene encoding the envelope protein of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2).
orf4 gene (SARS-CoV-2)
E gene (SARS-CoV-2)
A gene encoding the membrane glycoprotrein M protein of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2).
orf5 gene (SARS-CoV-2)
M gene (SARS-CoV-2)
A gene encoding the nucleocapsid phosphoprotein of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2).
orf9 gene (SARS-CoV-2)
N gene (SARS-CoV-2)
A gene encoding the Spike protein of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2).
orf2 gene (SARS-CoV-2)
Spike gene (SARS-CoV-2)
A gene encoding the replicase polyprotein 1ab of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2).
rep gene (SARS-CoV-2)
orf1ab gene (SARS-CoV-2)
A gene encoding the polyprotein 1a of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2).
pp1a gene (SARS-CoV-2)
orf1a gene (SARS-CoV-2)
A gene encoding the nonstructural protein 11 of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2).
nsp11 gene (SARS-CoV-2)
A gene encoding the nonstructural protein 1 of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2).
nsp1 gene (SARS-CoV-2)
A gene encoding the nonstructural protein 2 of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2).
nsp2 gene (SARS-CoV-2)
A gene encoding the nonstructural protein 3 of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2).
nsp3 gene (SARS-CoV-2)
A gene encoding the nonstructural protein 4 of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2).
nsp4 gene (SARS-CoV-2)
A gene encoding the nonstructural protein 5 of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2).
nsp5 gene (SARS-CoV-2)
A gene encoding the nonstructural protein 6 of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2).
nsp6 gene (SARS-CoV-2)
A gene encoding the nonstructural protein 7 of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2).
nsp7 gene (SARS-CoV-2)
A gene encoding the nonstructural protein 8 of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2).
nsp8 gene (SARS-CoV-2)
A gene encoding the nonstructural protein 9 of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2).
nsp9 gene (SARS-CoV-2)
A gene encoding the nonstructural protein 10 of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2).
nsp10 gene (SARS-CoV-2)
A gene encoding the RNA-dependent RNA polymerase (RdRp) of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2).
nsp12 gene (SARS-CoV-2)
RdRp gene (SARS-CoV-2)
A gene encoding the helicase (hel) of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2).
nsp13 gene (SARS-CoV-2)
hel gene (SARS-CoV-2)
A gene encoding the nonstructural protein 14 of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2).
nsp14 gene (SARS-CoV-2)
exoN gene (SARS-CoV-2)
A gene encoding the nonstructural protein 15 of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2).
nsp15 gene (SARS-CoV-2)
A gene encoding the nonstructural protein 16 of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2).
nsp16 gene (SARS-CoV-2)
A gene encoding the viroporin ORF3a of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2).
orf3a gene (SARS-CoV-2)
A gene encoding the polyprotein ORF3b of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2).
orf3b gene (SARS-CoV-2)
ns6 gene (SARS-CoV-2)
orf6 gene (SARS-CoV-2)
A gene encoding a transmembrane protein of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2).
orf7a gene (SARS-CoV-2)
A gene encoding the polyprotein ORF7b of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2).
ns7b gene (SARS-CoV-2)
orf7b gene (SARS-CoV-2)
ns8 gene (SARS-CoV-2)
orf8 gene (SARS-CoV-2)
A gene encoding the viral accessory protein ORF9b of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2).
orf9b gene (SARS-CoV-2)
A gene encoding the membrane-associated protein ORF9c of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2).
orf9c gene (SARS-CoV-2)
A gene encoding the polyprotein ORF10 of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2).
orf10 gene (SARS-CoV-2)
A gene encoding the uncharacterized protein ORF14 of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2).
orf14 gene (SARS-CoV-2)
A genomic region that is untranslated at the 5' end of the genome of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2).
SARS-COV-2 5' UTR
SARS-CoV-2 5' untranslated region
SARS-CoV-2 5'-UTR
5' UTR (SARS-CoV-2)
A process occuring within or in the vicinity of a human with a confirmed case of COVID-19 that exposes the recipient organism to SARS-CoV-2.
Contact with Known COVID-19 Case
contact with known COVID19 case
contact with known COVID-19 case exposure process
A process occuring within or in the vicinity of a human patient that exposes the recipient organism to a material entity.
Contact with Patient
contact with patient exposure process
A process occuring within or in the vicinity of a human with a probable case of COVID-19 that exposes the recipient organism to SARS-CoV-2.
Contact with Probable COVID-19 Case
contact with probable COVID19 case
contact with probable COVID-19 case exposure process
A process occuring within or in the vicinity of a human with acute respiratory illness that exposes the recipient organism to said acute respiratory illness.
Contact with Person with Acute Respiratory Illness
contact with person with acute respiratory illness exposure process
A process occuring within or in the vicinity of a human with a fever and/or cough that exposes the recipient organism to the causative agent.
Contact with Person with Fever and/or Cough
contact with person with fever and/or cough exposure process
A process occuring within or in the vicinity of a human, who recently travelled, that exposes the recipient organism to a material entity.
Contact with Person who Recently Travelled
contact with person who recently travelled exposure process
A process occuring within or in the vicinity of a human residential environment that exposes the recipient organism to a material entity.
Occupational, Residency or Patronage Exposure
occupational, residency or patronage exposure process
A process occuring within or in the vicinity of an animal rescue facility that exposes the recipient organism to a material entity.
Animal Rescue
animal rescue exposure process
A process occuring within or in the vicinity of a human childcare environment that exposes the recipient organism to a material entity.
Childcare
childcare exposure process
A process occuring within or in the vicinity of a human daycare environment that exposes the recipient organism to a material entity.
Daycare
daycare exposure process
A process occuring within or in the vicinity of a human nursery that exposes the recipient organism to a material entity.
Nursery
nursery exposure process
A process occuring within or in the vicinity of a community service centre that exposes the recipient organism to a material entity.
Community Service Centre
community service centre exposure process
A process occuring within or in the vicinity of a correctional facility that exposes the recipient organism to a material entity.
Correctional Facility
correctional facility exposure process
A process occuring within or in the vicinity of a dormitory that exposes the recipient organism to a material entity.
Dormitory
dormitory exposure process
A process occuring within or in the vicinity of a first nations reserve that exposes the recipient organism to a material entity.
First Nations Reserve
first nations reserve exposure process
A process occuring within or in the vicinity of a fgroup home that exposes the recipient organism to a material entity.
Funeral Home
funeral home exposure process
A process occuring within or in the vicinity of a group home that exposes the recipient organism to a material entity.
Group Home
group home exposure process
A process occuring within or in the vicinity of a healthcare environment that exposes the recipient organism to a material entity.
Healthcare Setting
healthcare setting exposure process
A process occuring within or in the vicinity of an ambulance that exposes the recipient organism to a material entity.
Ambulance
ambulance exposure process
A process occuring within or in the vicinity of an acute care facility that exposes the recipient organism to a material entity.
Acute Care Facility
acute care facility exposure process
A process occuring within or in the vicinity of a medical clinic that exposes the recipient organism to a material entity.
Clinic
clinic exposure process
A process occuring within or in the vicinity of a community health centre that exposes the recipient organism to a material entity.
Community Health Centre
community health centre exposure process
A process occuring within or in the vicinity of an emergency department that exposes the recipient organism to a material entity.
Emergency Department
emergency department exposure process
A process occuring within or in the vicinity of an ICU that exposes the recipient organism to a material entity.
intensive care unit exposure process
A process occuring within or in the vicinity of a hospital ward that exposes the recipient organism to a material entity.
Ward
ward exposure process
A process occuring within or in the vicinity of a long-term care facility that exposes the recipient organism to a material entity.
Long-Term Care Facility
long-term care facility exposure process
A process occuring within or in the vicinity of a pharmacy that exposes the recipient organism to a material entity.
Pharmacy
pharmacy exposure process
A process occuring within or in the vicinity of a physician's office that exposes the recipient organism to a material entity.
Physician's Office
physician's Office exposure process
A process occuring within or in the vicinity of a household that exposes the recipient organism to a material entity.
Household
household exposure process
A process occuring that exposes the recipient organism to a material entity as a consequence of said organism having insecure housing.
Insecure Housing (Homeless)
homeless
insecure housing exposure process
A process occuring within or in the vicinity of a human occupational environment that exposes the recipient organism to a material entity.
Occupational Exposure
occupational exposure process
A process occuring within or in the vicinity of an office that exposes the recipient organism to a material entity.
Worksite
worksite exposure process
A process occuring outdoors that exposes the recipient organism to a material entity.
Outdoors
outdoors exposure process
A process that exposes the recipient organism to a material entity as a consequence of hiking.
Hiking Trail
hiking trail exposure process
A process occuring within or in the vicinity of a ski resort that exposes the recipient organism to a material entity.
Ski Resort
ski resort exposure process
A directive information entity which realizes sample strategy specifications.
sampling strategy specification
A process occuring within or in the vicinity of a place of worship that exposes the recipient organism to a material entity.
Place of Worship
place of worship exposure process
A process occuring within or in the vicinity of a church that exposes the recipient organism to a material entity.
Church
church exposure process
A process occuring within or in the vicinity of a mosque that exposes the recipient organism to a material entity.
Mosque
mosque exposure process
A process occuring within or in the vicinity of a temple that exposes the recipient organism to a material entity.
Temple
temple exposure process
A process occuring within or in the vicinity of a school that exposes the recipient organism to a material entity.
School
school exposure process
A process occuring within or in the vicinity of a temporary residence that exposes the recipient organism to a material entity.
Temporary Residence
temporary residence exposure process
A process occuring within or in the vicinity of a homeless shelter that exposes the recipient organism to a material entity.
Homeless Shelter
homeless shelter exposure process
A process occuring within or in the vicinity of a hotel exposure that exposes the recipient organism to a material entity.
Hotel
hotel exposure process
A process occuring within or in the vicinity of a veterinary facility that exposes the recipient organism to a material entity.
Veterinary Care Clinic
veterinary care clinic exposure process
A process occuring as a result of travel that exposes the recipient organism to a material entity.
Travel Exposure
travel exposure process
A process occuring within or in the vicinity of a cruise ship that exposes the recipient organism to a material entity.
Travelled on a Cruise Ship
travelled on a cruise ship exposure process
A process occuring within or in the vicinity of an airplane that exposes the recipient organism to a material entity.
Travelled on a Plane
travelled on a plane exposure process
A process occuring within or in the vicinity of ground transport that exposes the recipient organism to a material entity.
Travelled on Ground Transport
travelled on ground transport exposure process
An absence of antiviral treatment administered prior to the current regimen or test.
no prior antiviral treatment
An infection that occurred within a host prior to the current infection.
prior infection
A process occuring that exposes the recipient organism to a material entity.
Other Exposure Setting
other exposure setting exposure process
An absence of infection that occurred within a host prior to the current infection.
no prior infection
A type of social behavior in which a sufficent number of humans gather together such that there is potential strain on community resources.
Mass Gathering
mass gathering exposure datum
A human mass gathering in which humans meet at an arranged place and time in order to discuss or engage in some common interest.
Convention
convention exposure datum
A human social gathering in which a group of humans formally assemble for a specific purpose.
Convocation
convocation exposure datum
A human social gathering at which humans gather for a planned or social occasion to carry out activities relevant to agriculture.
Agricultural Event
agricultural event exposure datum
A type of social behavior in which a collection of humans intentionally gathers together on a temporary basis to engage in a religious activity.
Religious Gathering
religious gathering exposure datum
A human eucharistic liturgical gathering in which humans perform public worship.
Mass
mass exposure datum
A human social event in which human family members congregate.
Family Gathering
family gathering exposure datum
A human social event in which many human members of an extended family congregate.
Family Reunion
family reunion exposure datum
A human social event in which humans gather for a ceremony connected with the final disposition of a corpse, such as a burial or cremation.
Funeral
funeral exposure datum
Contact via airborne transmission or contact with contaminated surfaces.
A type of contact in which an individual does not come in direct contact with a source of infection.
indirect contact
A type of indirect contact where an individual sustains unprotected exposure by being within 6 feet of an infected individual over a sustained period of time.
face-to-face contact
close indirect contact
A type of indirect contact where an individual may at the same location at the same time as a positive case; however, they may have been there only briefly, or it may have been a location that carries a lower risk of transmission.
casual indirect contact
A role inhering in a person that is realized when the bearer is present on a given occasion or at a given place.
Attendee
attendee role
A role inhering in a person that is realized when the bearer travels in a vehicle but bears little to no responsibility for vehicle operation nor arrival at its destination.
Passenger
passenger role
A role inhering in a person that is realized when the bearer maintains residency in a given place.
Resident
resident role
A role inhering in a person that is realized when the bearer pays a visit to a specific place or event.
Visitor
visitor role
A role inhering in a person that is realized when the bearer enters into any service of their own free will.
Volunteer
volunteer role
A role inhering in a person that is realized when the bearer performs labor for a living.
Work
work role
A role inhering in a person that is realized when the bearer is engaged in administration or administrative work.
Administrator
administrator role
A role inhering in a person that is realized when the bearer is among the first to arrive at the scene of an emergency and has specialized training to provide assistance.
First Responder
first responder role
A role inhering in a person that is realized when the bearer is a rescuer extensively trained in firefighting.
Firefighter
firefighter role
A role inhering in a person that is realized when the bearer is a healthcare professional who responds to emergency calls for medical help outside of a hospital.
Paramedic
paramedic role
A role inhering in a person that is realized when the bearer is a warranted law employee of a police force.
Police Officer
police officer role
A role inhering in a person that is realized when the bearer is an individual who performs cleaning duties and/or is responsible for the supervision of cleaning staff.
Housekeeper
housekeeper role
A role inhering in a person that is realized when the bearer is an employee that performs labor in a kitchen.
Kitchen Worker
kitchen worker role
A role inhering in a person that is realized when the bearer is an employee that performs labor in a laboratory.
Laboratory Worker
laboratory worker role
A role inhering in a person that is realized when the bearer works to help another person complete their daily activities.
Personal Care Aid
personal care aide role
personal care aid role
A role inhering in a person that is realized when the bearer is a health professional who specializes in dispensing prescription drugs at a healthcare facility.
Pharmacist
pharmacist role
A role inhering in a person that is realized when the bearer is a professional who practices veterinary medicine.
Veterinarian
veterinarian role
A role inhering in a person that is realized when the bearer is in a state of being acquainted with a person.
Acquaintance of case
acquaintance role
A role inhering in a person that is realized when the bearer is a relative of the case.
Relative of case
relative role
A role inhering in a person that is realized when the bearer is a person younger than the age of majority.
Child of case
child role
A role inhering in a person that is realized when the bearer is a caregiver of the offspring of their own species.
Parent of case
guardian of case role
parent of caserole
A role inhering in a person that is realized when the bearer is the male parent of a child.
Father of case
father role
A role inhering in a person that is realized when the bearer is the female parent of a child.
Mother of case
mother role
A role inhering in a person that is realized when the bearer is a significant other in a marriage, civil union, or common-law marriage.
Spouse of case
spouse role
A variant surveillance strategy in which a sample is sequenced because the individual from which the sample is derived has a known epidemiological link to a variant case.
Sample has epidemiological link to Variant of Concern (VoC)
sample has epidemiological link to VoC
sample has epidemiological link to Variant of Concern strategy
A variant surveillance strategy in which a sample is sequenced because the individual from which the sample is derived has a known epidemiological link to an Omicron variant case.
Sample has epidemiological link to Omicron Variant
sample has epidemiological link to Omicron variant strategy
A domestic travel-associated surveillance strategy in which individuals are selected if their travel occurred within a state/province within a nation.
Interstate/ interprovincial travel surveillance
interstate/ interprovincial travel surveillance strategy
A domestic travel-associated surveillance strategy in which individuals are selected if their travel occurred between states/provinces within a nation.
Intra-state/ intra-provincial travel surveillance
intra-state/ intra-provincial travel surveillance strategy
A data field which describes whether the sample was collected from an individual in quarantine.
sample collected in quarantine
sample collected in quarantine slot
Example Guidance: Whether a sample was collected under quarantine conditions (e.g. self-quarantining, medically isolated, staying at a quarantine hotel) can inform public health measure assessments. Use the picklist provided in the template.
sample collected in quarantine field
Jitter added to publicly shared collection dates to prevent re-identifiability.
A data field which describes how any data elements were altered to preserve patient privacy.
data abstraction details
data abstraction details slot
Example Guidance: If applicable, provide a description of how each data element was abstracted.
data abstraction details field
A variant designation which is 1) a variant of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), 2) containing genetic mutates that may increase binding affinity to human cells, 3) linked to rapid spread in human populations, 4) is being monitored, and 5) denoted as a lower risk than a Variant of Interest (VOI).
Variant Under Monitoring (VUM)
VBM
VUM
Variant Being Monitored
PHA4GE Definition: A category used for indicating that a variant of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) containing genetic mutations that may increase binding affinity to human cells and linked to rapid spread in human populations is being monitored. This category denotes less risk than a Variant of Interest (VOI).
variant under monitoring (SARS-CoV-2)
A data field which describes the county or region of origin of the sample.
geo_loc name (county/region)
geographical location county or region name
geo_loc name (county/region) slot
geographical location county or region name field
geographical location county or region name slot
Example Guidance: Provide the county/region name from the GAZ geography ontology. Search for geography terms here: https://www.ebi.ac.uk/ols/ontologies/gaz
geo_loc name (county/region) field
A data field which describes the identifier used to specify an epidemiologically detected case of disease.
case ID
case ID slot
case identifier field
case identifier slot
Example Guidance: Provide the case identifer. The case ID greatly facilitates linkage between laboratory and epidemiological data. The case ID may be considered identifiable information. Consult the data steward before sharing.
epidemiology case ID field
An identifier data field which describes the user-defined Global Initiative on Sharing Avian Influenza Data (GISAID) virus name assigned to the sequence.
GISAID virus name
GISAID virus name slot
Global Initiative on Sharing Avian Influenza Data virus name field
Global Initiative on Sharing Avian Influenza Data virus name slot
Example Guidance: GISAID virus names should be in the format .hCoV-19/Country/Identifier/year..
GISAID virus name field
URI example: http://portal.vertnet.org/o/fmnh/mammals?id=33e55cfe-330b-40d9-aaae-8d042cba7542, INSDC triplet example: UAM:Mamm:52179
A data field which describes the identifier for the physical specimen.
host specimen voucher
host specimen voucher ID slot
host specimen voucher identifier field
host specimen voucher identifier slothost specimen voucher ID field
host specimen voucher slot
Example Guidance: Include a URI (Uniform Resource Identifier) in the form of a URL providing a direct link to the physical host specimen. If the specimen was destroyed in the process of analysis, electronic images (e-vouchers) are an adequate substitute for a physical host voucher specimen. If a URI is not available, a museum-provided globally unique identifier (GUID) can be used. If no persistent unique identifier is available, follow the INSDC guidance for populating the voucher_specimen attribute using standard triplets for institution codes (i.e., /specimen_voucher=.[<institution-code>:[<collection-code>:]]<specimen_id>.): http://www.insdc.org/controlled-vocabulary-specimenvoucher-qualifier
host specimen voucher field
A data field which describes the name of the source collection and unique culture identifier.
culture collection
culture collection slot
Example Guidance: Format: .<institution-code>:[<collection-code>:]<culture_id>.. For more information, see http://www.insdc.org/controlled-vocabulary-culturecollection-qualifier.
culture collection ID field
A data field which describes the name of the sample plan implemented for sample collection.
sample plan name
sample plan name slot
Example Guidance: Provide the name and version of the sample plan outlining the sample strategy.
sample plan name field
A specimen datum which describes the collection, isolate production, sequencing, or storage of specimen material or data.
An organism datum which contains additional contextual details regarding the health or disease status of a host at the time of sample collection.
host health status details at time of specimen collection
A personal health datum which specifies host health complications at time of specimen collection.
host health complications at time of specimen collection
A personal health datum which specifies host pre-existing conditions and risk factors at time of specimen collection.
pre-existing conditions and risk factors at time of specimen collection
A personal health datum which specifies host signs and symptoms at time of specimen collection.
signs and symptoms at time of specimen collection
An infection detail datum which is used for classifying a variant of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), determined by the risk it poses based on available scientific evidence.
variant designation (SARS-CoV-2)
A material entity encoding a genomic region of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2).
SARS-CoV-2 genomic region
A data item that describes an event in which exposure to a stressor may have occurred.
exposure datum
A process in which a recipient organism is exposed to a material entity.
exposure process
obsolete: cell line cell
A patient as host datum which indicates the vaccination status of the patient.
vaccination status
A genomic region encoding a gene of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2).
SARS-CoV-2 gene
A data enumeration which references a set of named signs and symptoms entities.
health signs and symptoms enumeration
A data enumeration which references a set of named pre-existing conditions and risk factors entities.
pre-existing conditions and risk factors enumeration
A data enumeration which references a set of named complications entities.
health complications enumeration
A data enumeration which references a set of named person role entities.
person role enumeration
A data field which describes the latitude coordinates of the geographical location of sample collection.
geo_loc latitude
geographical location latitude
geo_loc latitude slot
geographical location latitude field
geographical location latitude slot
Example Guidance: Provide latitude coordinates if available. Do not use the centre of the city/region/province/state/country or the location of your agency as a proxy, as this implicates a real location and is misleading. Specify as degrees latitude in format .d[d.dddd] N|S..
geo_loc latitude field
A data field which describes the longitude coordinates of the geographical location of sample collection.
geo_loc longitude
geographical location longitude
geo_loc longitude slot
geographical location longitude field
geographical location longitude slot
Example Guidance: Provide longitude coordinates if available. Do not use the centre of the city/region/province/state/country or the location of your agency as a proxy, as this implicates a real location and is misleading. Specify as degrees longitude in format .d[dd.dddd] W|E..
geo_loc longitude field
25 swabs were pooled and further prepared as a single sample during library prep.
A data field which describes detailed information regarding the processing applied to a sample during or after receiving the sample.
specimen processing details
specimen processing details slot
Example Guidance: Provide a free text description of any processing details applied to a sample.
specimen processing details field
A host data field which describes the self-identified ethnicity(ies) of the host.
host ethnicity
host ethnicity slot
Example Guidance: If known, provide the self-identified ethnicity or ethnicities of the host as a free text description. This is highly sensitive information which must be treated respectfully and carefully when sharing. The information may have implications for equitable access and benefit sharing. Consult your privacy officer, data steward and/or cultural services representative.
host ethnicity field
A data field which describes the name of the vaccine administered as the first dose of a vaccine regimen.
vaccination dose 1 vaccine name
vaccination dose one vaccine name
vaccination dose 1 vaccine name slot
vaccination dose one vaccine name field
vaccination dose one vaccine name slot
Example Guidance: Provide the name and the corresponding manufacturer of the COVID-19 vaccine administered as the first dose by selecting a value from the pick list
vaccination dose 1 vaccine name field
A host data field which describes the date the first dose of a vaccine was administered.
vaccination dose 1 vaccination date
vaccination dose one vaccination date
vaccination dose 1 vaccination date slot
vaccination dose one vaccination date field
vaccination dose one vaccination date slot
Example Guidance: Provide the date the first dose of COVID-19 vaccine was administered. The date should be provided in ISO 8601 standard format .YYYY-MM-DD..
vaccination dose 1 vaccination date field
A data field which describes the name of the vaccine administered as the second dose of a vaccine regimen.
vaccination dose 2 vaccine name
vaccination dose two vaccine name
vaccination dose 2 vaccine name slot
vaccination dose two vaccine name field
vaccination dose two vaccine name slot
Example Guidance: Provide the name and the corresponding manufacturer of the COVID-19 vaccine administered as the second dose by selecting a value from the pick list
vaccination dose 2 vaccine name field
A host data field which describes the date the second dose of a vaccine was administered.
vaccination dose 2 vaccination date
vaccination dose two vaccination date
vaccination dose 2 vaccination date slot
vaccination dose two vaccination date field
vaccination dose two vaccination date slot
Example Guidance: Provide the date the second dose of COVID-19 vaccine was administered. The date should be provided in ISO 8601 standard format .YYYY-MM-DD..
vaccination dose 2 vaccination date field
A data field which describes the name of the vaccine administered as the third dose of a vaccine regimen.
vaccination dose 3 vaccine name
vaccination dose three vaccine name
vaccination dose 3 vaccine name slot
vaccination dose three vaccine name field
vaccination dose three vaccine name slot
Example Guidance: Provide the name and the corresponding manufacturer of the COVID-19 vaccine administered as the third dose by selecting a value from the pick list
vaccination dose 3 vaccine name field
A host data field which describes the date the third dose of a vaccine was administered.
vaccination dose 3 vaccination date
vaccination dose three vaccination date
vaccination dose 3 vaccination date slot
vaccination dose three vaccination date field
vaccination dose three vaccination date slot
Example Guidance: Provide the date the third dose of COVID-19 vaccine was administered. The date should be provided in ISO 8601 standard format .YYYY-MM-DD..
vaccination dose 3 vaccination date field
A data field which describes the name of the vaccine administered as the fourth dose of a vaccine regimen.
vaccination dose 4 vaccine name
vaccination dose four vaccine name
vaccination dose 4 vaccine name slot
vaccination dose four vaccine name field
vaccination dose four vaccine name slot
Example Guidance: Provide the name and the corresponding manufacturer of the COVID-19 vaccine administered as the fourth dose by selecting a value from the pick list
vaccination dose 4 vaccine name field
A host data field which describes the date the fourth dose of a vaccine was administered.
vaccination dose 4 vaccination date
vaccination dose four vaccination date
vaccination dose 4 vaccination date slot
vaccination dose four vaccination date field
vaccination dose four vaccination date slot
Example Guidance: Provide the date the fourth dose of COVID-19 vaccine was administered. The date should be provided in ISO 8601 standard format .YYYY-MM-DD..
vaccination dose 4 vaccination date field
Pfizer-BioNTech (Comirnaty); 2021-03-01; Pfizer-BioNTech (Comirnaty); 2022-01-15
A host data field which describes the description of the vaccines received and the administration dates of a series of vaccinations against a specific disease or a set of diseases.
vaccination history
vaccination history slot
Example Guidance: Free text description of the dates and vaccines administered against a particular disease/set of diseases. It is also acceptable to concatenate the individual dose information (vaccine name, vaccination date) separated by semicolons.
vaccination history field
A role inhering in a person that is realized when the bearer is an employee that performs labor in a healthcare setting.
Healthcare Worker
healthcare worker role
A role inhering in a person that is realized when the bearer is an employee that performs labor which rotates according to a schedule.
Rotational Worker
rotational worker role
A role inhering in a person that is realized when the bearer is an employee that performs labor according to a seasonal schedule.
Seasonal Worker
seasonal worker role
A sampling strategy in which stored samples from past events are sequenced.
Retrospective sequencing
retrospective sequencing strategy
A type of contact in which an individual comes in contact with an infected person, either directly or indirectly.
contact with infected individual
A data field which describes the type of entry point a traveler arrives through.
travel point of entry type
travel point of entry type slot
Example Guidance: Select the point of entry type.
travel point of entry type field
A data field which describes the day a traveller was tested on or after arrival at their point of entry.
border testing test day type
border testing test day type slot
Example Guidance: Select the test day.
border testing test day type field
A process occuring within or in the vicinty of a the individual home where the patient or client is living and health care or supportive care is being being delivered, as opposed to care provided in group accommodations like clinics or nursing home.
Community Healthcare (At-Home) Setting
at-home community healthcare exposure process
A data field which describes the name of the agency, organization or institution responsible for sequencing the isolate's genome.
Not to be confused with 'sequence_submitted_by' http://purl.obolibrary.org/obo/GENEPIO_0001159.
sequenced by
sequenced_by
sequenced by slot
Example Guidance: The name of the agency should be written out in full, (with minor exceptions) and be consistent across multiple submissions. If submitting specimens rather than sequencing data, please put the .National Microbiology Laboratory (NML)..
sequenced by field
A mass gathering event where the primary emphasis is on recreation.
Recreational Event
recreational event datum
A recreational event where the primary emphasis is on a concert performance.
Concert
concert event datum
A recreational event where the primary emphasis is a sporting deemonstration or athletic competition.
Sporting Event
sporting event datum
A role inhering in a person that is realized when the bearer a professional caregiver that provides health care or supportive care in the individual home where the patient or client is living, as opposed to care provided in group accommodations like clinics or nursing home.
Community Healthcare Worker
community healthcare worker
A data field which describes the email address of the contact responsible for follow-up regarding the sequence.
Not to be confused with 'sequence submitter contact email' http://purl.obolibrary.org/obo/GENEPIO_0001165
sequenced by contact email
sequenced_by_contact_email
sequenced by contact email slot
Example Guidance: The email address can represent a specific individual or lab e.g. johnnyblogs@lab.ca, or RespLab@lab.ca
sequenced by contact email field
A data field which describes the mailing address of the agency submitting the sequence.
Not to be confused with 'sequence submitter contact address' http://purl.obolibrary.org/obo/GENEPIO_0001167
sequenced by contact address
sequenced by contact address slot
Example Guidance: The mailing address should be in the format: Street number and name, City, Province/Territory, Postal Code, Country
sequenced by contact address field
A data field which describes an alternative sample identifier assigned to the sample by another organization.
alternative sample ID
alternative sample identifier
alternative_sample_ID
alternative sample ID slot
alternative sample identifier field
alternative sample identifier slot
Example Guidance: Provide any alternative identifiers for the sample here, separated by commas. Alternative identifiers assigned to the sample should be tracked along with original IDs to establish chain of custody. If the information is unknown or cannot be provided, leave blank or provide a null value.
alternative sample ID field
A data field which describes the specific laboratory affiliation of the sample collector.
sample collected by laboratory name
sample_collected_by_laboratory_name
sample collected by laboratory name slot
Example Guidance: Provide the name of the specific laboratory that collected the sample (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value.
sample collected by laboratory name field
A data field which describes the project/initiative/program for which the sample was collected.
sample collection project name
sample_collection_project_name
sample collection project name slot
Example Guidance: Provide the name of the project and/or the project ID here. If the information is unknown or cannot be provided, leave blank or provide a null value.
sample collection project name field
National Microbiological Baseline Study in Broiler Chicken
A data field which describes the name of the study design for a surveillance project.
sample_plan_name
Example Guidance: Provide the name of the sample plan used for sample collection. If the information is unknown or cannot be provided, leave blank or provide a null value.
A data field which describes the identifier of the study design for a surveillance project.
sample plan ID
sample plan identifier
sample_plan_ID
sample plan ID slot
sample plan identifier field
sample plan identifier slot
Example Guidance: Provide the identifier of the sample plan used for sample collection. If the information is unknown or cannot be provided, leave blank or provide a null value.
sample plan ID field
A data field which describes the name or job title of the contact responsible for follow-up regarding the sample.
sample collector contact name
sample_collector_contact_name
sample collector contact name slot
Example Guidance: Provide the name of an individual or their job title. As personnel turnover may render the contact's name obsolete, it is more preferable to provide a job title for ensuring accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value.
sample collector contact name field
Antimicrobial pre-treatment [GENEPIO:0100537]
A data field which describes the activities or variables introduced upstream of sample collection that may affect the sample collected.
presampling activity
presampling_activity
presampling activity slot
Example Guidance: If there was presampling activity that would affect the sample prior to collection (this is different than sample processing which happens after the sample is collected), provide the experimental activities by selecting one or more values from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value.
presampling activity field
Chicken feed containing X amount of novobiocin was fed to chickens for 72 hours prior to collection of litter.
A data field which describes the details of the activities or variables introduced upstream of sample collection that may affect the sample collected.
presampling activity details
presampling_activity_details
presampling activity details slot
Example Guidance: Briefly describe the presampling activity details using free text.
presampling activity details field
A data field which describes the processing applied to samples post-collection, prior to further testing, characterization, or isolation procedures.
specimen_processing
Example Guidance: Provide the sample processing information by selecting a value from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value.
A data field which describes the name of a specific geographical location (i.e. toponym).
geo_loc name (site)
geographical location site name
geo_loc name (site) slot
geographical location site name field
geographical location site name slot
Example Guidance: Provide the name of the specific geographical site using a specific noun (a word that names a certain place, thing).
geo_loc name (site) field
A data field which describes the country of origin of a food product.
food product origin geo loc name (country)
food product origin geographical location country name
food_product_origin geo_loc_name (country)
food product origin geo loc name (country) slot
food product origin geographical location country name field
food product origin geographical location country name slot
Example Guidance: If a food product was sampled and the food product was manufactured outside of Canada, provide the name of the country where the food product originated by selecting a value from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value.
food product origin geo loc name (country) field
A host geographical location field which describes the country of origin of the host.
host origin geo loc name (country)
host origin geographical location name
host_origin geo_loc_name (country)
host origin geo loc name (country) slot
host origin geographical location name field
host origin geographical location name slot
Example Guidance: If a sample is from a human or animal host that originated from outside of Canada, provide the the name of the country where the host originated by selecting a value from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value.
host origin geo loc name (country) field
A data field which describes the original sample description provided by the sample collector.
original sample description
original_sample_description
original sample description slot
Example Guidance: Provide the sample description provided by the original sample collector. The original description is useful as it may provide further details, or can be used to clarify higher level classifications.
original sample description field
A data field which describes the depth of some water.
water depth
water_depth
water depth slot
Example Guidance: Provide the depth of water with a value and unit.
water depth field
A data field which describes the temperature of some air.
air temperature
air_temperature
air temperature slot
Example Guidance: Provide the temperature of the air with a value and unit. Do not provide a symbol for degree e.g. oC
air temperature field
A data field which describes the state of the atmosphere at a place and time.
Regarding heat, dryness, sunshine, wind, rain, etc.
weather type
weather_type
weather type slot
Example Guidance: Provide the weather conditions at the time of sample collection.
weather type field
A data field which describes the type of animal or plant population inhabiting an area.
animal or plant population
animal_or_plant_population
animal or plant population slot
Example Guidance: This field should be used when a sample is taken from an environmental location inhabited by many individuals of a specific type, rather than describing a sample taken from one particular host. If applicable, provide the standardized term and ontology ID for the animal or plant population name. The standardized term can be sourced from this look-up service: https://www.ebi.ac.uk/ols/ontologies/genepio. If not applicable, leave blank.
animal or plant population field
Feather meal [FOODON:00003927]; Bone meal [ENVO:02000054]; Chicken breast [FOODON:00002703]
A data field which describes material consumed and digested for nutritional value or enjoyment.
food_product
food product slot
Example Guidance: This field includes animal feed. If applicable, provide the standardized term and ontology ID for the anatomical material. The standardized term can be sourced from this look-up service: https://www.ebi.ac.uk/ols/ontologies/foodon. If not applicable, leave blank.
food product field
Food (chopped) [FOODON:00002777]; Ready-to-eat (RTE) [FOODON:03316636]
A data field which describes any characteristic of the food product pertaining to its state, processing, a label claim, or implications for consumers.
food product properties
food_product_properties
food product properties slot
Example Guidance: Provide any characteristics of the food product including whether it has been cooked, processed, preserved, any known information about its state (e.g. raw, ready-to-eat), any known information about its containment (e.g. canned), and any information about a label claim (e.g. organic, fat-free).
food product properties field
A data field which describes the animal from which the food product was derived.
animal source of food
animal_source_of_food
animal source of food slot
Example Guidance: Provide the common name of the animal. If not applicable, leave blank. Multiple entries can be provided, separated by a comma.
animal source of food field
A data field which describes the type of packaging used to contain a food product.
food_packaging
food packaging slot
Example Guidance: If known, provide information regarding how the food product was packaged.
food packaging field
A data field which describes the way that a specimen is or was stored.
sample storage method
sample_storage_method
sample storage method slot
Example Guidance: Provide a description of how the same was stored.
sample storage method field
A data field which describes the material or matrix in which a sample is stored.
sample storage medium
sample_storage_medium
sample storage medium slot
Example Guidance: Provide a description of the material or matrix used to store the sample.
sample storage medium field
A host field which describes the biotype resulting from selection in a particular habitat.
host (ecotype)
host (ecotype) slot
Example Guidance: Provide the name of the ecotype of the host organism.
host (ecotype) field
A host field which describes a specific group of domestic animals or plants having homogeneous appearance, homogeneous behavior, and other characteristics that distinguish it from other animals or plants of the same species and that were arrived at through selective breeding.
host (breed)
host (breed) slot
Example Guidance: Provide the name of the breed of the host organism.
host (breed) field
A host field which describes the name of the host at a certain stage of food production, which may depend on its age or stage of sexual maturity.
host (food production name)
host (food production name) slot
Example Guidance: Select the host's food production name from the pick list.
host (food production name) field
An instance of the "strain and isolation information field category" that contains the "isolate received date field".
An instance of the "strain and isolation information field category" that contains the "microbiological method field".
A data field category which refers to strain and isolation information fields.
strain and isolation information
strain and isolation information slot category
strain and isolation information field category
A data field which describes the laboratory method used to grow, prepare, and/or isolate the microbial isolate.
microbiological method
microbiological method slot
Example Guidance: Provide the name and version number of the microbiological method. The ID of the method is also acceptable if the ID can be linked to the laboratory that created the procedure.
microbiological method field
A data field which describes the strain identifier.
strain
strain slot
Example Guidance: A population or type of organisms that is genetically different from others of the same species and possessing a set of defined characteristics. If the isolate represents or is derived from, a lab reference strain or strain from a type culture collection, provide the strain identifier.
strain field
A data field which describes the identifier of the specific isolate.
isolate
isolate ID
isolate ID slot
isolate field
isolate identifier field
isolate identifier slot
isolate slot
Example Guidance: This identifier should be an unique, indexed, alpha-numeric ID within your laboratory. If submitted to the INSDC, the .isolate. name is propagated throughtout different databases. As such, structure the .isolate. name to be ICTV/INSDC compliant in the following format: .SARS-CoV-2/host/country/sampleID/date..
isolate ID field
A data field which describes an isolate identifier assigned to the isolate by another organization.
alternative isolate ID
alternative isolate identifier
alternative_isolate_ID
alternative isolate ID slot
alternative isolate identifier field
alternative isolate identifier slot
Example Guidance: If one or more alternative isolate_IDs are available, record them all here, separated by a comma.
alternative isolate ID field
A data field which describes the identifier assigned to a progenitor isolate derived from an isolate that was directly obtained from a sample.
progeny isolate ID
progeny isolate identifier
progeny_isolate_ID
progeny isolate ID slot
progeny isolate identifier field
progeny isolate identifier slot
Example Guidance: If your sequence data pertains to progeny of an original isolate, provide the progeny_isolate_ID.
progeny isolate ID field
A data field which describes the identifier of the isolate in the Integrated Rapid Infectious Disease Analysis (IRIDA) platform.
IRIDA isolate ID
IRIDA isolate identifier
IRIDA_isolate_ID
IRIDA isolate ID slot
IRIDA isolate identifier field
IRIDA isolate identifier slot
Integrated Rapid Infectious Disease Analysis isolate ID field
Integrated Rapid Infectious Disease Analysis isolate ID slot
Integrated Rapid Infectious Disease Analysis isolate identifier field
Integrated Rapid Infectious Disease Analysis isolate identifier slot
Example Guidance: Provide the .sample ID. used to track information linked to the isolate in IRIDA. IRIDA sample IDs should be unqiue to avoid ID clash. This is very important in large Projects, especially when samples are shared from different organizations. Download the IRIDA sample ID and add it to the sample data in your spreadsheet as part of good data management practices.
IRIDA isolate ID field
A data field which describes the identifier of the project in the Integrated Rapid Infectious Disease Analysis (IRIDA) platform.
IRIDA project ID
IRIDA project identifier
IRIDA project ID slot
IRIDA project identifier field
IRIDA project identifier slot
Integrated Rapid Infectious Disease Analysis project ID field
Integrated Rapid Infectious Disease Analysis project ID slot
Integrated Rapid Infectious Disease Analysis project identifier field
Integrated Rapid Infectious Disease Analysis project identifier slot
Example Guidance: Provide the IRIDA .project ID..
IRIDA project ID field
Public Health Agency of Canada (PHAC) [GENEPIO:0100551]
A data field which describes the name of the agency, organization or institution with which the individual who performed the isolation procedure is affiliated.
isolated by
isolated_by
isolated by slot
Example Guidance: Provide the name of the agency, organization or institution that isolated the original isolate in full (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value.
isolated by field
A data field which describes the specific laboratory affiliation of the individual who performed the isolation procedure.
isolated by laboratory name
isolated_by_laboratory_name
isolated by laboratory name slot
Example Guidance: Provide the name of the specific laboratory that that isolated the original isolate (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value.
isolated by laboratory name field
A data field which describes the name or title of the contact responsible for follow-up regarding the isolate.
isolated by contact name
isolated_by_contact_name
isolated by contact name slot
Example Guidance: Provide the name of an individual or their job title. As personnel turnover may render the contact's name obsolete, it is prefereable to provide a job title for ensuring accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value.
isolated by contact name field
A data field which describes the email address of the contact responsible for follow-up regarding the isolate.
isolated by contact email
isolated_by_contact_email
isolated by contact email slot
Example Guidance: Provide the email associated with the listed contact. As personnel turnover may render an individual's email obsolete, it is more prefereable to provide an address for a position or lab, to ensure accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value.
isolated by contact email field
A date field which describes the date on which the isolate was isolated from a sample.
isolate collection date
isolation date
isolation_date
isolate collection date field
isolate collection date slot
isolation date slot
Example Guidance: Provide the date according to the ISO 8601 standard .YYYY-MM-DD., .YYYY-MM. or .YYYY..
isolation date field
A date field which describes the date on which the isolate was received by the laboratory.
isolate_received_date
isolate received date slot
isolate received date field
A data field which describes the serovar of the organism.
serovar
serotype field
serotype slot
serovar slot
Example Guidance: Only include this information if it has been determined by traditional serological methods or a validated in silico prediction tool e.g. SISTR.
serovar field
A data field which describes the method used to determine the serovar.
serotyping method
serotyping_method
serotyping method slot
Example Guidance: If the serovar was determined via traditional serotyping methods, put “Traditional serotyping”. If the serovar was determined via in silico methods, provide the name and version number of the software.
serotyping method field
A data field which describes the phagetype of the organism.
phagetype
phagetype slot
Example Guidance: Provide if known. If unknown, put “missing”.
phagetype field
A data field which describes the specific laboratory affiliation of those responsible for sequencing the isolate's genome.
sequenced by laboratory name
sequenced by laboratory name slot
Example Guidance: Provide the name of the specific laboratory that that performed the sequencing in full (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value.
sequenced by laboratory name field
A data field which describes the name or title of the contact responsible for follow-up regarding the sequence.
Not to be confused with 'sequence submitted by contact name' http://purl.obolibrary.org/obo/GENEPIO_0100474
sequenced by contact name
sequenced_by_contact_name
sequenced by contact name slot
Example Guidance: Provide the name of an individual or their job title. As personnel turnover may render the contact's name obsolete, it is more prefereable to provide a job title for ensuring accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value.
sequenced by contact name field
A data field which describes the name of the project/initiative/program for which sequencing was performed.
sequencing project name
sequencing_project_name
sequencing project name slot
sequencing project name field
A data field which describes the platform technology used to perform the sequencing.
sequencing platform
sequencing_platform
sequencing platform slot
Example Guidance: Provide the name of the company that created the sequencing instrument by selecting a value from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value.
sequencing platform field
A data field which describes the name or title of the contact responsible for follow-up regarding the submission of the sequence to a repository or database.
Not to be confused with 'sequenced by contact name' http://purl.obolibrary.org/obo/GENEPIO_0100471
sequence submitted by contact name
sequence_submitted_by_contact_name
sequence submitted by contact name slot
sequence submitted by contact name field
A data field which describes the identifier for a publication.
publication ID
publication identifier
publication_ID
publication ID slot
publication identifier field
publication identifier slot
Example Guidance: If the isolate is associated with a published work which can provide additional information, provide the PubMed identifier of the publication. Other types of identifiers (e.g. DOI) are also acceptable.
publication ID field
A data field which describes the attribute package used to structure metadata in an International Nucleotide Sequence Database Collaboration (INSDC) BioSample.
attribute package
attribute_package
attribute package slot
Example Guidance: If the sample is from a specific human or animal, put “Pathogen.cl”. If the sample is from an environmental sample including food, feed, production facility, farm, water source, manure etc, put “Pathogen.env”.
attribute package field
An instance of the "public repository information field category" that contains the "publication ID field".
A data field category which refers to public repository information fields.
public repository information
public repository information slot category
public repository information field category
An instance of the "risk assessment information field category" that contains the "prevalence metrics field".
A data field category which refers to risk assessment information fields.
risk assessment information
risk assessment information slot category
risk assessment information field category
An instance of the "antimicrobial resistance field category" that contains the "AMR* laboratory typing method field". *AMR = antimicrobial resistance
A data field category which refers to antimicrobial resistance fields.
antimicrobial resistance
antimicrobial resistance slot category
antimicrobial resistance field category
Number of total samples collected, Number of positive samples
A data field which describes metrics regarding the prevalence of the pathogen of interest obtained from a surveillance project.
prevalence metrics
prevalence_metrics
prevalence metrics slot
Example Guidance: Risk assessment requires detailed information regarding the quantities of a pathogen in a specified location, commodity, or environment. As such, it is useful for risk assessors to know what types of information are available through documented methods and results. Provide the metric types that are available in the surveillance project sample plan by selecting them from the pick list. The metrics of interest are . Number of total samples collected., .Number of positive samples., .Average count of hazard organism., .Average count of indicator organism.. You do not need to provide the actual values, just indicate that the information is available.
prevalence metrics field
Hazard organism counts (i.e. Salmonella) do not distinguish between serovars.
A data field which describes the details pertaining to the prevalence metrics from a surveillance project.
prevalence metrics details
prevalence_metrics_details
prevalence metrics details slot
Example Guidance: If there are details pertaining to samples or organism counts in the sample plan that might be informative, provide details using free text.
prevalence metrics details field
A data field which describes the stage of food production.
stage of production
stage_of_production
stage of production slot
Example Guidance: Provide the stage of food production from which the sample was taken. Select a value form the pick list provided.
stage of production field
A data field which describes the category of the experimental intervention applied in the food production system.
experimental intervention
experimental_intervention
experimental intervention slot
Example Guidance: In some surveys, a particular intervention in the food supply chain in studied. If there was an intervention specified in the sample plan, select the intervention category from the pick list provided.
experimental intervention field
a data field which describes the details of the experimental intervention applied in the food production system.
experiment intervention details
experiment_intervention_details
experiment intervention details slot
Example Guidance: If an experimental intervention was applied in the survey, provide details in this field as free text.
experiment intervention details field
A role inhering in a person that is realized when the bearer is engaged in child care or education work.
Child Care/Education Worker
child care or education worker
A role inhering in a person that is realized when the bearer is engaged in operations and services that are essential to ensure the continuity of critical infrastructure operations.
Essential Worker
essential worker
A role inhering in a person that is realized when the bearer is an employee that performs labor internationally.
International worker
international worker
A role inhering in a person that is realized when the bearer is engaged in transportation.
Transport Worker
transport worker
A transport worker role inhering in a person that is realized when the bearer is the driver of a transport truck.
Transport Truck Driver
transport truck driver
A role inhering in a person that is realized when the bearer is a sexual partner of the case.
Sexual partner of case
sexual partner role
A process occuring within or in the vicinity of a human with a confirmed case of COVID-19 that exposes the recipient organism to Monkeypox.
Contact with Known Monkeypox Case
contact with known Monkeypox case
contact with known Monkeypox case exposure process
A process occuring within or in the vicinity of a human with a probable case of COVID-19 that exposes the recipient organism to Monkeypox.
Contact with Probable Monkeypox Case
contact with probable Monkeypox case
contact with probable Monkeypox case exposure process
Canadian Food Inspection Agency (CFIA) [GENEPIO:0100552]
A data field which describes the name of the organization that performed the antimicrobial resistance (AMR) testing.
AMR testing by
AMR_testing_by
antimicrobial resistance testing by
AMR testing by slot
antimicrobial resistance testing by field
antimicrobial resistance testing by slot
Example Guidance: Provide the name of the agency, organization or institution that performed the AMR testing, in full (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value.
AMR testing by field
A data field which describes the name of the lab within the organization that performed the antimicrobial resistance (AMR) testing.
AMR testing by laboratory name
AMR_testing_by_laboratory_name
antimicrobial resistance testing by laboratory name
AMR testing by laboratory name slot
antimicrobial resistance testing by laboratory name field
antimicrobial resistance testing by laboratory name slot
Example Guidance: Provide the name of the specific laboratory that performed the AMR testing (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value.
AMR testing by laboratory name field
A data field which describes the name of the individual or the individual's role in the organization that performed the antimicrobial resistance (AMR) testing.
AMR testing by contact name
AMR_testing_by_contact_name
antimicrobial resistance testing by contact name
AMR testing by contact name slot
antimicrobial resistance testing by contact name field
antimicrobial resistance testing by contact name slot
AMR testing by contact name field
A data field which describes the email of the individual or the individual's role in the organization that performed the antimicrobial resistance (AMR) testing.
AMR testing by contact email
AMR_testing_by_contact_email
antimicrobial resistance testing by contact email
AMR testing by contact email slot
antimicrobial resistance testing by contact email field
antimicrobial resistance testing by contact email slot
Example Guidance: Provide the email associated with the listed contact. As personnel turnover may render an individual's email obsolete, it is more preferable to provide an address for a position or lab, to ensure accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value.
AMR testing by contact email field
A data field which describes the date the antimicrobial resistance (AMR) testing was performed.
AMR testing date
AMR_testing_date
antimicrobial resistance testing date
AMR testing date slot
antimicrobial resistance testing date field
antimicrobial resistance testing date slot
AMR testing date field
An antimicrobial resistance (AMR) field which describes the maximum measurement for a sample to be considered “sensitive” to this antibiotic.
Dependent on the units specified in the 'AMR measurement units field' [GENEPIO:0100523].
AMR testing susceptible breakpoint
AMR_testing_susceptible_breakpoint
antimicrobial resistance testing susceptible breakpoint
AMR testing susceptible breakpoint slot
antimicrobial resistance testing susceptible breakpoint field
antimicrobial resistance testing susceptible breakpoint slot
Example Guidance: This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied.
AMR testing susceptible breakpoint field
An antimicrobial resistance (AMR) field which describes intermediate measurement(s) where a sample would be considered to have an “intermediate” phenotype for this antibiotic.
AMR testing intermediate breakpoint
AMR_testing_intermediate_breakpoint
antimicrobial resistance testing intermediate breakpoint
AMR testing intermediate breakpoint slot
antimicrobial resistance testing intermediate breakpoint field
antimicrobial resistance testing intermediate breakpoint slot
Example Guidance: This field should only contain a number (either an integer or a number with decimals), since the qualifier is implied.
AMR testing intermediate breakpoint field
An antimicrobial resistance (AMR) field which describes minimum measurement for a sample to be considered “resistant” to this antibiotic.
AMR testing resistant breakpoint
AMR_testing_resistant_breakpoint
antimicrobial resistance testing resistant breakpoint
AMR testing resistant breakpoint slot
antimicrobial resistance testing resistant breakpoint field
antimicrobial resistance testing resistant breakpoint slot
Example Guidance: This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied.
AMR testing resistant breakpoint field
27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017.
An antimicrobial resistance (AMR) field which describes additional details associated with the testing standard used for determination of resistance phenotype.
AMR testing standard details
AMR_testing_standard_details
antimicrobial resistance testing standard details
AMR testing standard details slot
antimicrobial resistance testing standard details field
antimicrobial resistance testing standard details slot
Example Guidance: This information may include the year or location where the testing standard was published. If not applicable, leave blank.
AMR testing standard details field
A data field which describes the name of the agent that kills or slows the growth of microorganisms, including bacteria, viruses, fungi and protozoans.
antimicrobial agent name
antimicrobial_agent_name
antimicrobial agent name slot
Example Guidance: The names of the drug have already been matched with measurement, breakpoint, and phenotype fields in the template. No need to add these unless the drug of interest is not present. Use the Term Request System to request the addition of other agents.
antimicrobial agent name field
A data field which describes the measured value of antimicrobial resistance (AMR).
Dependent on the value specified in the 'antimicrobial agent name field' [GENEPIO:0100521]
AMR measurement
AMR_measurement
antimicrobial resistance measurement
AMR measurement slot
antimicrobial resistance measurement field
antimicrobial resistance measurement slot
Example Guidance: This field should only contain a number (either an integer or a number with decimals).
AMR measurement field
A data field which describes the units of the antimicrobial resistance (AMR) measurement.
Dependent on the numerical value specified in the 'AMR measurement field' [GENEPIO:0100522]
AMR measurement units
AMR_measurement_units
antimicrobial resistance measurement units
AMR measurement units slot
antimicrobial resistance measurement units field
antimicrobial resistance measurement units slot
Example Guidance: Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary.
AMR measurement units field
A data field which describes the qualifier associated with the antibiotic resistance (AMR) measurement.
AMR measurement sign
AMR_measurement_sign
antimicrobial resistance measurement sign
AMR measurement sign slot
antimicrobial resistance measurement sign field
antimicrobial resistance measurement sign slot
Example Guidance: Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary.
AMR measurement sign field
Susceptible antimicrobial phenotype [ARO:3004302]
A data field which describes an antimicrobial resistance (AMR) phenotype, as determined by the antibiotic susceptibility measurement and testing standard for the antibiotic specified.
AMR phenotype
AMR_phenotype
antimicrobial resistance phenotype
AMR phenotype slot
antimicrobial resistance phenotype field
antimicrobial resistance phenotype slot
Example Guidance: Select a phenotype from the pick list provided.
AMR phenotype field
An antimicrobial resistance (AMR) field which describes the general method used for antibiotic susceptibility testing.
AMR laboratory typing method
AMR_laboratory_typing_method
antimicrobial resistance laboratory typing method
AMR laboratory typing method slot
antimicrobial resistance laboratory typing method field
antimicrobial resistance laboratory typing method slot
Example Guidance: Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary.
AMR laboratory typing method field
An antimicrobial resistance (AMR) field which describes the brand/platform used for antibiotic susceptibility testing.
AMR laboratory typing platform
AMR_laboratory_typing_platform
antimicrobial resistance laboratory typing platform
AMR laboratory typing platform slot
antimicrobial resistance laboratory typing platform field
antimicrobial resistance laboratory typing platform slot
Example Guidance: Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary.
AMR laboratory typing platform field
An antimicrobial resistance (AMR) field which describes the specific name and version of the plate, panel, or other platform used for antibiotic susceptibility testing.
AMR laboratory typing platform version
AMR_laboratory_typing_platform_version
antimicrobial resistance laboratory typing platform version
AMR laboratory typing platform version slot
antimicrobial resistance laboratory typing platform version field
antimicrobial resistance laboratory typing platform version slot
Example Guidance: Include any additional information about the antimicrobial susceptibility test such as the drug panel details.
AMR laboratory typing platform version field
An antimicrobial resistance (AMR) field which describes the name of the vendor of the testing platform used.
AMR vendor name
AMR_vendor_name
antimicrobial resistance vendor name
AMR vendor name slot
antimicrobial resistance vendor name field
antimicrobial resistance vendor name slot
Example Guidance: Provide the full name of the company (avoid abbreviations).
AMR vendor name field
Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366]
An antimicrobial resistance (AMR) field which describes testing standard used for determination of resistance phenotype.
AMR testing standard
AMR_testing_standard
antimicrobial resistance testing standard
AMR testing standard slot
antimicrobial resistance testing standard field
antimicrobial resistance testing standard slot
Example Guidance: Select a testing standard from the pick list provided.
AMR testing standard field
An antimicrobial resistance (AMR) field which describes version number associated with the testing standard used for determination of resistance phenotype. If applicable, include a version number for the testing standard used.
AMR testing standard version
AMR_testing_standard_version
antimicrobial resistance testing standard version
AMR testing standard version slot
antimicrobial resistance testing standard version field
antimicrobial resistance testing standard version slot
Example Guidance: If applicable, include a version number for the testing standard used.
AMR testing standard version field
A data field which describes the absence or presence of a prior Monkeypox infection.
prior Monkeypox infection
prior Monkeypox infection slot
Example Guidance: If known, provide information about whether the individual had a previous Monkeypox infection. Select a value from the pick list.
prior Monkeypox infection field
A data field which describes the date of diagnosis of the prior Monkeypox infection.
prior Monkeypox infection date
prior Monkeypox infection date slot
Example Guidance: Provide the date that the most recent prior infection was diagnosed. Provide the prior Monkeypox infection date in ISO 8601 standard format .YYYY-MM-DD..
prior Monkeypox infection date field
A data field which describes the absence or presence of antiviral treatment for a prior Monkeypox infection.
prior Monkeypox antiviral treatment
prior Monkeypox antiviral treatment slot
Example Guidance: If known, provide information about whether the individual had a previous Monkeypox antiviral treatment. Select a value from the pick list.
prior Monkeypox antiviral treatment field
AZT was administered for HIV infection during the prior Monkeypox infection.
A data field which describes the antiviral treatment for any infection during the prior Moneypox infection period.
prior antiviral treatment during prior Monkeypox infection
prior antiviral treatment during prior Monkeypox infection slot
Example Guidance: Provide a description of any antiviral treatment administered for viral infections (not including Monkeypox treatment) during the prior Monkeypox infection period. This field is meant to capture concurrent treatment information.
prior antiviral treatment during prior Monkeypox infection field
A sampling strategy in which environments are sampled in the context of testing for the presence of, or change in the levels of, chemicals, pathogens or other phenomena.
Environmental testing
environmental testing sampling
A sampling strategy in which individuals are sampled in the context of experiments or observations performed as part of clinical research.
Clinical trial
clinical trial sampling
clinical trial sampling strategy
A sampling strategy in which samples are taken during real-life experiments which test directly whether proposed interventions actually work.
Field experiment
field experiment sampling
A data field which describes the name of the method used to assess whether a sequence passed a predetermined quality control threshold.
quality control method name
qc method name field
qc method name slot
quality control method name field
quality control method name slot
A data field which describes the version number of the method used to assess whether a sequence passed a predetermined quality control threshold.
quality control method version
qc method version field
qc method version slot
quality control method version field
quality control method version slot
sequence failed quality control [GENEPIO:0100564]
A data field which describes the determination of a quality control assessment.
quality control determination
qc determination field
qc determination slot
quality control determination field
quality control determination slot
low average genome coverage [GENEPIO:0100570]
A data field which describes the reason contributing to, or causing, a low quality determination in a quality control assessment.
quality control issues
qc issues field
qc issues slot
quality control issues field
quality control issues slot
CT value of 39. Low viral load. Low DNA concentration after amplification.
A data field which describes the details surrounding a low quality determination in a quality control assessment.
quality control details
qc details field
qc details slot
quality control details field
quality control details slot
A data item which is a statement confirming that quality control processes were carried out and no quality issues were detected.
no quality control issues identified
Example: This statement may be used in conjunction with the quality control determination statement "sequence passed quality control" to confirm that no issues were identified. It is possible that a sequence may pass QC but still have some issues worthy of noting e.g. novel indel detected. Note: quality control here refers to quality of the raw reads, consensus sequence or assembly, not the qaulity of analytical results e.g. lineage assignment.
no quality control issues identified datum
A data item which is a statement confirming that quality control processes were carried out and that the sequence met the assessment criteria.
sequence passed quality control
Example: Use this statement to indicate that quality control processes were carried out and that the sequence met the assessment criteria. Note: quality control here refers to quality of the raw reads, consensus sequence or assembly, not the qaulity of analytical results e.g. lineage assignment.
sequence passed quality control datum
A data item which is a statement confirming that quality control processes were carried out and that the sequence did not meet the assessment criteria.
sequence failed quality control
Example: Use this statement to indicate that quality control processes were carried out and that the sequence failed to meet the assessment criteria. Note: quality control here refers to quality of the raw reads, consensus sequence or assembly, not the qaulity of analytical results e.g. lineage assignment.
sequence failed quality control datum
A data item which is a statement confirming that quality control processes were carried out and that the sequence did not meet the assessment criteria, however the issues detected were minor.
minor quality control issues identified
Example: This statement may be used in conjunction with the quality control determination statement "sequence failed quality control" to communicate that the reasons why the sequence did not meet the assessment criteria. Minor issues may include phenomena that the analyst should review e.g. amplicons detected in the negative control sequence or more mutations than expected based on the reference sequence. The details of the issues can be described in the "quality control details" field. Note: quality control here refers to quality of the raw reads, consensus sequence or assembly, not the qaulity of analytical results e.g. lineage assignment.
minor quality control issues identified datum
A data item which is a statement confirming that quality control processes were carried out however it is unclear whether the sequence meets the assessment criteria and the assessment requires review.
sequence flagged for potential quality control issues
Example: This statement may be used in conjunction with other quality control determination statements to indicate potential sequence quality issues. Note: quality control here refers to quality of the raw reads, consensus sequence or assembly, not the qaulity of analytical results e.g. lineage assignment.
sequence flagged for potential quality control issues datum
A data item which is a statement confirming that quality control processes have not been carried out.
quality control not performed
Example: Use this statement to indicate that quality control processes have not been performed. Note: quality control here refers to quality of the raw reads, consensus sequence or assembly, not the qaulity of analytical results e.g. lineage assignment.
quality control not performed datum
A data item that describes sequence data that does not meet quality control thresholds.
low quality sequence
low quality sequence datum
A data item that describes sequence data that contains reads from unintended targets (e.g. other organisms, other samples) due to contamination so that it does not faithfully represent the genetic information from the biological source.
sequence contaminated
sequence contaminated datum
A data item that describes sequence data in which the entire length of the genome is not sufficiently sequenced (low breadth of coverage), or particular positions of the genome are not sequenced a prescribed number of times (low depth of coverage).
low average genome coverage
low average genome coverage datum
A data item that describes sequence data in which the entire length of the genome is not sufficiently sequenced (low breadth of coverage).
low percent genome captured
low percent genome captured datum
A data item that describes average sequence read lengths that are below the expected size range given a particular sequencing instrument, reagents and conditions.
read lengths shorter than expected
read lengths shorter than expected datum
A data item that describes sequence data containing errors generated during the polymerase chain reaction (PCR) amplification process during library generation (e.g. mutations, altered read distribution, amplicon dropouts).
sequence amplification artifacts
sequence amplification artifacts datum
A data item that describes sequence data containing more errors or undetermined bases (noise) than sequence representing the biological source (signal).
low signal to noise ratio
low signal to noise ratio datum
A data item that describes sequence data that contains a lower than expected number of mutations that are usually observed in the reference sequence.
low coverage of characteristic mutations
low coverage of characteristic mutations datum
Tecovirimat used to treat current Monkeypox infection; AZT administered for concurrent HIV infection
A data field which describes treatment of viral infections with agents that prevent viral replication in infected cells without impairing the host cell function.
antiviral therapy
antiviral therapy slot
Example Guidance: Provide details of all current antiviral treatment during the current Monkeypox infection period. Consult with the data steward prior to sharing this information.
antiviral therapy field
A collection of contextual data attributes pertaining to a pathogen in an environmental sample, as specified by the International Nucleotide Sequence Database Collaboration (INSDC).
Environmental Pathogen Attribute Package (Pathogen.env)
A sampling strategy in which individuals and/or materials are sampled for surveillance performed for research purposes.
Survey study
survey study sampling
survey study sampling strategy
A data field which describes the type of planned process by which an organismal entity is associated with a taxon or taxa.
taxonomic identification process
taxonomic_identification_process
taxonomic identification process slot
Example Guidance: Provide the type of method used to determine the taxonomic identity of the organism by selecting a value from the pick list. If the information is unknown or cannot be provided, leave blank or provide a null value.
taxonomic identification process field
A data field which describes the details of the process used to determine the taxonomic identification of an organism.
taxonomic identification process details
taxonomic_identification_process_details
taxonomic identification process details slot
Example Guidance: Briefly describe the taxonomic identififcation method details using free text.
taxonomic identification process details field
The "specimen collector sample ID" is where one can store sample identifiers given by the specimen collector.
A data item which is a location for a predetermined type of data.
data slot
data field
A data specification established for use by The Public Health Alliance for Genomic Epidemiology (PHA4GE) project for SARS-CoV-2 contextual data (metadata) harmonization and curation across data providers.
PHA4GE SARS-CoV-2 contextual data specification
Public Health Alliance for Genomic Epidemiology SARS-CoV-2 specification
Public Health Alliance for Genomic Epidemiology severe acute respiratory syndrome coronavirus 2 specification
PHA4GE SARS-CoV-2 specification
Manuscript: https://doi.org/10.1093/gigascience/giac003
GitHub: https://github.com/pha4ge/SARS-CoV-2-Contextual-Data-Specification
A data specification established for pathogen genomics contextual data (metadata) harmonization and curation across Canadian data providers.
Canadian pathogen genomics specification
A data specification established for use by The Canadian Genomics Research & Development Initiative (GRDI) Antimicrobial Resistance (AMR) project for contextual data (metadata) harmonization and curation across data providers.
Genomics Research & Development Initiative Antimicrobial Resistance One Health specification
GRDI AMR One Health specification
A data specification established for Monkeypox pathogen genomics contextual data (metadata) harmonization and curation across Canadian data providers.
Canadian Monkeypox specification
A data specification established for Monkeypox pathogen genomics contextual data (metadata) harmonization and curation across international data providers.
International Monkeypox specification
A data item which is a duration for which a specimen is stored before analysis.
obsolete: specimen storage duration
The refrigerator provided a sample storage temperature of -80 degree Celsius
A data item which is a temperature at which a specimen is stored.
Domain appropriate replacement identified in OBIB
obsolete: specimen storage temperature
molecular lab was recorded as the sample storage location.
A data item which indicates the location where a specimen is stored, usually of a room or freezer.
obsolete: specimen storage location
The sequence data for "Zika virus envelope protein (E) gene, partial cds" is stored in a file named "AF372422-1.fasta".
A sequence data item which is the name of a file containing molecular sequence data.
When a new genome is sequenced, it is constructed from a series of overlapping sequences known as contigs. Each contig receives an identifier code that contains a unique numerical identifier, in addition to project and assembly information, to differentiate an individual contig from others within a squence collection.
A sequence data which specifies a particular contig in a sequence collection.
The "123" gene ORF is oriented in the 5' -> 3' direction on the DNA sense (coding) strand.
A sequence data which is the orientation of a genomic element on a double stranded molecule.
A sequence data which is the short name of a gene typically derived from the gene name.
A sequence data which is the name of a gene (typically) assigned by a person and/or according to a naming scheme.
The breadth of coverage of the sequence of interest to the reference sequence was 75%.
A data item which is breadth of coverage datum as a percentage.
The breadth of coverage of the sequence of interest to the reference sequence was 3:4.
A data item which is breadth of coverage datum as a ratio.
The BLAST results for two sequences of interest resulted in a sequence identity of 50%; i.e. only 50% of the sequences matched in both nucleotide content and corresponding positions when performing a theoretically optimal local alignment.
A data item which is the number of matches (identical characters) in positions from an alignment of two molecular sequences as a percentage.
I used the NCBI reference sequence "RefSeq" database as a reference database for the identification and characterization of novel prokaryote sequences.
A data item which is an identifier of a reference bioinformatics database.
See editor note of http://purl.obolibrary.org/obo/IAO_0000650
The reference SARS-CoV-2 genome provided a basis for the design of PCR primers and probes to be utilized in SARS-CoV-2 detection.
A sequence data which is any sequence that is used as a basis for comparison against another sequence.
A sequence Accession number without a version suffix always refers to the latest version of the sequence.
A unique identifier given to a sequence record to allow for tracking of different versions of that sequence record and the associated sequence over time in a single data repository.
The "Homo sapiens DRD2 mRNA" sequence has the NCBI reference sequence identifier NM_000795.
A centrally registered identifier symbol that specifies an individual sequence record in a public sequence repository and used as a basis for comparison against another sequence.
The sequence length measurement datum for the Zika virus E protein gene (AF372422.1) is 830 bp.
A length measurement datum which is the number of base pairs in a sequence.
reference sequence length measurement datum
The sequence length measurment datum for the SARS-CoV-2 reference sequence (NC_045512.2) is 29903 bp.
A sequence length measurement datum which describes the number of base pairs of a reference sequence.
The sequence length measurment datum for the SARS-CoV-2 reference sequence (NC_045512.2) ORF1ab gene (43740578) is 21289 bp.
A reference sequence length measurement datum which describes the number of base pairs of a gene retrieved from a reference sequence.
The sequence length measurment datum for the SARS-CoV-2 reference sequence (NC_045512.2) nps13_ZBD protein (YP_009725308.1) is 1802 bp.
A reference sequence length measurement datum which describes the number of positions of a reference protein.
A sequence length measurement datum about a input sequence being analyzed.
input gene sequence length measurement datum
A sequence length measurement datum which describes the number of base pairs of a gene of interest undergoing analysis.
input protein sequence length measurement datum
A sequence length measurement datum which describes the number of positions of a protein undergoing analysis.
A processed material which is a medium designed to promote longevity of a viral sample.
A data field which describes the date recommended for the use of a product while at peak quality, this date is not a reflection of safety unless used on infant formula.
food quality date
food_quality_date
food quality date slot
Example Guidance: This date is typically labeled on a food product as .best if used by., best by., .use by., or .freeze by. e.g. 5/24/2020. If the date is known, leave blank or provide a null value.
food quality date field
A data field which descibes the food product's packaging date as marked by a food manufacturer or retailer.
food packaging date
food_packaging_date
food packaging date slot
Example Guidance: The packaging date should not be confused with, nor replaced by a Best Before date or other food quality date. If the date is known, leave blank or provide a null value.
food packaging date field
A data item which describes an organism bearing a host role.
host column
host slot; host organism field; host organism slot
host field
A data field which describes a geographical location.
geo_loc field
geo_loc slot
geographical location column
geographical location slot
geographical location field
A field that describes the host country of reisdence.
A data field which describes the geographical location of a host organism.
host geo_loc
host geographical location column
host geographical location slot
host geographical location field
A data field which describes a symbol that is part of a centrally registered identifier database (CRID) and that is sufficient to look up a record from the CRID's registry.
ID column
identifier column
ID field
ID slot
identifier slot
identifier field
A data field which describes the particular day, month and/or year an event has happened or will happen.
date column
date slot
date field
A data field which describes the vaccination information of a host organism.
host vaccination column
host vaccination slot
host vaccination field
This "or" class is just to represent an equivalency with a commonly used classification, it should not have subclasses under it. (2022-12-22)
State or Province or Territory
A data field which describes antimicrobial information.
antimicrobial column
antimicrobial slot
antimicrobial field
A data field which describes antimicrobial resistance information.
AMR column
antimicrobial resistance column
AMR field
AMR slot
antimicrobial resistance slot
antibiotic field
antimicrobial resistance field
A data field which describes the exposure information of a host organism.
exposure column
exposure slot
exposure field
A data field which describes prior infection information of a host organism.
prior infection column
prior infection slot
prior infection field
A data field which describes the name of the gene used in the diagnostic reverse transcription polymerase chain reaction (RT-PCR) test.
gene name slot
gene name field
A data field which describes the name and version number of the reverse transcription polymerase chain reaction (RT-PCR) protocol used for diagnostic marker amplification.
diagnostic pcr protocol slot
diagnostic polymerase chain reaction protocol field
diagnostic polymerase chain reaction protocol slot
diagnostic pcr protocol field
A data field which describes the cycle threshold (Ct) value result from a diagnostic reverse transcription polymerase chain reaction (RT-PCR) test.
diagnostic pcr Ct value slot
diagnostic polymerase chain reaction cycle threshold field
diagnostic polymerase chain reaction cycle threshold slot
diagnostic pcr Ct value field
A small moistened piece of plastic or cloth fabric.
A data specification established by the Public Health Alliance for Genomic Epidemiology (PHA4GE) for genomics contextual data (metadata) harmonization and curation.
Public Health Alliance for Genomic Epidemiology specification
PHA4GE genomics specification
PHA4GE QC contextual data tags specification
PHA4GE QC tags specification
PHA4GE quality control contextual data tags specification
PHA4GE QC specification
Public Health Alliance for Genomic Epidemiology quality control specification
PHA4GE quality control specification
GitHub: https://github.com/pha4ge/contextual_data_QC_tags
A data field which describes quality control information.
qc column
quality control column
qc field
qc slot
quality control slot
quality control field
quality control datum
A data enumeration which references a set of named quality control determination entities.
quality control determination enumeration
A data enumeration which references a set of named quality control issues entities.
quality control issues enumeration
A role inhering in a person that is realized when the bearer is engaged in child care work.
childcare worker role
A role inhering in a person that is realized when the bearer is engaged in education work.
education worker role
A data field which describes the type of data that is available.
The data may or may not require permission to access.
available data types
available_data_types
available data types slot
Example Guidance: This field provides information about additional data types that are available that may provide context for interpretation of the sequence data. Provide a term from the picklist for additional data types that are available. Additional data types may require special permission to access. Contact the data provider for more information.
available data types field
A data field which describes the depth of some sediment.
sediment depth
sediment_depth
sediment depth slot
Example Guidance: Provide the depth of sediment with a value and unit.
sediment depth field
A data field which describes the temperature of some water.
water temperature
water_temperature
water temperature slot
Example Guidance: Provide the temperature of the water with a value and unit. Do not provide a symbol for degree e.g. oC
water temperature field
A data field which describes a production pathway incorporating the processes, material entities, and conditions that participate in the generation of a particular commodity.
Material entities examples: equipment, animals, locations
production stream
production_stream
production stream slot
Example Guidance: Provide the name of the agricultural production stream from the picklist.
production stream field
A data field which describes a 3D anatomical region in space without well-defined compartmental boundaries.
anatomical region
anatomical_region
anatomical region slot
Example Guidance: This field captures more granular spatial information on a host anatomical part e.g. dorso-lateral region vs back. Select a term from the picklist.
anatomical region field
A dataset may be annotated with the "mollusc shell length tag" to indicate the presence mollusc shell length data attributes such as a "mollusc shell length" field and "mollusc shell length unit" field.
A data item which indicates the presence of specific data attributes within a dataset.
dataset component tag
dataset data type
dataset tag
dataset attribute bundle
A dataset attribute bundle which indicates the presence of documentation data.
https://en.wikipedia.org/wiki/Documentation used as a partial source for the "Example Guidance".
documentation
documentation attribute bundle
documentation data type
Example Guidance: Use this tag to indicate additional data is available that provides information that is used to describe, explain or instruct regarding some attributes of an object, system or procedure.
documentation data tag
A documentation data tag which indicates the presence of data that describes experimental parameters.
experimental parameters documentation
experimental parameters documentation data type
Example Guidance: Use this tag to indicate additional data is available that provides documentation describing parameters of the experiment.
experimental parameters documentation tag
A documentation data tag which indicates the presence of data that describes feed history.
http://purl.obolibrary.org/obo/ENVO_02000047 used as a partial source for the "Example Guidance".
feed history
feed history data type
Example Guidance: Use this tag to indicate additional data is available that provides a history of food material given to meet nutritional requirements.
feed history documentation tag
A documentation data tag which indicates the presence of data that describes land use information.
https://www.epa.gov/report-environment/land-use used as a partial source for the "Example Guidance".
land use information
land use information data type
Example Guidance: Use this tag to indicate additional data is available that provides information describing human use of the land.
land use information documentation tag
A documentation data tag which indicates the presence of data that describes a history of therapeutic administration.
therapeutic administration history
therapeutic administration history documentation data type
Example Guidance: Use this tag to indicate additional data is available that provides a history of therapeutics admnistered to a subject.
therapeutic administration history documentation tag
A dataset attribute bundle which indicates the presence of chemical characterization data.
chemical characterization
chemical characterization attribute bundle
chemical characterization data type
Example Guidance: Use this tag to indicate additional data is available that provides characterization information from chemical properties.
chemical characterization data tag
A chemical characterization data tag which indicates the presence of data that describes a measurement of pH.
http://purl.obolibrary.org/obo/GENEPIO_0001736 used as a partial source for the "Example Guidance".
pH measurement characterization data tag
Example Guidance: Use this tag to indicate additional data is available that provides characterization information from the measurement of pH, where pH is a numeric scale used to specify the acidity or basicity (alkalinity) of an aqueous solution.
pH measurement characterization tag
A chemical characterization data tag which indicates the presence of data that describes a measurement of dissolved oxygen.
https://www.epa.gov/national-aquatic-resource-surveys/indicators-dissolved-oxygen used as a partial source for the "Example Guidance".
dissolved oxygen measurement
dissolved oxygen measurement characterization data tag
Example Guidance: Use this tag to indicate additional data is available that provides characterization information from the amount of oxygen that is present in water.
dissolved oxygen measurement characterization tag
A chemical characterization data tag which indicates the presence of data that descibes a measurement of nitrate.
http://purl.obolibrary.org/obo/NCIT:C161352 used as a partial source for the "Example Guidance".
nitrate measurement
nitrate measurement characterization data tag
Example Guidance: Use this tag to indicate additional data is available that provides characterization information from the determination of the amount of nitrate present in a sample.
nitrate measurement characterization tag
A chemical characterization data tag which indicates the presence of data that descibes a measurement of nitrite.
http://purl.obolibrary.org/obo/NCIT:C64810 used as a partial source for the "Example Guidance".
nitrite measurement
nitrite measurement characterization data tag
Example Guidance: Use this tag to indicate additional data is available that provides characterization information from the quantitative measurement of the amount of nitrite present in a sample.
nitrite measurement characterization tag
A chemical characterization data tag which indicates the presence of data that describes a measurement of phosphorus.
phosphorous measurement
phosphorous measurement characterization data tag
Example Guidance: Use this tag to indicate additional data is available that provides characterization information from the quantitative measurement of the amount of phosphorus present in a sample.
phosphorous measurement characterization tag
A chemical characterization data tag which indicates the presence of data that describes a measurement of salinity.
salinity measurement
salinity measurement characterization data tag
Example Guidance: Use this tag to indicate additional data is available that provides characterization information from the quantitative measurement of the amount of salt dissolved in a body of water.
salinity measurement characterization tag
A dataset attribute bundle which indicates the presence of microbiological characterization data.
microbiological characterization
microbiological characterization attribute bundle
microbiological characterization data type
Example Guidance: Use this tag to indicate additional data is available that provides characterization information based on microbiological properties.
microbiological characterization data tag
A microbiological characterization data tag which indicates the presence of microbiological identification data.
microbiological identification
microbiological identification data type
Example Guidance: Use this tag to indicate additional data is available that provides identification information from microbiological properties.
microbiological identification data tag
A microbiological characterization data tag which indicates the presence of microbiological identification data derived using the Beckson Dickson BBL Crystal identification system.
microbiological identification (Beckson Dickson BBL Crystal)
microbiological identification data type (Beckson Dickson BBL Crystal)
Example Guidance: Use this tag to indicate additional data is available that provides identification information from microbiology properties generated using Beckson Dickson BBL Crystal.
microbiological identification tag (Beckson Dickson BBL Crystal)
A microbiological characterization data tag which indicates the presence of microbiological identification data dervied using the bioMérieux API identification system.
microbiological identification (bioMérieux API)
microbiological identification data type (bioMérieux API)
Example Guidance: Use this tag to indicate additional data is available that provides identification information from microbiology properties generated using bioMérieux API.
microbiological identification tag (bioMérieux API)
A microbiological characterization data tag which indicates the presence of microbiological identification data derived using the Biolog identification system.
microbiological identification (Biolog)
microbiological identification data type (Biolog)
Example Guidance: Use this tag to indicate additional data is available that provides identification information from microbiology properties generated using Biolog.
microbiological identification tag (Biolog)
A microbiological characterization data tag which indicates the presence of microbiological identification data derived using the Fatty acid methyl esters (FAME) identification system.
microbiological identification (FAME)
microbiological identification data type (Fatty acid methyl esters)
Example Guidance: Use this tag to indicate additional data is available that provides identification information from microbiology properties generated using FAME.
microbiological identification tag (Fatty acid methyl esters (FAME))
A microbiological characterization data tag which indicates the presence of microbiological identification data derived using the Sensititre identification system.
microbiological identification (Sensititre)
microbiological identification data type (Sensititre)
Example Guidance: Use this tag to indicate additional data is available that provides identification information from microbiology properties generated using Sensititre.
microbiological identification tag (Sensititre)
A microbiological characterization data tag which indicates the presence of microbiological identification data derived using the ViTek identification system.
microbiological identification (ViTek)
microbiological identification data type (ViTek)
Example Guidance: Use this tag to indicate additional data is available that provides identification information from microbiology properties generated using ViTek.
microbiological identification tag (ViTek)
A microbiological characterization data tag which indicates the presence of microbiological identification data derived using phage type identification.
phage type
phage type data type
Example Guidance: Use this tag to indicate additional data is available that provides identification information from phage typing.
phage type identification tag
A microbiological characterization data tag which indicates the presence of microbiological identification data derived using serotype identification.
https://www.cdc.gov/salmonella/reportspubs/salmonella-atlas/serotyping-importance.html used as a partial source for the "Example Guidance".
serotype
serotype data type
Example Guidance: Use this tag to indicate additional data is available that provides identification information from serotyping, a subtyping test based on differences in microbial surfaces.
serotype identification tag
A microbiological characterization data tag which indicates the presence of phenotypic microbiological characterization data.
https://www.merriam-webster.com/dictionary/phenotyping used as a partial source for the "Example Guidance".
phenotypic microbiological characterization
phenotypic microbiological characterization attribute bundle
phenotypic microbiological characterization data type
Example Guidance: Use this tag to indicate additional data is available that provides characterization information from determining, analyzing, or predicting all or part of a microorganism's phenotype.
phenotypic microbiological characterization data tag
A phenotypic microbiological characterization data tag which indicates the presence of antimicrobial resistance (AMR) phenotypic testing characterization data.
AMR phenotypic testing
AMR phenotypic testing data type
AMR phenotypic testing tag
antimicrobial resistance phenotypic testing data type
Example Guidance: Use this tag to indicate additional data is available that provides phenotypic characterization using AMR testing.
antimicrobial resistance (AMR) phenotypic testing characterization tag
A phenotypic microbiological characterization data tag which indicates the presence of biolog phenotype microarray characterization data.
biolog phenotype microarray
biolog phenotype microarray data type
Example Guidance: Use this tag to indicate additional data is available that provides phenotypic characterization using biolog microarray technology.
biolog phenotype microarray characterization tag
A dataset attribute bundle which indicates the presence of microbiological quantification data.
microbiological quantification
microbiological quantification attribute bundle
microbiological quantification data type
Example Guidance: Use this tag to indicate additional data is available that provides quantification information from microbiological properties.
microbiological quantification data tag
A microbiological quantification data tag which indicates the presence of colony count data.
colony count
colony count data type
Example Guidance: Use this tag to indicate additional data is available that provides quantification information from microbial colony counts.
colony count microbiological quantification tag
A colony count microbiological quantification data tag which indicates the presence of data that describes total colony count of coliforms.
total coliform count
total coliform count data type
Example Guidance: Use this tag to indicate additional data is available that provides quantification information from microbial total coliform counts.
total coliform count microbiological quantification tag
A colony count microbiological quantification data tag that indicates the presence of data which describes total colony count of fecal coliforms.
total fecal coliform count
total fecal coliform count data type
Example Guidance: Use this tag to indicate additional data is available that provides quantification information from microbial total colony count of coliforms that generally originate in the intestines of warm-blooded animals.
total fecal coliform count microbiological quantification tag
A microbiological quantification data tag which indicates the presence of infectivity assay data.
infectivity assay
infectivity assay data type
Example Guidance: Use this tag to indicate additional data is available that provides quantification information from infectivity assay(s).
infectivity assay tag
A microbiological quantification data tag which indicates the presence of data which describes enzyme-linked immunosorbent assay (ELISA) toxin binding.
ELISA toxin binding
ELISA toxin binding data type
enzyme-linked immunosorbent assay (ELISA) toxin binding data type
Example Guidance: Use this tag to indicate additional data is available that provides quantification data from ELISA toxin binding assay(s).
enzyme-linked immunosorbent assay (ELISA) toxin binding tag
A dataset attribute bundle which indicates the presence of molecular characterization data.
Molecular characterization
molecular characterization data type
Example Guidance: Use this tag to indicate additional data is available that provides characterization information from molecular properties.
molecular characterization data tag
A molecular characterization data tag which indicates the presence of 16S rRNA Sanger sequencing characterization data.
16S rRNA Sanger sequencing
16S rRNA Sanger sequencing data type
Example Guidance: Use this tag to indicate additional data is available that provides characterization information from 16S rRNA Sanger sequencing.
16S rRNA Sanger sequencing characterization tag
A molecular characterization data tag which indicates the presence of polymerase chain reaction (PCR) marker detection characterization data.
PCR marker detection
PCR marker detection data type
Polymerase chain reaction (PCR) marker detection data type
Example Guidance: Use this tag to indicate additional data is available that provides characterization information from PCR marker detection.
polymerase chain reaction (PCR) marker detection characterization tag
A PCR marker detection characterization data tag which indicates the presence of BOX-A1R-based repetitive extragenic palindromic (BOX) PCR fingerprint data.
BOX PCR fingerprint
BOX PCR fingerprint tag
BOX-A1R-based repetitive extragenic palindromic (BOX) PCR fingerprint data type
Example Guidance: Use this tag to indicate additional data is available that provides characterization information from BOX PCR fingerprint assay(s).
BOX-A1R-based repetitive extragenic palindromic (BOX) PCR fingerprint tag
A PCR marker detection characterization data tag which indicates the presence of enterobacterial repetitive intergenic consensus (ERIC) PCR fingerprint data.
ERIC PCR fingerprint
ERIC PCR fingerprint data type
ERIC PCR fingerprint tag
enterobacterial repetitive intergenic consensus polymerase chain reaction fingerprint data type
Example Guidance: Use this tag to indicate additional data is available that provides characterization information from ERCI PCR fingerprint assay(s).
enterobacterial repetitive intergenic consensus (ERIC) PCR fingerprint tag
A molecular characterization data tag which indicates the presence of plasmid type characterization data.
plasmid type
plasmid type data type
Example Guidance: Use this tag to indicate additional data is available that provides characterization information from typing plasmids.
plasmid type characterization data tag
A molecular characterization data tag which indicates the presence of ribotype characterization data.
http://purl.obolibrary.org/obo/GENEPIO_0000063 used as a partial source for the "Example Guidance".
ribotype
ribotype data type
Example Guidance: Use this tag to indicate additional data is available that provides characterization information from ribotyping, which involves the fingerprinting of genomic DNA restriction fragments that contain all or part of the genes coding for the 16S and 23S rRNA.
ribotype characterization data tag
A dataset attribute bundle which indicates the presence of molecular quantification data.
molecular quantification
molecular quantification attribute bundle
molecular quantification data type
Example Guidance: Use this tag to indicate additional data is available that provides quantification information from molecular properties.
molecular quantification data tag
A molecular quantification data tag which indicates the presence of quantitative polymerase chain reaction (qPCR) marker organism quantification data.
qPCR marker organism quantification
qPCR marker organism quantification data type
qPCR marker organism quantification tag
quantitative polymerase chain reaction (qPCR) marker organism quantification data type
Example Guidance: Use this tag to indicate additional data is available that provides quantification information from qPCR marker organism assay(s).
quantitative polymerase chain reaction (qPCR) marker organism quantification tag
A dataset attribute bundle which indicates the presence of physical characterization data.
physical characterization
physical characterization attribute bundle
physical characterization data type
Example Guidance: Use this tag to indicate additional data is available that provides characterization information from physical properties.
physical characterization data tag
A physical characterization data tag which indicates the presence of data that describes conductivity measurement characterization.
conductivity measurement
conductivity measurement data type
Example Guidance: Use this tag to indicate additional data is available that provides physical characterization via measurement of conductivity, including the units of measurement.
conductivity measurement characterization tag
A physical characterization data tag which indicates the presence of data that describes a measurement of a mollusc shell.
mollusc shell measurement
mollusc shell measurement data type
Example Guidance: Use this tag to indicate additional data is available that provides a measurement of the mollusc shell, including the units of measurement.
mollusc shell measurement characterization tag
A physical characterization data tag which indicates the presence of data that describes the length of a mollusc shell.
mollusc shell length
mollusc shell length data type
Example Guidance: Use this tag to indicate additional data is available that provides the length of the mollusc shell, including the units of measurement.
mollusc shell length tag
A physical characterization data tag which indicates the presence of matter compostion characterization data.
matter compostion
matter compostion data type
Example Guidance: Use this tag to indicate additional data is available that provides the composition of the mass of something.
matter compostion characterization tag
A matter composition characterization data tag which indicates the presence of data that describes dry matter composition.
dry matter composition
dry matter composition data type
Example Guidance: Use this tag to indicate additional data is available that provides the composition of the mass of something when water is completely removed.
dry matter composition tag
A matter composition characterization data tag which indicates the presence of data that describes organic matter composition.
organic matter composition
organic matter composition data type
Example Guidance: Use this tag to indicate additional data is available that provides the composition of the mass of something comprised of organic compounds.
organic matter composition tag
A physical characterization data tag which indicates the presence of data that describes turbidity measurement.
http://purl.obolibrary.org/obo/NCIT_C74723 used as a partial source for the "Example Guidance".
turbidity measurement
turbidity measurement data type
Example Guidance: Use this tag to indicate additional data is available that provides the determination of the sample opacity, including the units of measurement.
turbidity measurement tag
available data types enumeration
Undigested food material, microbiota, and other materials found in the digestive tract.
Undigested food material, microbiota, and other materials found in the cecum
Undigested food material, microbiota, and other materials found in the intestine.
A specimen collection device that is designed to collect sediment samples from the hard bottoms of a body of water i.e. sand, gravel, consolidated marl or clay.
A specimen collection device designed to penetrate soil with a hollow tube to collect soil sample cores.
A specimen collection process that is used to dig out an amount of sample using a scoop.
A specimen collection process that is used to collect a sediment sample.
A specimen collection process that is used to collect soil sample cores.
A coordinate system, and a set of reference points, used to locate places on the Earth (or similar objects).
Josh Hanna
Damion Dooley's note: This coordinate system must reference the particulars of a spheroid - its "radius = fn(lat,long)" formula - in order to yeild any distance metrics. Alternate definition: A geographic coordinate system is a 2 dimensional coordinate system superimposed onto the surface of a spheroid.
geodetic datum
The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter or a transporter complex, a pore or a motor protein.
Note that this term should not be used for direct annotation. It should be possible to make a more specific annotation to one of the children of this term, for e.g. to transmembrane transport, to microtubule-based transport or to vesicle-mediated transport.
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.
1. Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation reviews. 2. While a broader definition of behavior encompassing plants and single cell organisms would be justified on the basis of some usage (see PMID:20160973 for discussion), GO uses a tight definition that limits behavior to animals and to responses involving the nervous system, excluding plant responses that GO classifies under development, and responses of unicellular organisms that has general classifications for covering the responses of cells in multicellular organisms (e.g. cell chemotaxis).
A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence.
A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence.
A process that emerges from two or more causally-connected macromolecular activities and has evolved to achieve a biological objective.
Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end.
A biological process is an evolved process
Note that, in addition to forming the root of the biological process ontology, this term is recommended for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this.
Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this.
biological process
A biological process that directly contributes to the process of producing new individuals by one or two organisms. The new individuals inherit some proportion of their genetic material from the parent or parents.
Any biological process, occurring at the level of a multicellular organism, pertinent to its function.
Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.
Behavior directed towards society, or taking place between members of the same species. Occurs predominantly, or only, in individuals that are part of a group.
Behavior such as predation which involves members of different species is not social. Communication between members of different species is also not social behavior.
Formation of hardened covering (a scab) at a wound site. The scab has multiple functions including limiting blood loss, providing structural stability to the wound and guarding against infection.
A process carried out by gene products in an organism that enable the organism to engage in a symbiotic relationship, a more or less intimate association, with another organism. The various forms of symbiosis include parasitism, in which the association is disadvantageous or destructive to one of the organisms; mutualism, in which the association is advantageous, or often necessary to one or both and not harmful to either; and commensalism, in which one member of the association benefits while the other is not affected. However, mutualism, parasitism, and commensalism are often not discrete categories of interactions and should rather be perceived as a continuum of interaction ranging from parasitism to mutualism. In fact, the direction of a symbiotic interaction can change during the lifetime of the symbionts due to developmental changes as well as changes in the biotic/abiotic environment in which the interaction occurs. Microscopic symbionts are often referred to as endosymbionts.
biological process involved in symbiotic interaction
Entry of a symbiont into the body, tissues, or cells of a host organism as part of the symbiont life cycle. The host is defined as the larger of the organisms involved in a symbiotic interaction.
Penetration by an organism into the body, tissues, or cells of the host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction.
entry into cell of other organism during symbiotic interaction
entry into host cell via penetration peg
entry into host via a specialized structure during symbiotic interaction
entry into host via enzymatic degradation of host anatomical structure
entry into host via enzymatic degradation of host cuticle
penetration into host via a specialized structure
penetration into host via a specialized structure during symbiotic interaction
Any process evolved to enable an interaction with an organism of a different species.
interspecies interaction between organisms
interspecies interaction with other organisms
biological process involved in interspecies interaction between organisms
The controlled release of a substance by a cell or a tissue.
Any process in which a cell, a substance, or a cellular entity, such as a protein complex or organelle, is transported, tethered to or otherwise maintained in a specific location. In the case of substances, localization may also be achieved via selective degradation.
establishment and maintenance of localization
establishment and maintenance of position
establishment and maintenance of cellular component location
establishment and maintenance of substance location
establishment and maintenance of substrate location
Any process that localizes a substance or cellular component. This may occur via movement, tethering or selective degradation.
An interaction between two organisms living together in more or less intimate association. The term host is used for the larger (macro) of the two members of a symbiosis; the various forms of symbiosis include parasitism, commensalism and mutualism.
biological process involved in interaction with host
Any process in which an organism has an effect on an organism of the same species.
intraspecies interaction between organisms
intraspecies interaction with other organisms
biological process involved in intraspecies interaction between organisms
A biological process which involves another organism of the same or different species.
An umbrella term often used in medical literature to include transgender persons and gender nonconforming people who may or may not be transgender.
transgender and gender nonconforming
An umbrella term often used in research to covered genderqueer and gender nonbinary identities, as well as gender nonconforming persons.
genderqueer, gender non-conforming, and gender nonbinary
genderqueer, gender nonconforming and gender nonbinary
genderqueer, gender nonconforming, and gender nonbinary
Either, a specific gender identity which is not male or female; or, more broadly, an umbrella term for gender identities not considered male or female.
gender non-binary
"Non-binary" (with the hyphen) is more common in the United Kingdom, whereas "nonbinary" (as one word) is more common in the United States.
Note that "nonbinary" as itself is preferable if the context in relationship to gender is known. Most therefore "nonbinary persons" not "gender nonbinary persons" can be used.
gender nonbinary
Equitable representation of persons of different genders.
diversité de genre
gender diversity
Having a feminine gender (identity) which is different from the sex one was assigned at birth.
trans feminine
transfemenino
transfeminin
transfeminine
Having a masculine gender (identity) which is different from the sex one was assigned at birth.
trans masculine
transmasculine
transmasculino
transmaskulin
noncisgender gender modality
non-cisgender gender modality
Population category defined using ancestry informative markers (AIMs) based on genetic/genomic data
Includes individuals who either self-report or have been described by authors as European, Caucasian, White or one of the sub-populations from this region (e.g Dutch). This category also includes individuals who genetically cluster with reference populations from this region, for example 1000 Genomes and/or HapMap CEU, FIN, GBR, IBS and TSI populations.
Includes individuals who either self-report or have been described by authors as South Asian or one of the sub-populations from this region (e.g Asian Indian). This category also includes individuals who genetically cluster with reference populations from this region, for example 1000 Genomes and/or HapMap BEB, GIH, ITU, PJL and STU populations.
Includes individuals who either self-report or have been described by authors as South East Asian or one of the sub-populations from this region (e.g Vietnamese). This category also includes includes individuals who genetically cluster with reference populations from this region, for example 1000 Genomes KHV population. We note that East Asian and South East Asian populations are often conflated. However, recent studies indicate a unique genetic background for South East Asian populations.
Includes individuals that either self-report or have been described as Asian but there was not sufficient information to allow classification as East Asian, Central Asian, South Asian or South-East Asian.
Includes individuals who either self-report or have been described by authors as East Asian or one of the sub-populations from this region (e.g Chinese). This category also includes individuals who genetically cluster with reference populations from this region, for example 1000 Genomes and/or HapMap CDX, CHB, CHS and JPT populations.
Includes individuals that either self-report or have been described as African, but there was not sufficient information to allow classification as African American, AfroCaribbean or Sub-Saharan African.
African unspecified
Includes individuals who either self-report or have been described by authors as SubSaharan African or one of the subpopulations from this region (e.g. Yoruban). This category also includes individuals who genetically cluster with reference populations from this region for example 1000 Genomes and/or HapMap ESN, LWK, GWD, MSL, MKK and YRI populations.
Includes indigenous individuals of North, Central and South America, descended from the original human migration into the Americas from Siberia. We note that there does not appear to be a suitable reference population for this category and efforts are required to fill this gap.
Class previously labelled as "Native American". Use of this term, alongside other terms such as "First Nations", should be discontinued in favour of the more appropriate "Indigenous American", which includes indigenous communities across the Americas while the former serve as political designations in the USA and Canada, respectively.
Indigenous American
Includes individuals who either self-report or are described by authors as Hispanic, Latino, Latin American or one of the sub-populations from this region. This category includes individuals with known admixture of primarily European, African and Native American ancestries, though some may have also a degree of Asian (e.g. Peru). We also note that the levels of admixture vary depending on the country, with Caribbean countries carrying higher levels of African admixture when compared to South American countries, for example. This category also includes individuals who genetically cluster with reference populations from this region, for example 1000 Genomes and/or HapMap CLM, MXL, PEL and PUR populations
Includes individuals who self-report or were described by authors as Middle Eastern, North African, Persian or one of the subpopulations from this region (e.g. Saudi Arabian). We note there is heterogeneity in this category with different degrees of admixture as well as levels of genetic isolation. We note that there does not appear to be a suitable reference population for this category and efforts are required to fill this gap.
Greater Middle Eastern (Middle Eastern or North African or Persian)
Includes individuals who either self-report or have been described by authors as African American or Afro-Caribbean. This category also includes individuals who genetically cluster with reference populations from this region, for example 1000 Genomes and/or HapMap ACB or ASW populations. We note that there is likely to be significant admixture with European ancestry populations.
Includes individuals that either self-report or have been described by authors as Oceanian or one of the sub-populations from this region (e.g. Native Hawaiian). We note that there does not appear to be a suitable reference population for this category and efforts are required to fill this gap.
A population for which specific ancestry information is known but that does not fall into any of the defined ancestry categories
Includes individuals who either self-report or have been described by authors as Central Asian. We note that there does not appear to be a suitable reference population for this population and efforts are required to fill this gap.
Central Asian
A population with increased genetic homogeneity and reduced genetic variation due to cultural or geographic isolation
genetically isolated population
Italian
Sardinian
Val Borbera
Friuli Venezia Giulia
Carlantino
Old Order Amish
Sorb
Hutterite
Amish
Erasmus Rucphen
Orcadian
Korčulan
Dutch
Finnish
Finnish founder
Dutch founder
Sudanese
Anguillan
Antiguan or Barbudan
Barbadian
Haitian
Jamaican
Tajikistani
Turkmen
Uzbekistani
Afghan
Kazakhstani
Kyrgyzstani
Albanian
Andorran
Australian
Austrian
Belarusian
Belgian
Bermudian
Bosnian or Herzegovinian
Brazilian
Bulgarian
Canadian
Channel Islander
Chilean
Croatian
Czech
Danish
Estonian
Faroese
Falkland Islander
French
German
Gibraltarian
Greek
Greenlander
Hungarian
Icelandic
Manx
Latvian
Liechtensteiner
Lithuanian
Luxembourgish
Maltese
Monegasque
Montenegrin
New Zealander
Norfolk Islander
Norwegian
Polish
Portugese
Irish
Moldovan
Romanian
Russian
Saint-Pierrais or Miquelonnais
Sammarinese
Serb
Slovak
Slovene
Spanish
Swedish
Swiss
Macedonian
Ukrainian
Argentine
Bahamian
Belizean
Bolivian
British Virgin Islander
Caymanian
Colombian
Costa Rican
Cuban
Dominican
Ecuadorian
Salvadoran
French Guianese
Grenadian
Guatemalan
Guyanese
Honduran
Martinican
Mexican
Montserratian
Nicaraguan
Panamanian
Paraguayan
Peruvian
Puerto Rican
Kittitian or Nevisian
Saint Lucian
Saint Vincentian
Surinamese
Trinidadian or Tobagonian
Turks and Caicos Islander
Virgin Islander
Uruguayan
Venezuelan
Algerian
Armenian
Azerbaijani
Bahraini
Cypriote
Georgian
Iranian
Iraqi
Israeli
Jordanian
Kuwaiti
Lebanese
Libyan
Moroccan
Palestinian
Omani
Qatari
Saudi
Tunisian
Turkish
Emirati
Yemeni
Aruban
Christmas Islander
Cocos Islander
Curacaoan
Kosovar
Northern Mariana Islander
South Sudanese
Syrian
British
American
American Samoan
Cook Islander
Fijian
French Polynesian
Guamanian
I-Kiribati
Marshallese
Micronesian
Nauruan
New Caledonian
Niuean
Palauan
Papua New Guinean
Pitcairn Islander
Samoan
Solomon Islander
Tokelauan
Tongan
Tuvaluan
Ni-Vanuato
Wallis and Futuna Islander
Bangladeshi
Bhutanese
Indian
Maldivian
Nepalese
Pakistani
Sri Lankan
Bruneian
Cambodian
Indonesian
Lao
Malaysian
Burmese
Filipino
Thai
Timorese
Vietnamese
Cameroonian
Cape Verdean
Chadian
Ethiopian
Kenyan
Liberian
Mauritanian
Mauritian
Mahoran
Namibian
Sao Tomean
Senegalese
Sierra Leonean
South African
St. Helenian
Ugandan
Angolan
Beninese
Motswana
Burkinabe
Burundian
Comoran
Congolese
Ivoirian
Djiboutian
Equatorial Guinean
Eritrean
Gabonese
Gambian
Ghanaian
Guinean
Bissau-Guinean
Mosotho
Malawian
Malian
Mozambican
Nigerien
Nigerian
Rwandan
Togolese
Tanzanian
Zambian
Zimbabweian
genetically homogenous Irish
Includes individuals who either self-report or have been described by authors as Australian Aboriginal. These are expected to be descendents of early human migration into Australia from Eastern Asia and can be distinguished from other Asian populations by mtDNA and Y chromosome variation.
Individuals who have at least six great-grandparents born in the Central Valley of Costa Rica, to ensure descent from the founder population, composed primarily of Europeans and Native Americans
Population for which insufficient information is available to allocate it to a specific ancestral group or which contain individuals from a range of known ancestry categories, eg American
Individuals who self-identify or are reported by authors as belonging to a group of indigenous Americans living in an area consisting of what is now central and southern Arizona, as well as northwestern Mexico in the states of Sonora and Chihuahua. The majority population of the two current bands of the Akimel O'odham in the United States are based in two reservations: the Keli Akimel Oʼodham on the Gila River Indian Community (GRIC) and the On'k Akimel O'odham on the Salt River Pima-Maricopa Indian Community (SRPMIC).
Individuals who self-identify or are reported by authors as belonging to the indigenous peoples who have historically lived on the Interior Plains (the Great Plains and Canadian Prairies) of North America
Includes individuals who either self-report or have been described by authors as Aboriginal Australian of Martu ancestry. The Martu Australian Aboriginal people are from the Western Desert region located across the Pilbara in Western Australia
Native people residing in the Arctic of Alaska, northern Canada, Greenland, or eastern Siberia
Class previously labelled as "Eskimo", which is outdated and culturally inappropriate. Outdated label may be added as an appropriately flagged synonym at a later stage.
Includes individuals with ethnic origins in the Semitic people populating the Arabian Peninsula and other countries in the Middle East and Northern Africa
Includes individuals who either self-report or have been described by authors as Singaporean Malay.
Includes individuals who either self-report or have been described by authors as Singaporean Indian.
Includes indigenous individuals of North and Central America, descended from the original human migration into the Americas from Siberia.
Indigenous in North America
Includes indigenous individuals of Central and South America, descended from the original human migration into the Americas from Siberia.
Indigenous in South America
Individuals who self-identify or are reported by authors as belonging to a group of indigenous people of Mexico inhabiting the central Mexican Plateau (Altiplano) region.
Otomi
Individuals who self-identify or are reported by authors as belonging to the Mayan ethnolinguistic group of indigenous peoples of Mesoamerica.
Maya
Individuals who self-identify or are reported by authors as belonging to the Zapotec ethnolinguistic group of indigenous people of Mexico. The Zapotec population is concentrated in the southern state of Oaxaca, but Zapotec communities also exist in neighboring states
Zapoteco
Individuals who self-identify or are reported by authors as belonging to the Mazatecan ethnolinguistic group of indigenous peoples in the area known as the Sierra Mazateca, which is in the northern part of the state of Oaxaca in southern Mexico, as well as in adjacent areas of the states of Puebla and Veracruz
Mazateco
Individuals who self-identify or are reported by authors as belonging to a group of indigenous people of the Americas living in the state of Chihuahua in Mexico
Rarámuri
Individuals who self-identify or are reported by authors as belonging to a group of the indigenous people of Mexico, El Salvador, Guatemala, Honduras, and Nicaragua
Nahua
Individuals who self-identify or are reported by authors as belonging to indigenous Mesoamerican peoples of Mexico inhabiting the region known as La Mixteca of Oaxaca and Puebla as well as La Montaña Region and Costa Chica Regions of the state of Guerrero
Mixteco
Individuals who self-identify or are reported by authors as belonging to the Wayúu indigenous people of the Guajira Peninsula in northernmost part of Colombia and northwest Venezuela.
Wayúu
Individuals who self-identify or are reported by authors as belonging to an Arawakan ethnolinguistic group in Colombia and Venezuela
Piapoco
Individuals who self-identify or are reported by authors as belonging to a group of indigenous people native to the Nariño region of southern Colombia and neighbouring Equador
Pastos
Individuals who self-identify or are reported by authors as belonging to a group of indigenous people of South America who speak the Quechua languages. Although most Quechua speakers are native to Peru, there are some significant populations in Ecuador, Bolivia, Chile, Colombia, and Argentina
Quechua
Individuals who self-identify or are reported by authors as belonging to a group of indigenous people in the Andes and Altiplano regions of South America; about 2.3 million live in northwest Argentina, Bolivia, Chile and Peru.
Aymara
Individuals who self-identify or are reported by authors as belonging to a group of South American indigenous people native to the Chilean Norte Chico and the Argentine Northwest.
Diaguita
Individuals who self-identify or are reported by authors as belonging to a group of indigenous people of present-day south-central Chile and southwestern Argentina, including parts of present-day Patagonia
Mapuche
Individuals who self-identify or are reported by authors as belonging to a group of culturally-related indigenous peoples of South America, living primarily in present-day Paraguay between the Paraná River and lower Paraguay River, the Misiones Province of Argentina, southern Brazil as far east as Rio de Janeiro, and parts of Uruguay and Bolivia.
Guaraní
Individuals who self-identify or are reported by authors as belonging to an indigenous people of Brazil, who now live in three indigenous territories (Terras Indígenas in Portuguese), Caieiras Velhas, Pau-Brasil and Comboiosare, located near the cities of Santa Cruz and Vila do Riacho in the municipality of Aracruz in northern Espírito Santo state, southeastern Brazil.
Tupiniquim
Individuals who self-identify or are reported by authors as belonging to an Chibchan-speaking indigenous people of Colombia, descended from the Tairona culture, concentrated in northern Colombia in the Sierra Nevada de Santa Marta.
Ica
Individuals who self-identify or are reported by authors as belonging to an indigenous people living in the rainforests of Peru and in the State of Acre, Brazil. Their ancestral lands are in the forests of Junín, Pasco, Huánuco and part of Ucayali in Peru.
Asháninka
A population made up of 10 samples from Bantu individuals recruited in Kenya as part of the Human Genome Diversity Project. The population was assigned by the collecting project to the superpopulation African.
A population made up of 4 samples from Bantu individuals recruited in South Africa as part of the Human Genome Diversity Project. The population was assigned by the collecting project to the superpopulation African.
A population made up of 24 samples from Biaka individuals recruited in Central African Republic as part of the Human Genome Diversity Project. The population was assigned by the collecting project to the superpopulation African.
Biaka in Central African Republic (HGDP)
A population made up of 20 samples from Mandenka individuals recruited in Senegal as part of the Human Genome Diversity Project. The population was assigned by the collecting project to the superpopulation African.
A population made up of 13 samples from Mbuti individuals recruited in Democratic Republic of Congo as part of the Human Genome Diversity Project. The population was assigned by the collecting project to the superpopulation African. Samples from this population were used in data collections for HGDP Transcriptome.
Mbuti in Democratic Republic of Congo (HGDP)
A population made up of 4 samples from San individuals recruited in Namibia as part of the Human Genome Diversity Project. The population was assigned by the collecting project to the superpopulation African.
A population made up of 18 samples from Yoruba individuals recruited in Nigeria as part of the Human Genome Diversity Project. The population was assigned by the collecting project to the superpopulation African.
A population made up of 2 samples from Bantu Herero individuals recruited in Botswana Or Namibia as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation African.
Bantu Herero in Botswana Or Namibia (SGDP)
A population made up of 2 samples from Bantu Kenya individuals recruited in Kenya as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation African.
A population made up of 2 samples from Bantu Tswana individuals recruited in Botswana Or Namibia as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation African.
Bantu Tswana in Botswana Or Namibia (SGDP)
A population made up of 2 samples from Biaka individuals recruited in Central African Republic as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation African.
Biaka in Central African Republic (SGDP)
A population made up of 3 samples from Dinka individuals recruited in Sudan as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation African.
A population made up of 2 samples from Esan individuals recruited in Nigeria as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation African.
A population made up of 2 samples from Gambian individuals recruited in Gambia as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation African.
A population made up of 4 samples from Ju|'hoan North individuals recruited in Namibia as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation African.
A population made up of 2 samples from Khomani San individuals recruited in South Africa as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation African.
A population made up of 2 samples from Luhya individuals recruited in Kenya as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation African.
A population made up of 2 samples from Luo individuals recruited in Kenya as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation African.
A population made up of 3 samples from Mandenka individuals recruited in Senegal as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation African.
A population made up of 3 samples from Masai individuals recruited in Kenya as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation African.
A population made up of 4 samples from Mbuti individuals recruited in Congo as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation African.
A population made up of 2 samples from Mende individuals recruited in Sierra Leone as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation African.
A population made up of 2 samples from Mozabite individuals recruited in Algeria as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation African.
A population made up of 2 samples from Saharawi individuals recruited in Western Sahara (Morocco) as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation African.
Saharawi in Western Sahara (Morocco) (SGDP)
A population made up of 1 samples from Somali individuals recruited in Kenya as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation African.
A population made up of 3 samples from Yoruba individuals recruited in Nigeria as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation African.
A population made up of 113 samples from African Ancestry individuals recruited in Southwest US as part of the 1000 Genomes Project. The population was assigned by the collecting project to the superpopulation African.
A population made up of 123 samples from African Caribbean individuals recruited in Barbados as part of the 1000 Genomes Project. The population was assigned by the collecting project to the superpopulation African.
A population made up of 173 samples from Esan individuals recruited in Nigeria as part of the 1000 Genomes Project. The population was assigned by the collecting project to the superpopulation African.
A population made up of 100 samples from Fula individuals recruited in Western Division, The Gambia as part of the Gambian Genome Variation Project. The population was assigned by the collecting project to the superpopulation African.
Gambian in Western Division, The Gambia - Fula
A population made up of 100 samples from Jola individuals recruited in Western Division, The Gambia as part of the Gambian Genome Variation Project. The population was assigned by the collecting project to the superpopulation African.
Gambian in Western Division, The Gambia - Jola
A population made up of 280 samples from Mandinka individuals recruited in Western Division, The Gambia as part of the 1000 Genomes Project. The population was assigned by the collecting project to the superpopulation African.
Gambian in Western Division, The Gambia - Mandinka
A population made up of 100 samples from Wolof individuals recruited in Western Division, The Gambia as part of the Gambian Genome Variation Project. The population was assigned by the collecting project to the superpopulation African.
Gambian in Western Division, The Gambia - Wolof
A population made up of 117 samples from Luhya individuals recruited in Webuye, Kenya as part of the 1000 Genomes Project. The population was assigned by the collecting project to the superpopulation African.
A population made up of 129 samples from Mende individuals recruited in Sierra Leone as part of the 1000 Genomes Project. The population was assigned by the collecting project to the superpopulation African.
A population made up of 187 samples from Yoruba individuals recruited in Ibadan, Nigeria as part of the 1000 Genomes Project. The population was assigned by the collecting project to the superpopulation African.
A population made up of 5 samples from Colombian individuals recruited in Colombia as part of the Human Genome Diversity Project. The population was assigned by the collecting project to the superpopulation Latin or Admixed American.
A population made up of 9 samples from Karitiana individuals recruited in Brazil as part of the Human Genome Diversity Project. The population was assigned by the collecting project to the superpopulation Latin or Admixed American.
A population made up of 21 samples from Maya individuals recruited in Mexico as part of the Human Genome Diversity Project. The population was assigned by the collecting project to the superpopulation Latin or Admixed American.
A population made up of 12 samples from Pima individuals recruited in Mexico as part of the Human Genome Diversity Project. The population was assigned by the collecting project to the superpopulation Latin or Admixed American.
A population made up of 6 samples from Surui individuals recruited in Brazil as part of the Human Genome Diversity Project. The population was assigned by the collecting project to the superpopulation Latin or Admixed American.
A population made up of 1 samples from Chane individuals recruited in Argentina as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation Latin or Admixed American.
A population made up of 3 samples from Karitiana individuals recruited in Brazil as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation Latin or Admixed American.
A population made up of 2 samples from Mayan individuals recruited in Mexico as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation Latin or Admixed American.
A population made up of 3 samples from Mixe individuals recruited in Mexico as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation Latin or Admixed American.
A population made up of 2 samples from Mixtec individuals recruited in Mexico as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation Latin or Admixed American.
A population made up of 2 samples from Piapoco individuals recruited in Colombia as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation Latin or Admixed American.
A population made up of 2 samples from Pima individuals recruited in Mexico as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation Latin or Admixed American.
A population made up of 3 samples from Quechua individuals recruited in Peru as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation Latin or Admixed American.
A population made up of 2 samples from Surui individuals recruited in Brazil as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation Latin or Admixed American.
A population made up of 2 samples from Zapotec individuals recruited in Mexico as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation Latin or Admixed American.
A population made up of 148 samples from Colombian individuals recruited in Medellin, Colombia as part of the 1000 Genomes Project. The population was assigned by the collecting project to the superpopulation Latin or Admixed American.
A population made up of 107 samples from Mexican Ancestry individuals recruited in Los Angeles, California as part of the 1000 Genomes Project. The population was assigned by the collecting project to the superpopulation Latin or Admixed American.
Mexican Ancestry in Los Angeles, California
A population made up of 130 samples from Peruvian individuals recruited in Lima, Peru as part of the 1000 Genomes Project. The population was assigned by the collecting project to the superpopulation Latin or Admixed American.
A population made up of 150 samples from Puerto Rican individuals recruited in Puerto Rico as part of the 1000 Genomes Project. The population was assigned by the collecting project to the superpopulation Latin or Admixed American.
A population made up of 2 samples from Aleut individuals recruited in Russia as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation Central Asian and Siberian.
A population made up of 1 samples from Altaian individuals recruited in Russia as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation Central Asian and Siberian.
A population made up of 1 samples from Chukchi individuals recruited in Russia as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation Central Asian and Siberian.
A population made up of 1 samples from Eskimo Chaplin individuals recruited in Russia as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation Central Asian and Siberian.
A population made up of 2 samples from Eskimo Naukan individuals recruited in Russia as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation Central Asian and Siberian.
A population made up of 2 samples from Eskimo Sireniki individuals recruited in Russia as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation Central Asian and Siberian.
A population made up of 3 samples from Even individuals recruited in Russia as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation Central Asian and Siberian.
A population made up of 1 samples from Itelman individuals recruited in Russia as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation Central Asian and Siberian.
A population made up of 2 samples from Kyrgyz individuals recruited in Kyrgyzystan as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation Central Asian and Siberian.
A population made up of 2 samples from Mansi individuals recruited in Russia as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation Central Asian and Siberian.
A population made up of 2 samples from Mongola individuals recruited in China as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation Central Asian and Siberian.
A population made up of 2 samples from Tlingit individuals recruited in Russia as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation Central Asian and Siberian.
A population made up of 2 samples from Tubalar individuals recruited in Russia as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation Central Asian and Siberian.
A population made up of 2 samples from Ulchi individuals recruited in Russia as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation Central Asian and Siberian.
A population made up of 2 samples from Yakut individuals recruited in Russia as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation Central Asian and Siberian.
A population made up of 22 samples from Balochi individuals recruited in Pakistan as part of the Human Genome Diversity Project. The population was assigned by the collecting project to the superpopulation Central South Asian.
A population made up of 23 samples from Brahui individuals recruited in Pakistan as part of the Human Genome Diversity Project. The population was assigned by the collecting project to the superpopulation Central South Asian.
A population made up of 22 samples from Burusho individuals recruited in Pakistan as part of the Human Genome Diversity Project. The population was assigned by the collecting project to the superpopulation Central South Asian.
A population made up of 18 samples from Hazara individuals recruited in Pakistan as part of the Human Genome Diversity Project. The population was assigned by the collecting project to the superpopulation Central South Asian.
A population made up of 21 samples from Kalash individuals recruited in Pakistan as part of the Human Genome Diversity Project. The population was assigned by the collecting project to the superpopulation Central South Asian.
A population made up of 23 samples from Makrani individuals recruited in Pakistan as part of the Human Genome Diversity Project. The population was assigned by the collecting project to the superpopulation Central South Asian.
A population made up of 23 samples from Pathan individuals recruited in Pakistan as part of the Human Genome Diversity Project. The population was assigned by the collecting project to the superpopulation Central South Asian.
A population made up of 22 samples from Sindhi individuals recruited in Pakistan as part of the Human Genome Diversity Project. The population was assigned by the collecting project to the superpopulation Central South Asian.
A population made up of 8 samples from Uygur individuals recruited in China as part of the Human Genome Diversity Project. The population was assigned by the collecting project to the superpopulation Central South Asian.
A population made up of 9 samples from Cambodian individuals recruited in Cambodia as part of the Human Genome Diversity Project. The population was assigned by the collecting project to the superpopulation East Asian.
A population made up of 5 samples from Dai individuals recruited in China as part of the Human Genome Diversity Project. The population was assigned by the collecting project to the superpopulation East Asian.
A population made up of 9 samples from Daur individuals recruited in China as part of the Human Genome Diversity Project. The population was assigned by the collecting project to the superpopulation East Asian.
A population made up of 30 samples from Han individuals recruited in China as part of the Human Genome Diversity Project. The population was assigned by the collecting project to the superpopulation East Asian.
A population made up of 7 samples from Hezhen individuals recruited in China as part of the Human Genome Diversity Project. The population was assigned by the collecting project to the superpopulation East Asian.
A population made up of 27 samples from Japanese individuals recruited in Japan as part of the Human Genome Diversity Project. The population was assigned by the collecting project to the superpopulation East Asian.
A population made up of 6 samples from Lahu individuals recruited in China as part of the Human Genome Diversity Project. The population was assigned by the collecting project to the superpopulation East Asian.
A population made up of 8 samples from Miao individuals recruited in China as part of the Human Genome Diversity Project. The population was assigned by the collecting project to the superpopulation East Asian.
A population made up of 8 samples from Mongolian individuals recruited in China as part of the Human Genome Diversity Project. The population was assigned by the collecting project to the superpopulation East Asian.
A population made up of 6 samples from Naxi individuals recruited in China as part of the Human Genome Diversity Project. The population was assigned by the collecting project to the superpopulation East Asian.
A population made up of 10 samples from Northern Han individuals recruited in China as part of the Human Genome Diversity Project. The population was assigned by the collecting project to the superpopulation East Asian.
A population made up of 7 samples from Oroqen individuals recruited in China as part of the Human Genome Diversity Project. The population was assigned by the collecting project to the superpopulation East Asian.
A population made up of 8 samples from She individuals recruited in China as part of the Human Genome Diversity Project. The population was assigned by the collecting project to the superpopulation East Asian.
A population made up of 8 samples from Tu individuals recruited in China as part of the Human Genome Diversity Project. The population was assigned by the collecting project to the superpopulation East Asian.
A population made up of 8 samples from Tujia individuals recruited in China as part of the Human Genome Diversity Project. The population was assigned by the collecting project to the superpopulation East Asian.
A population made up of 7 samples from Xibo individuals recruited in China as part of the Human Genome Diversity Project. The population was assigned by the collecting project to the superpopulation East Asian.
A population made up of 23 samples from Yakut individuals recruited in Siberia as part of the Human Genome Diversity Project. The population was assigned by the collecting project to the superpopulation East Asian.
A population made up of 8 samples from Yi individuals recruited in China as part of the Human Genome Diversity Project. The population was assigned by the collecting project to the superpopulation East Asian.
A population made up of 2 samples from Ami individuals recruited in Taiwan as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation East Asian.
A population made up of 1 samples from Atayal individuals recruited in Taiwan as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation East Asian.
A population made up of 2 samples from Burmese individuals recruited in Myanmar as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation East Asian.
A population made up of 2 samples from Cambodian individuals recruited in Cambodia as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation East Asian.
A population made up of 4 samples from Dai individuals recruited in China as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation East Asian.
A population made up of 1 samples from Daur individuals recruited in China as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation East Asian.
A population made up of 3 samples from Han individuals recruited in China as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation East Asian.
A population made up of 2 samples from Hezhen individuals recruited in China as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation East Asian.
A population made up of 3 samples from Japanese individuals recruited in Japan as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation East Asian.
A population made up of 2 samples from Kinh individuals recruited in Vietnam as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation East Asian.
A population made up of 2 samples from Korean individuals recruited in Korea as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation East Asian.
A population made up of 2 samples from Lahu individuals recruited in China as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation East Asian.
A population made up of 2 samples from Miao individuals recruited in China as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation East Asian.
A population made up of 3 samples from Naxi individuals recruited in China as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation East Asian.
A population made up of 2 samples from Oroqen individuals recruited in China as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation East Asian.
A population made up of 2 samples from She individuals recruited in China as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation East Asian.
A population made up of 2 samples from Thai individuals recruited in Thailand as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation East Asian.
A population made up of 2 samples from Tu individuals recruited in China as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation East Asian.
A population made up of 2 samples from Tujia individuals recruited in China as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation East Asian.
A population made up of 2 samples from Uygur individuals recruited in China as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation East Asian.
A population made up of 2 samples from Xibo individuals recruited in China as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation East Asian.
A population made up of 2 samples from Yi individuals recruited in China as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation East Asian.
A population made up of 109 samples from Chinese Dai individuals recruited in Xishuangbanna, China as part of the 1000 Genomes Project. The population was assigned by the collecting project to the superpopulation East Asian.
A population made up of 112 samples from Han Chinese individuals recruited in Beijing, China as part of the 1000 Genomes Project. The population was assigned by the collecting project to the superpopulation East Asian.
A population made up of 105 samples from Japanese individuals recruited in Tokyo, Japan as part of the 1000 Genomes Project. The population was assigned by the collecting project to the superpopulation East Asian.
A population made up of 124 samples from Kinh individuals recruited in Ho Chi Minh City, Vietnam as part of the 1000 Genomes Project. The population was assigned by the collecting project to the superpopulation East Asian.
A population made up of 171 samples from Han Chinese South individuals recruited in China as part of the 1000 Genomes Project. The population was assigned by the collecting project to the superpopulation East Asian.
A population made up of 15 samples from Adygei individuals recruited in Caucasus, Russia as part of the Human Genome Diversity Project. The population was assigned by the collecting project to the superpopulation European.
A population made up of 22 samples from Basque individuals recruited in France as part of the Human Genome Diversity Project. The population was assigned by the collecting project to the superpopulation European.
A population made up of 10 samples from Bergamo Italian individuals recruited in Bergamo, Italy as part of the Human Genome Diversity Project. The population was assigned by the collecting project to the superpopulation European.
Bergamo Italian in Bergamo, Italy (HGDP)
A population made up of 24 samples from French individuals recruited in France as part of the Human Genome Diversity Project. The population was assigned by the collecting project to the superpopulation European.
A population made up of 13 samples from Orcadian individuals recruited in Orkney as part of the Human Genome Diversity Project. The population was assigned by the collecting project to the superpopulation European.
A population made up of 23 samples from Russian individuals recruited in Russia as part of the Human Genome Diversity Project. The population was assigned by the collecting project to the superpopulation European.
A population made up of 24 samples from Sardinian individuals recruited in Italy as part of the Human Genome Diversity Project. The population was assigned by the collecting project to the superpopulation European.
A population made up of 6 samples from Tuscan individuals recruited in Italy as part of the Human Genome Diversity Project. The population was assigned by the collecting project to the superpopulation European.
A population made up of 107 samples from British individuals recruited in England and Scotland as part of the 1000 Genomes Project. The population was assigned by the collecting project to the superpopulation European.
A population made up of 184 samples from individuals resident in Utah (CEPH) with Northern and Western European ancestry recruited in Utah, USA as part of the 1000 Genomes Project. The population was assigned by the collecting project to the superpopulation European.
Utah residents (CEPH) with Northern and Western European ancestry
A population made up of 105 samples from Finnish individuals recruited in Finland as part of the 1000 Genomes Project. The population was assigned by the collecting project to the superpopulation European.
A population made up of 162 samples from Iberian populations individuals recruited in Spain as part of the 1000 Genomes Project. The population was assigned by the collecting project to the superpopulation European.
A population made up of 112 samples from Toscani individuals recruited in Italy as part of the 1000 Genomes Project. The population was assigned by the collecting project to the superpopulation European.
A population made up of 44 samples from Bedouin individuals recruited in Negev, Israel as part of the Human Genome Diversity Project. The population was assigned by the collecting project to the superpopulation Greater Middle Eastern (Middle Eastern or North African or Persian).
A population made up of 40 samples from Druze individuals recruited in Carmel, Israel as part of the Human Genome Diversity Project. The population was assigned by the collecting project to the superpopulation Greater Middle Eastern (Middle Eastern or North African or Persian).
A population made up of 27 samples from Mozabite individuals recruited in Mzab, Algeria as part of the Human Genome Diversity Project. The population was assigned by the collecting project to the superpopulation Greater Middle Eastern (Middle Eastern or North African or Persian).
A population made up of 43 samples from Palestinian individuals recruited in Central, Israel as part of the Human Genome Diversity Project. The population was assigned by the collecting project to the superpopulation Greater Middle Eastern (Middle Eastern or North African or Persian).
A population made up of 11 samples from Bougainville individuals recruited in Bougainville as part of the Human Genome Diversity Project. The population was assigned by the collecting project to the superpopulation Oceanian.
A population made up of 6 samples from Papuan Highlands individuals recruited in New Guinea as part of the Human Genome Diversity Project. The population was assigned by the collecting project to the superpopulation Oceanian.
A population made up of 8 samples from Papuan Sepik individuals recruited in New Guinea as part of the Human Genome Diversity Project. The population was assigned by the collecting project to the superpopulation Oceanian.
A population made up of 2 samples from Australian individuals recruited in Australia as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation Oceanian.
A population made up of 2 samples from Bougainville individuals recruited in Papua New Guinea as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation Oceanian.
A population made up of 2 samples from Dusun individuals recruited in Brunei as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation Oceanian.
A population made up of 1 samples from Hawaiian individuals recruited in USA as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation Oceanian.
A population made up of 2 samples from Igorot individuals recruited in Philippines as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation Oceanian.
A population made up of 1 samples from Maori individuals recruited in New Zealand as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation Oceanian.
A population made up of 15 samples from Papuan individuals recruited in Papua New Guinea as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation Oceanian.
A population made up of 2 samples from Balochi individuals recruited in Pakistan as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation South Asian.
A population made up of 2 samples from Bengali individuals recruited in Bangladesh as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation South Asian.
A population made up of 2 samples from Brahmin individuals recruited in India as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation South Asian.
A population made up of 2 samples from Brahui individuals recruited in Pakistan as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation South Asian.
A population made up of 2 samples from Burusho individuals recruited in Pakistan as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation South Asian.
A population made up of 2 samples from Hazara individuals recruited in Pakistan as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation South Asian.
A population made up of 2 samples from Irula individuals recruited in India as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation South Asian.
A population made up of 2 samples from Kalash individuals recruited in Pakistan as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation South Asian.
A population made up of 2 samples from Kapu individuals recruited in India as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation South Asian.
A population made up of 1 samples from Khonda Dora individuals recruited in India as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation South Asian.
A population made up of 2 samples from Kusunda individuals recruited in Nepal as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation South Asian.
A population made up of 1 samples from Madiga individuals recruited in India as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation South Asian.
A population made up of 2 samples from Makrani individuals recruited in Pakistan as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation South Asian.
A population made up of 2 samples from Pathan individuals recruited in Pakistan as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation South Asian.
A population made up of 4 samples from Punjabi individuals recruited in Pakistan as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation South Asian.
A population made up of 2 samples from Relli individuals recruited in India as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation South Asian.
A population made up of 2 samples from Sindhi individuals recruited in Pakistan as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation South Asian.
A population made up of 2 samples from Yadava individuals recruited in India as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation South Asian.
A population made up of 144 samples from Bengali individuals recruited in Bangladesh as part of the 1000 Genomes Project. The population was assigned by the collecting project to the superpopulation South Asian.
A population made up of 113 samples from Gujarati Indians individuals recruited in Houston, TX as part of the 1000 Genomes Project. The population was assigned by the collecting project to the superpopulation South Asian.
A population made up of 158 samples from Punjabi individuals recruited in Lahore, Pakistan as part of the 1000 Genomes Project. The population was assigned by the collecting project to the superpopulation South Asian.
A population made up of 128 samples from Sri Lankan Tamil individuals recruited in the UK as part of the 1000 Genomes Project. The population was assigned by the collecting project to the superpopulation South Asian.
A population made up of 118 samples from Indian Telugu individuals recruited in the UK as part of the 1000 Genomes Project. The population was assigned by the collecting project to the superpopulation South Asian.
A population made up of 2 samples from Abkhasian individuals recruited in Abkhazia or Russia as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation West Eurasian.
A population made up of 2 samples from Adygei individuals recruited in Russia(Caucasus) as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation West Eurasian.
A population made up of 1 samples from Albanian individuals recruited in Albania as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation West Eurasian.
A population made up of 2 samples from Armenian individuals recruited in Armenia as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation West Eurasian.
A population made up of 2 samples from Basque individuals recruited in France as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation West Eurasian.
A population made up of 2 samples from Bedouin B individuals recruited in Israel(Negev) as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation West Eurasian.
A population made up of 2 samples from Bergamo individuals recruited in Italy(Bergamo) as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation West Eurasian.
A population made up of 2 samples from Bulgarian individuals recruited in Bulgaria as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation West Eurasian.
A population made up of 1 samples from Chechen individuals recruited in Russia as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation West Eurasian.
A population made up of 2 samples from Crete individuals recruited in Greece as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation West Eurasian.
A population made up of 1 samples from Czech individuals recruited in Czechoslovakia(pre1989) as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation West Eurasian.
A population made up of 2 samples from Druze individuals recruited in Israel(Carmel) as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation West Eurasian.
A population made up of 2 samples from English individuals recruited in England as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation West Eurasian.
A population made up of 2 samples from Estonian individuals recruited in Estonia as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation West Eurasian.
A population made up of 3 samples from Finnish individuals recruited in Finland as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation West Eurasian.
A population made up of 3 samples from French individuals recruited in France as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation West Eurasian.
A population made up of 2 samples from Georgian individuals recruited in Georgia as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation West Eurasian.
A population made up of 2 samples from Greek individuals recruited in Greece as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation West Eurasian.
A population made up of 2 samples from Hungarian individuals recruited in Hungary as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation West Eurasian.
A population made up of 2 samples from Icelandic individuals recruited in Iceland as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation West Eurasian.
A population made up of 2 samples from Iranian individuals recruited in Iran as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation West Eurasian.
A population made up of 2 samples from Iraqi Jew individuals recruited in Iraq as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation West Eurasian.
A population made up of 3 samples from Jordanian individuals recruited in Jordan as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation West Eurasian.
A population made up of 2 samples from Lezgin individuals recruited in Russia as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation West Eurasian.
A population made up of 2 samples from North Ossetian individuals recruited in Russia as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation West Eurasian.
A population made up of 1 samples from Norwegian individuals recruited in Norway as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation West Eurasian.
A population made up of 2 samples from Orcadian individuals recruited in Orkney Islands as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation West Eurasian.
A population made up of 3 samples from Palestinian individuals recruited in Israel(Central) as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation West Eurasian.
A population made up of 1 samples from Polish individuals recruited in Poland as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation West Eurasian.
A population made up of 2 samples from Russian individuals recruited in Russia as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation West Eurasian.
A population made up of 2 samples from Saami individuals recruited in Finland as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation West Eurasian.
A population made up of 1 samples from Samaritan individuals recruited in Israel as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation West Eurasian.
A population made up of 3 samples from Sardinian individuals recruited in Italy as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation West Eurasian.
A population made up of 2 samples from Spanish individuals recruited in Spain as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation West Eurasian.
A population made up of 2 samples from Tajik individuals recruited in Tajikistan as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation West Eurasian.
A population made up of 2 samples from Turkish individuals recruited in Turkey as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation West Eurasian.
A population made up of 2 samples from Tuscan individuals recruited in Italy(Tuscany) as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation West Eurasian.
A population made up of 2 samples from Yemenite Jew individuals recruited in Yemen as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation West Eurasian.
Includes individuals who either self-report or have been described by authors as Indigenous Siberan. This covers any indigenous groups from the northern part of the Asian contient that is commonly referred to as Siberia and which reaches from the Ural Mountains in the west to the Pacific Ocean in the east, and from the Arctic Ocean in the north to the northern borders of Kazakhstan, Mongolia and China in the south. We note that there does not appear to be a suitable reference population for this population and efforts are required to fill this gap, although smaller reference populations were defined by the SGDP. Principal-component analysis of samples from this population suggest a close genetic relatedness with some Indigenous North American populations, such as the Chipewyan.
Indigenous peoples of Siberia
Root of all terms in the Human Phenotype Ontology.
The pattern in which a particular genetic trait or disorder is passed from one generation to the next.
While there is a close conceptual relationship between allelic requirement and inheritance, they serve different purposes; allelic requirement is necessary for variant annotation pipelines and to determine if a given variant in a specific context is relevant to the phenotype of the patient e.g. a heterozygous variant (in the absence of compound heterozygosity) is relevant for dominant but not for recessive disease; while inheritance is used for describing the mode of inheritance of a phenotype and is particularly applicable in the clinical setting for communicating recurrence risk, to guide family screening, and to guide reproductive advice.
The kidney is a paired organ whose primary function is the production of urine.
A reduction in the level of performance of the kidneys in areas of function comprising the concentration of urine, removal of wastes, the maintenance of electrolyte balance, homeostasis of blood pressure, and calcium metabolism.
symptom
This is the root of the phenotypic abnormality subontology of the HPO.
The presence of any abnormality of the genitourinary system.
Abnormality of the oral cavity, i.e., the opening or hollow part of the mouth.
Dryness of the mouth due to salivary gland dysfunction.
Abnormality of the region around the eyes
Anomaly of the orbital region of the face
Deformity of the orbital region of the face
Malformation of the orbital region of the face
Epistaxis, or nosebleed, refers to a hemorrhage localized in the nose.
An inability to perceive odors. This is a general term describing inability to smell arising in any part of the process of smelling from absorption of odorants into the nasal mucous overlying the olfactory epithelium, diffusion to the cilia, binding to olfactory receptor sites, generation of action potentials in olfactory neurons, and perception of a smell.
Any abnormality of the eye, including location, spacing, and intraocular abnormalities.
The conjunctiva is a thin, sparsely vascularized transparent membrane that covers and protects the sclera (the bulbar conjunctiva), and forms the inner lining of the eyelids (the tarsal conjunctiva).
Abnormality of eyesight (visual perception).
The upper eyelid margin is positioned 3 mm or more lower than usual and covers the superior portion of the iris (objective); or, the upper lid margin obscures at least part of the pupil (subjective).
Either a morphological abnormality or hearing deficit. This should be split more cleanly in the future.
An anomaly of the pharynx, i.e., of the tubular structure extending from the base of the skull superiorly to the esophageal inlet inferiorly.
The pharynx is tubular structure extending from base of skull superiorly to esophageal inlet inferiorly, and is composed of three distinct areas: the nasopharynx, the oropharynx, and the hypopharynx, with the pharyngeal walls being composed of the superior, middle, and inferior pharyngeal constrictor muscles. It is part of the digestive system and of the conducting zone of the respiratory system.
Lack of sharpness of vision resulting in the inability to see fine detail.
This is a very nonspecific term and it is preferable to describe the correlates of blurred vision with the corresponding terms if possible.
The nervous system comprises the neuraxis (brain, spinal cord, and ventricles), the autonomic nervous system, the enteric nervous system, and the peripheral nervous system.
Atypical behavior is an abnormality in a person's actions that can be controlled or modulated by the will of the individual. While abnormal behaviors can be difficult to control, they are distinct from other abnormal actions that cannot be affected by the individual's will.
Atypical behaviors should include or directly affect observable actions. While behavioral disorders often encompass abnormal thoughts, feelings, perceptions, or other cognitions, these alone would not be considered atypical behavioral features.
A proneness to anger, i.e., a tendency to become easily bothered or annoyed.
The presence of blood in the urine. Hematuria may be gross hematuria (visible to the naked eye) or microscopic hematuria (detected by dipstick or microscopic examination of the urine).
The endocrine system is composed of glands that secrete hormones directly into the bloodstream and includes the following glands: thyroid, parathyroids, adrenals, pancreas, gonads (testicles and ovaries), and pituitary. Many other organs, such as the kidney, liver, and heart, have secondary endocrine functions.
A group of abnormalities characterized by hyperglycemia and glucose intolerance.
The presence of chronic increased pressure in the systemic arterial system.
Hypertension is sustained elevation of resting systolic BP (140 mm Hg or higher), diastolic BP (90 mm Hg or higher), or both.
Bluish discoloration of the skin and mucosa due to poor circulation or inadequate oxygenation of arterial or capillary blood.
Eczema is a form of dermatitis that is characterized by scaly, pruritic, erythematous lesions located on flexural surfaces.
The term eczema is broadly applied to a range of persistent skin conditions and can be related to a number of underlying conditions. Manifestations of eczema can include dryness and recurring skin rashes with redness, skin edema, itching and dryness, crusting, flaking, blistering, cracking, oozing, or bleeding. Eczema has several forms including atopic dermatitis, contact dermatitis, dyshidrotic eczema, nummular eczema, seborrheic dermatitis, and stasis dermatitis.
An abnormal accumulation of fluid beneath the skin, or in one or more cavities of the body.
Edema may be related to one or more of the following factors: 1) increased capillary hydrostatic pressure, 2) decreased osmotic pressure of plasma, 3) decreased tissue tension and lymphatic drainage, 4) increased osmotic pressure of tissue fluids, and 5) increased capillary permeability.
Dermatological manifestations of systemic disorders
Bluish discoloration of the skin of the hands or feet.
Cyanosis is caused by increased levels of deoxygenated hemoglobin.
Hard, pebble-like deposits that form within the gallbladder.
Gallstones range in size from as small as a grain of sand to as large as a golf ball. Cholesterol gallstones are the most common type of gallstone. Gallstones resulting from too much bilirubin in the bile are referred to as pigment stones.
An abnormality of the fetus or the birth of the fetus, excluding structural abnormalities.
Abnormality of prenatal development or birth
Because of the close link between prenatal developmental abnormalities and abnormalities of the birth process, a single term is chosen to subsume both classes of abnormality.
A seizure is an intermittent abnormality of nervous system physiology characterized by a transient occurrence of signs and/or symptoms due to abnormal excessive or synchronous neuronal activity in the brain.
A type of electrographic seizure has been proposed in neonates which does not have a clinical correlate, it is electrographic only. The term epilepsy is not used to describe recurrent febrile seizures. Epilepsy presumably reflects an abnormally reduced seizure threshold.
The complete absence of wakefulness and consciousness, which is evident through a lack of response to any form of external stimuli.
Coma is generally a result of diffuse or extensive involvement of both hemispheres of the brain or lesions in the brainstem.
Lack of clarity and coherence of thought, perception, understanding, or action.
Sudden impairment of blood flow to a part of the brain due to occlusion or rupture of an artery to the brain.
Encephalopathy is a term that means brain disease, damage, or malfunction. In general, encephalopathy is manifested by an altered mental state.
This term and its children are general and bundled terms that are kept for convenience. For new annotations, it is recommended that the specific phenotypic abnormalities be noted.
It is important clinical to distinguish between muscle weakness, fatigue, and asthenia. Fatigue describes the inability to continue performing a task after multiple repetitions; in contrast, a patient with primary weakness is unable to perform the first repetition of the task. Asthenia is a sense of weariness or exhaustion in the absence of muscle weakness. Conditions that result in intrinsic muscle weakness can be divided into several main categories: infectious, neurologic, endocrine, inflammatory, rheumatologic, genetic, metabolic, electrolyte-induced, or drug-induced.
Abnormal coordination of muscles involved in speech.
An abnormal structure or form of the joints, i.e., one or more of the articulations where two bones join.
A reduction in the freedom of movement of one or more joints.
Joint stiffness is a perceived sensation of tightness in a joint or joints when attempting to move them after a period of inactivity. Joint stiffness typically subsides over time.
Steatosis is a term used to denote lipid accumulation within hepatocytes.
Although steatosis is the hallmark of the fatty liver disease, it is not a specific feature because it can be seen as part of other disease processes, such as drug injury, Wilson disease, or hepatitis C virus infection (especially genotype-3). Involvement of less than 5% of the hepatocytes by steatosis is considered clinically insignificant and within reference range. Based on the morphologic appearance and the size of the lipid droplets within the cytoplasm of the hepatocytes, steatosis is characterized as macrovesicular or microvesicular. Macrovesicular steatosis is characterized by large lipid droplets occupying the cytoplasm, displacing the nucleus to the periphery (large droplet macrovesicular steatosis) or multiple small lipid droplets of variable size occupying the cytoplasm with the nucleus maintaining its central location (small droplet macrovesicular steatosis). Microvesicular steatosis is characterized by innumerable tiny, relatively uniform lipid vacuoles that result in a bubbly appearance of the hepatocytes.
Reduced ability of the liver to perform its functions.
Accumulation of substantial excess body fat.
A thrusting or bulging out of the abdomen.
An abnormality of the integument, which consists of the skin and the superficial fascia.
This term describes any abnormality of the voice, i.e., of the sounds produced by humans by the passage of air through the larynx and over the vocal cords, and then modified by the resonance organs, the nasopharynx, and the mouth.
Any abnormality of the cardiovascular system.
Abnormality of the cardiovascular system
The cardiovascular system consists of the heart, vasculature, and the lymphatic system.
The presence of an abnormality of cardiac function that is responsible for the failure of the heart to pump blood at a rate that is commensurate with the needs of the tissues or a state in which abnormally elevated filling pressures are required for the heart to do so. Heart failure is frequently related to a defect in myocardial contraction.
A structural anomaly of the muscle layer of the heart wall.
A myocardial disorder in which the heart muscle is structurally and functionally abnormal, in the absence of coronary artery disease, hypertension, valvular disease and congenital heart disease sufficient to cause the observed myocardial abnormality.
A rapid heartrate that exceeds the range of the normal resting heartrate for age.
Irreversible damage to heart tissue (myocardium) due to lack of oxygen after a heart attack (myocardial infarction).
Reduced ability to pass air through the nasal cavity often leading to mouth breathing.
An abnormality of the functioning of the vestibular apparatus.
The vestibular apparatus is the nonauditory portion of the inner ear that mediates the subjective sensation of motion and spatial orientation of the head, adjusts muscular activity and body position to maintain posture, and stabilizes in space the fixation point of the eyes when the head moves, in order to provide a stable image upon the retina. The functioning of the vestibular system is often checked clinically by means of the caloric test, in which the head is tilted backward by about 60 degrees and either warm or cold water is introduced into the external auditory meatus on one side. The immediate results are usually vertigo, nausea, nystagmus, and twisting of the head and body.
An abnormality of the hematopoietic system.
Abnormality of blood and blood-forming tissues
Abnormality of the haematopoietic system
The hematopoietic system comprises the organs that are involved in the production of blood, primarily the bone marrow, spleen, tonsils, and lymph nodes.
Any structural abnormality of erythrocytes (red-blood cells).
An abnormal susceptibility to bleeding, often referred to as a bleeding diathesis. A bleeding diathesis may be related to vascular, platelet and coagulation defects.
This term is kept for historical reasons. If possible, a more exact description of the phenotype (i.e., whether there is a vascular, platelet and coagulation defect) should be attempted.
A reduction in erythrocytes volume or hemoglobin concentration.
Low number of red blood cells or haemoglobin
Low number of red blood cells or hemoglobin
Anemia is not a specific entity but can result from many underlying pathologic processes. The three main causes of anemia are blood loss, decreased or faulty red blood cell production, and increased destruction of red blood cells. Various classifications are in clinical use including a classification according to the mean corpuscular volume (MCV) of the erythrocytes: microcytic, macrocytic, or normocytic. Anemias can also be classified according to variations in cell size and shape, as reflected by the red-cell distribution width (RDW). Additionally, anemias can be classified into those of inadequate production and hemolytic anemias.
Sudden loss of renal function, as manifested by decreased urine production, and a rise in serum creatinine or blood urea nitrogen concentration (azotemia).
Acute renal failure is usually classified into prerenal (response to severe volume depletion), intrinsic (response to acute cytotoxic, ischemic, or inflammatory insults) and postrenal (response to obstruction of the passage of urine) etiologies.
Body temperature elevated above the normal range.
Fever has been defined as a state of elevated core temperature, which is often, but not necessarily, part of the defensive responses of multicellular organisms (host) to the invasion of live (microorganisms) or inanimate matter recognized as pathogenic or alien by the host. The febrile response (of which fever is a component) is a complex physiologic reaction to disease, involving a cytokine-mediated rise in core temperature, generation of acute phase reactants, and activation of numerous physiologic, endocrinologic, and immunologic systems. The rise in temperature during fever is to be distinguished from that occurring during episodes of hyperthermia. Unlike fever, hyperthermia involves an unregulated rise in body temperature in which pyrogenic cytokines are not directly involved and against which standard antipyretics are ineffective. It represents a failure of thermoregulatory homeostasis, in which there is uncontrolled heat production, inadequate heat dissipation, or defective hypothalamic thermoregulation.
Glucose intolerance (GI) can be defined as dysglycemia that comprises both prediabetes and diabetes. It includes the conditions of impaired fasting glucose (IFG) and impaired glucose tolerance (IGT) and diabetes mellitus (DM).
Venous or arterial thrombosis (formation of blood clots) of spontaneous nature and which cannot be fully explained by acquired risk (e.g. atherosclerosis).
A structural abnormality of the central nervous system.
Abnormality of the central nervous system
Morphological abnormality of the central nervous system
Morphological central nervous system abnormality
An abnormality of the viscera of the abdomen.
The abdominal organs comprise the stomach, small and large intestines, liver, pancreas, bile tract, and spleen.
Forceful ejection of the contents of the stomach through the mouth by means of a series of involuntary spasmic contractions.
Abnormally increased frequency (usually defined as three or more) loose or watery bowel movements a day.
Nausea is a commonly encountered symptom that has been defined as an unpleasant painless subjective feeling that one will imminently vomit. Vomiting has been defined as the forceful expulsion of the contents of the stomach, duodenum, or jejunum through the oral cavity. While nausea and vomiting are often thought to exist on a temporal continuum, this is not always the case. There are situations when severe nausea may be present without emesis and less frequently, when emesis may be present without preceding nausea.
A sensation of unease in the stomach together with an urge to vomit.
Infrequent or difficult evacuation of feces.
An unpleasant sensation characterized by physical discomfort (such as pricking, throbbing, or aching) and perceived to originate in the abdomen.
Abdominal pain can be crampy, achy, dull, intermittent or sharp. The terms stomach ache and stomach cramps are nonmedical terms often used to describe pain in the mid- or upper abdominal area, even though it is not the case that the (smooth) muscles of the stomach or the abdomen have cramps. Stomach pain is another layperson term commonly used to refer to abdominal pain.
The presence of chronic diarrhea, which is usually taken to mean diarrhea that has persisted for over 4 weeks.
An inadequate sucking reflex, resulting in the difficult of newborns to be breast-fed.
Inflammation, or an inflammatory state in the large intestine.
Anorexia, or the loss of appetite for food, is a medical condition.
Please note that this term does not refer to the condition of anorexia nervosa, which is a disorder characterized by an obsessive desire to lose weight by refusing to eat.
Any structural abnormality of the telencephalon, which is also known as the cerebrum.
Migraine is a chronic neurological disorder characterized by episodic attacks of headache and associated symptoms.
An abnormality of the respiratory system, which include the airways, lungs, and the respiratory muscles.
An abnormality of the upper respiratory tract.
Abnormality of the upper respiratory tract
Inflammation of any part of the lung parenchyma.
Difficult or labored breathing. Dyspnea is a subjective feeling only the patient can rate, e.g., on a Borg scale.
Asthma is characterized by increased responsiveness of the tracheobronchial tree to multiple stimuli, leading to narrowing of the air passages with resultant dyspnea, cough, and wheezing.
An abnormality of the pulmonary pleura, the thin, transparent membrane which covers the lungs and lines the inside of the chest walls.
Coughing up (expectoration) of blood or blood-streaked sputum from the larynx, trachea, bronchi, or lungs.
Accumulation of air in the pleural cavity leading to a partially or completely collapsed lung.
Pneumothorax occurring without traumatic injury to the chest or lung.
Acute ischemic stroke (AIS) is defined by the sudden loss of blood flow to an area of the brain with the resulting loss of neurologic function. It is caused by thrombosis or embolism that occludes a cerebral vessel supplying a specific area of the brain. During a vessel occlusion, there is a core area where damage to the brain is irreversible and an area of penumbra where the brain has lost function owing to decreased blood flow but is not irreversibly injured.
An abnormality in the sound (volume) or cadence (rate) of speech.
The term Abnormal speech pattern includes both psychiatric and neurological conditions that affect the rate, rhythm, and volume of expressed speech.
The presence of an excessive amount of fluid in the pleural cavity.
An embolus (that is, an abnormal particle circulating in the blood) located in the pulmonary artery and thereby blocking blood circulation to the lung. Usually the embolus is a blood clot that has developed in an extremity (for instance, a deep venous thrombosis), detached, and traveled through the circulation before becoming trapped in the pulmonary artery.
Replacement of normal lung tissues by fibroblasts and collagen.
Pulmonary fibrosis leads to an irreversible impairment of alveolar oxygen transfer.
Hemorrhage affecting the gastrointestinal tract.
An abnormality of the intestine. The closely related term enteropathy is used to refer to any disease of the intestine.
The passage of blackish, tarry feces associated with gastrointestinal hemorrhage. Melena occurs if the blood remains in the colon long enough for it to be broken down by colonic bacteria. One degradation product, hematin, imbues the stool with a blackish color. Thus, melena generally occurs with bleeding from the upper gastrointestinal tract (e.g., stomach ulcers or duodenal ulcers), since the blood usually remains in the gut for a longer period of time than with lower gastrointestinal bleeding.
The large intestine comprises the cecum and colon.
Repeated episodes of diarrhea separated by periods without diarrhea.
Cephalgia, or pain sensed in various parts of the head, not confined to the area of distribution of any nerve.
Headache is one of the most common types of recurrent pain as well as one of the most frequent symptoms in neurology. In addition to occasional headaches, there are well-defined headache disorders that vary in incidence, prevalence and duration and can be divided into two broad categories. In secondary headache disorders, headaches are attributed to another condition, such as brain tumor or head injury; for the primary disorders the headache is not due to another condition.
An abnormal sensation of spinning while the body is actually stationary.
A disorder of the brain caused by an infectious agent that presents with fever, headache, and an altered level of consciousness. There may also be focal or multifocal neurologic deficits, and focal or generalized seizure activity.
Paroxysmal, recurrent episodes of vomiting.
The passage of fresh (red) blood per anus, usually in or with stools. Most rectal bleeding comes from the colon, rectum, or anus.
Bright red blood in stool, most frequentoly caused by hemorrhoids or diverticulosis.
Colitis refers to an inflammation of the colon and is often used to describe an inflammation of the large intestine (colon, cecum and rectum). Colitides may be acute and self-limited or chronic, and broadly fit into the category of digestive diseases.
Vomiting that ejects the gastric contents with great force.
Low Blood Pressure, vascular hypotension.
Formation of a blot clot in a deep vein. The clot often blocks blood flow, causing swelling and pain. The deep veins of the leg are most often affected.
Restriction of arterial blood supply to the brain associated with insufficient oxygenation to support the metabolic requirements of the tissue.
Disruption of blood oxygen supply to brain
The immune system is composed of organs and interdependent cell types that collectively protect the body from infections and from the growth of tumor cells. The organs of the immune system comprise the bone marrow, the spleen, the thymus,the lymph nodes, and the cell types comprise B cells, T cells, natural killer cells, granulocytes,dendritic cells, and macrophages.
Increased respiratory rate or depth of breathing
In adults, a beathing rate of between 12-20 breaths per minute is normal and tachypnea is present with a ventilatory rate greater than 20 breaths per minute.
An anomaly of the rhythm or depth of breathing.
Abnormal function of the respiratory system.
Arthralgia is distinct from Arthritis, which is not a symptom but a diagnosis with articular inflammation or signs of osteoarthritis.
A severe form of respiratory insufficiency characterized by inadequate gas exchange such that the levels of oxygen or carbon dioxide cannot be maintained within normal limits.
Respiratory failure is classified as type 1 with hypoxemia (arterial partial pressure of oxygen less than 60 mmHg) without hypercapnea, and type 2 with hypoxemia in the present of hypercapnea (partial pressure of carbon dioxide over 50 mmHg).
An abnormally decreased potassium concentration in the blood.
An abnormally decreased calcium concentration in the blood.
An abnormally decreased magnesium concentration in the blood.
Abnormality originating in one or more muscles, i.e., of the set of muscles of body.
An abnormality of the composition of urine or the levels of its components.
Abnormality of the homeostasis (concentration) of a monoatomic ion.
Breakdown of muscle fibers that leads to the release of muscle fiber contents (myoglobin) into the bloodstream.
Abdominal distention can be a secondary feature associated with a number of conditions such as bowel obstruction.
Paralysis of voluntary muscles means loss of contraction due to interruption of one or more motor pathways from the brain to the muscle fibers. Although the word paralysis is often used interchangeably to mean either complete or partial loss of muscle strength, it is preferable to use paralysis or plegia for complete or severe loss of muscle strength, and paresis for partial or slight loss. Motor paralysis results from deficits of the upper motor neurons (corticospinal, corticobulbar, or subcorticospinal). Motor paralysis is often accompanied by an impairment in the facility of movement.
A phenotypic abnormality that is present at birth.
Congenital onset literally means present at birth. Congenital abnormalities are thus generally acquired during fetal development. Congenital abnormalities are often but not always hereditary in nature. Whether a disease manifestation is diagnosed to be intrauterine or congenital may depend on the time at which diagnostic procedures are performed. Thus, most congenital abnormalities are also intrauterine. This term should be used for phenotypic abnormalities or diseases initially observed at the time of birth. For abnormalities observed prior to (e.g., by fetal ultrasound), use the term Antenatal onset (HP:0030674).
Onset of disease manifestations in adulthood, defined here as at the age of 16 years or later.
Onset of signs or symptoms of disease between 28 days to one year of life.
Onset of signs or symptoms of disease within the first 12 months of life.
Onset of signs or symptoms of disease between the age of 5 and 15 years.
Signs and symptoms begin before 15 years of age
Onset of signs or symptoms of disease within the first 28 days of life.
The age group in which disease manifestations appear.
Adolescent is defined by WHO as a person between 10-19 years of age.
Cases of the disease in question occur without a previous family history, i.e., as isolated cases without being transmitted from a parent and without other siblings being affected.
An abnormal, increased fatiguability of the musculature.
Death of the fetus in utero after at least 22 weeks of gestation.
The age at which fetal demise is legally classified asa a miscarriage varies between countries with the US being 20 gestational weeks and the UK being 24 gestational weeks. The HPO chooses the average of these age ranges.
An abnormal increase or decrease of weight or an abnormal distribution of mass in the body.
Any deviation from the normal concentration of calcium in the blood circulation.
Abnormal circulating calcium concentration
An abnormality of temperature homeostasis.
Abnormally diminished level of attention, responsiveness, or wakefulness.
Inflammation of the alimentary part of the gastrointestinal system.
A deficiency in the intake of energy and nutrients.
An anomaly in the ability to perceive and distinguish scents (odors).
A decreased sensitivity to odorants (that is, a decreased ability to perceive odors).
The formation of a blood clot inside an artery.
A tachycardia originating in the ventricles characterized by rapid heart rate (over 100 beats per minute) and broad QRS complexes (over 120 ms).
Ventricular tachycardia (VT) is a potentially life-threatening ventricular arrhythmia that presents as a wide QRS complex tachycardia, and is defined as three or more consecutive QRS complexes with a duration longer than 120 milliseconds (ms) and a rate of 100 beats per minute or more, whereby the complexes have a ventricular origin. VT can be subdivided as follows: (i) sustained VT persists for 30 seconds or more; (ii) non-sustained VT lasts less than 30 seconds; (iii) monomorphic VT displays a uniform QRS morphology; and (iv) polymorphic VT displays QRS morphologies that variy from beat to beat. VT is observed most commonly in individuals with structural heart disease or acute myocardial infarction (MI). VT may also be observed in in the setting of drug toxicity or electrolyte abnormalities or in individuals with Mendelian disease.
A state of respiratory distress that requires a life saving intervention in the form of gaining airway access and instituting positive pressure ventilation.
Respiratory distress necessitating mechanical ventilation
Respiratory distress requiring endotracheal intubation
Respiratory distress requiring mechanical ventilation
Respiratory failure requiring assisted ventilation
An abnormality of magnesium ion homeostasis.
Formation of a blood clot (thrombus) inside a vein, causing the obstruction of blood flow.
Watery voluminous diarrhea resulting from an imbalance between ion and water secretion and absorption.
A pregnancy that ends at a stage in which the fetus is incapable of surviving on its own, defined as the spontaneous loss of a fetus before the 22th week of pregnancy.
A type of diabetes mellitus initially characterized by insulin resistance and hyperinsulinemia and subsequently by glucose interolerance and hyperglycemia.
Persons with type II diabetes mellitus rarely develop ketoacidosis.
An anomaly that is characterized progressive airflow obstruction that is only partly reversible, inflammation in the airways, and systemic effects or comorbities.
COPD is usually conceptualized as a disease entity. It is heterogeneous histologically and pathogenically, and conventionally includes emphysema and chronic bronchitis, It is included as a phenotype term as COPD is often annotated as a feature of other diseases.
According to the definitions of the American and British Thoracic Societies, including pulmonary functional tests, X-rays, and CT scans for items such as fibrosis, bronchiectasis, bullae, emphysema, nodular or lymphomatous abnormalities.
Abnormality of the lung parenchyma extending to the pulmonary interstitium and leading to diffuse pulmonary fibrosis.
Abnormality in area between air sacs in lung
Abnormal pulmonary interstitial morphology
Obstruction of conducting airways of the lung.
Abnormality of the vasculature of the eye
Impaired feeding performance of an infant as manifested by difficulties such as weak and ineffective sucking, brief bursts of sucking, and falling asleep during sucking. There may be difficulties with chewing or maintaining attention.
Loss of elasticity of the upper and lower eyelids causing the skin to sag and bulge.
An abnormality of divalent inorganic cation homeostasis.
Abnormality of divalent inorganic cation homeostasis
Abnormal blood inorganic cation concentration
An abnormality of monovalent inorganic cation homeostasis.
Abnormality of monovalent inorganic cation homeostasis
Abnormal blood monovalent inorganic cation concentration
An abnormality of the upper urinary tract.
The upper urinary tract is a subdivision of urinary system which consists of the kidney and the ureters.
A functional abnormality of the immune system.
The speed at which disease manifestations appear and develop.
Sudden appearance of disease manifestations over a short period of time.
The word acute is applied to different time scales depending on the disease or manifestation and does not have an exact definition in minutes, hours, or days.
An abnormality of any process involved in the maintenance of an internal steady state of glucose within an organism or cell.
An abnormality of the gastrointestinal tract.
Abnormality of the gastrointestinal tract
Abnormal functionality of the cardiovascular system.
Abnormality of cardiovascular system physiology
Abnormal cardiovascular system physiology
The presence of hemorrhage within the body.
An abnormality of the regulation of body fluids.
A sudden flexion, extension, or mixed extension-flexion of predominantly proximal and truncal muscles that is usually more sustained than a myoclonic movement but not as sustained as a tonic seizure. Limited forms may occur: Grimacing, head nodding, or subtle eye movements. Epileptic spasms frequently occur in clusters. Infantile spasms are the best known form, but spasms can occur at all ages
The maximum age of onset is between 3 and 12 months, the peak being at 6 months. However, spasms may start from birth, or appear long after the age of 12 months, including into adulthood. Infantile spasms represent a specific type of seizure seen in an epilepsy syndrome of infancy and childhood known as West Syndrome. West Syndrome is characterized by infantile spasms, developmental regression, and hypsarrhythmia (as demonstrated by electroencephalography).
Any morphological abnormality of the skin.
Any abnormality of the physiological function of the skin.
The presence of inflammation of the skin. That is, an abnormality of the skin resulting from the local accumulation of fluid, plasma proteins, and leukocytes.
Abnormal tendency to infections of the skin
Abnormality of the urinary system physiology
An abnormality of the skin that is not localized to any one particular region.
An abnormality of the function of the inner ear.
The inner ear comprises the cochlea, three semicircular canals and the vestibule (labyrinth), and is directly responsible for hearing. Additionally, the vestibule and semicircular canals function to maintain balance or equilibrium.
Delivery of a fetus through surgical incisions made through the abdominal wall (laparotomy) and the uterine wall (hysterotomy).
The age group when the cessation of life happens.
An anomaly of the control or production of movement in the central nervous system.
Cognitive, psychiatric, or memory anomaly.
This includes abnormalities in speech, mood, emotions, behavior, and cognition.
A type of infection of the central nervous system that can be regarded as a sign of a pathological susceptibility to infection.
A subjective manifestation of disease localized to the abdomen.
Onset of disease at the age of between 1 and 5 years.
This term refers to ages up to but not including the fifth birthday (see Juvenile onset).
Feeding problem necessitating nasogastric tube feeding.
This is a severe form of feeding problems in infancy.
Feeding problem necessitating gastrostomy tube feeding.
This is an extremely severe form of feeding problems in infancy.
Any cardiac rhythm other than the normal sinus rhythm. Such a rhythm may be either of sinus or ectopic origin and either regular or irregular. An arrhythmia may be due to a disturbance in impulse formation or conduction or both.
An abnormality in the range and ease of motion of joints across their normal range.
A functional abnormality of a skeletal muscle.
A structural abnormality of a skeletal muscle.
An abnormality of the form, structure, or size of the skeletal system.
An abnormality of the function of the skeletal system.
Abnormality of musculoskeletal physiology
A type of abdominal pain that comes and goes in waves, most often starting and ending suddenly and being of severe intensity.
Colicky abdominal pain can be caused by kidney stones and gallstones, among other etiologies. This type of pain is thought to be caused by spasm, obstruction, or distension of any of the hollow viscera of the gastrointestinal system.
An infection of the upper or lower respiratory tract.
Impaired ability to eat related to problems gathering food and getting ready to suck, chew, or swallow it.
An abnormal functionality of the kidney.
A structural anomaly of the respiratory system.
An anomaly in the processes involved in the maintenance of an internal equilibrium.
A structural anomaly of the globe of the eye, or bulbus oculi.
A subjective feeling of tiredness characterized by a lack of energy and motivation.
Fatigue is distinct from muscle weakness.
A delay in the development of skills required to feed oneself in the toddler period (between one and three years of age).
Delayed self-feeding during toddler years
Inflammation of the large airways in the lung including any part of the bronchi from the primary bronchi to the tertiary bronchi.
An abnormality of the partial pressure of oxygen or carbon dioxide in the arterial blood.
Abnormally reduced blood carbon dioxide (CO2) level.
An abnormally low level of blood oxygen.
Note that hypoxemia is defined as a condition where arterial oxygen tension is below normal (80-100mmHg). Hypoxia is defined as the failure of oxygenation at the tissue level. Hypoxia is not measured directly by a standard laboratory value.
A structural anomaly of the gallbladder.
A structural abnormality of the brain, which has as its parts the forebrain, midbrain, and hindbrain.
Constipation for longer than three months with fewer than 3 bowel movements per week, straining, lumpy or hard stools, and a sensation of anorectal obstruction or incomplete defecation.
Constipation of sudden onset and lasting for less than three months.
An unpleasant sensory and emotional experience associated with actual or potential tissue damage, or described in terms of such damage.
An anomalous finding in the examination of the urine for cells.
Functional anomaly of the kidney persisting for at least three months.
A functional anomaly of the nervous system.
Abnormality of nervous system physiology
A structural anomaly of the nervous system.
Abnormality of nervous system morphology
Any anomaly of the inflammatory response, a response to injury or infection characterized by local vasodilation, extravasation of plasma into intercellular spaces and accumulation of white blood cells and macrophages.
A abnormal increase in the inflammatory response to injury or infection.
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
Abnormal functionality of the gastrointestinal tract.
Functional abnormality of the gastrointestinal tract
A sudden, audible expulsion of air from the lungs through a partially closed glottis, preceded by inhalation.
The European Respiratory Society Task Force recommended two possible definitions of cough: (1) A three-phase expulsive motor act characterized by an inspiratory effort (inspiratory phase) followed by a forced expiratory effort against a closed glottis (compressive phase) and then by opening of the glottis and rapid expiratory airflow (expulsive phase);and (2) A forced expiratory maneuver, usually against a closed glottis and associated with a characteristic sound. The term Cough or any of its more specific descendents can be modified by the terms Acute (HP:0011009), Subacute (HP:0011011), and Chronic (HP:0011010). In adults, an acute cough lasts less than 3 weeks, a subacute cough from 3 to 8 weeks, and a chronic cough longer than 8 weeks. In children aged less than 15 years a chronic cough is defined as a daily cough lasting for over 4 weeks.
This subontology is designed to provide terms to characterize and specify the phenotypic abnormalities defined in the Phenotypic abnormality subontology, with respect to severity, laterality, age of onset, and other aspects.
Note that some of the terms, such as Intellectual disability, have children terms such as Severe intellectual disability that represent precomposed combinations of modifiers and phenotypic abnormality terms. This done where the medical community commonly uses these terms with a fixed meaning (for instance, the Intellectual disability terms are used with specific IQ ranges). For computational reasoning, the semantics are intended to be the same as if there was a combination of the phenotype term and the clinical modifier term.
position of phenotype abnormality
A motor seizure is a type of seizure that is characterized at onset by involvement of the skeletal musculature. The motor event could consist of an increase (positive) or decrease (negative) in muscle contraction to produce a movement.
This term describes the initial semiology of the seizure without specifying whether the onset is focal or generalized.
Any anomaly of the digestive system, a collection of organs that is made up of the gastrointestinal tract and the liver, pancreas, and gallbladder. The gastrointestinal tract is a series of hollow organs joined in a long, twisting tube from the mouth to the anus, including the mouth, esophagus, stomach, small intestine, large intestine and anus.
A functional anomaly of the digestive system.
Abnormality of digestive system physiology
A structural anomaly of the digestive system.
Abnormality of digestive system morphology
The anterior abdominal wall is sunken and presents a concave rather than a convex contour.
Scaphoid abdomen can be observed in diseases such as congenital diaphragmatic hernia (since the abdominal contents can be in the thorax).
Passage of many stools containing blood.
Diarrhea that contains bright red or maroon-colored blood may be referred to as hematochezia, while melena is used to describe black, tarry, and smelly diarrhea.
Passage of many stools containing blood and mucus.
Vomiting of material that is of fecal origin.
Feculent vomiting is usually due to mechanical intestinal obstruction but it can be due to paralytic obstruction (adynamic ileus).
A sudden violent, spasmodic, audible expiration of breath through the nose and mouth.
A symptom or manifestation indicating a systemic or general effect of a disease and that may affect the general well-being or status of an individual.
Note that we use the preferred term label constitutional symptom because this reflects common usage, but we do not restrict the term or its descendents to the narrow meaning of symptom, i.e., a complaint related by a patient to a physician. There is no generally accepted classification of what defines a constitutional symptom, but examples include weight loss, fatigue, general weakness, night sweats, shaking, chills, fever, and vomiting.
The word chills can also refer to an episode of shivering, accompanied by paleness and feeling cold.
Involuntary contraction or twitching of the muscles.
Shivering is a physiologic method of heat production in man and other mammals. Shivering is a bodily function in response to fever, early hypothermia or feeling cold.
Severe chills with violent shivering. A rigor is an episode of shaking or exaggerated shivering which can occur with a high fever.
A sudden attack of severe shivering accompanied by chills (a feeling of coldness) is called a rigor and may be associated with a marked rise in body temperature. Patients often describe rigors as an attack of uncontrollable shaking. Rigors are often a sign of infection, particularly bacterial infection.
A functional anomaly of the hepatobiliary system
Abnormality of hepatobiliary system physiology
Any physiological abnormality of the esophagus.
Functional abnormality of the oesophagus
A reddish appearance over the white part (sclera) of the eye ranging from a few enlarged blood vessels appearing as wiggly lines over the sclera to a bright red color completely covering to sclera.
A state characterized by a feeling of weakness and loss of strength leading to a generalized weakness of the body.
Asthenia is to be distinguished from fatigue, because asthenia refers to a sensation of exhaustion which occurs before any effort. Asthenia is to be distinguished from myasthenia, which means a specific weakness of one or more muscles. Asthenia and fatigue can coexist.
Any anomaly of the vocalizing of an infant's crying, i.e.,the typically loud voice production that is accompanied by tears and agitation.
Inflammation (due to infection or irritation) of the pharynx.
An abscess is a localized collection of purulent material surrounded by inflammation and granulation.
Any functional anomaly of the neck region.
A necrotic lesion in the cerebrum resulting from a sudden insufficiency of arterial or venous blood supply due to emboli, thrombi or mechanical factors.
An anomaly in intensity, frequency, or duration of the verbal or behavioral expression of emotions, feelings, or thoughts.
Affect includes a combination of emotion in terms of feelings and its expression either in the verbal or behavioral (action) level. Normal expressions are often relatively short lived and familiar to the person while pathological expressions may be intense and extended and considered out of character for the individual. Affect encompasses: 1) emotions, 2) volition, and 3) what is termed the intellect or cognitive elements expressing (communicating) emotion and volition. Affect includes an internal feeling (emotion), an internal drive (will), and a motor component expression (typically speech, but also reflected in thoughts).
An anomaly of the amount or nature of abdominal sounds. Abdominal sounds (bowel sounds) are made by the movement of the intestines as they promote passage of abdominal contents by peristalsis.
Abnormally increased gurgling/rumbling sounds made by the movement of fluid and gas in the intestines.
Complete lack of abdominal sounds as assayed by examination of the abdomen with a stethoscope.
This feature reflects lack of intestinal activity.
Severely decreased cardiac output with evidence of inadequate end-organ perfusion (i.e., tissue hypoxia) in the presence of adequate intravascular volume.
Cardiogenic shock can result from a number of different of cardiac insults, the most common of which is acute myocardial infarction.
A structural anomaly of the adjacent structures (i.e., adnexa) of the eye, defined as the lacrimal apparatus, the extraocular muscles and the eyelids, eyelashes, eyebrows and the conjunctiva.
Any structural anomaly of the heart and blood vessels.
Abnormality of cardiovascular system morphology
Abnormal cardiovascular system morphology
An anomalous (adventitious) sound produced by the breathing process.
A functional anomaly of that portion of the cardiosvascular system that carries deoxygenated blood from the heart to the lungs and returns oxygenated blood back to the heart.
Feeding problem necessitating gastrojejunal tube feeding.
The rationale for gastrojejunal tube feeding is that placing the tip of the tube beyond the ligament of Treitz prevented duodenogastric reflux or gastro-esophageal reflux. Gastrojejunal feeding tubes have since been used in children who are deemed too unfit for antireflux surgery or where fundoplication has failed.
Dilatation of the blood vessels of the conjunctiva leading to a red appearance of the sclera.
An anomaly of the electrical conduction physiology of the heart.
Abnormality of cardiovascular system electrophysiology
A chronic deviation from normal pressure in the systemic arterial system.
Hepatocytes (liver parenchymal cells) exhibit a bloated appearance because of expansion of the cytoplasm by accumulated material.
Resistance of the extensor muscles of the neck to being bent forwards (i.e., impaired neck flexion) as a result of muscle spasm of the extensor muscles of the neck. Nuchal rigidity is not a fixed rigidity. Nuchal rigidity has been used as a bedside test for meningism, although its sensitivity for this purpose has been debated.
Meningism is resistance to neck flexion due to painful spasm of extensor muscles resulting from meningeal irritation. The diagnosis of meningism is made in someone whose symptoms simulate meningitis, but in which no actual inflammation of these membranes is present. Nuchal rigidity can thus be observed in individuals with meningitis or with meningism.
A cough that does not produce phlegm or mucus.
A distortion of the sense of taste, often characterized by the sensation of a metallic taste.
The state in which profound and widespread reduction of effective tissue perfusion leads first to reversible, and then if prolonged, to irreversible cellular injury.
A circumscribed area of pus or necrotic debris in the skin.
An unpleasant sensation of tightness or pressure in the chest.
Any deviation from the normal quantity of secretion of nasal mucus, a thick viscous liquid produced by the mucous membranes of the nose.
Increased discharge of mucus from the nose.
A type of ventricular tachycardia that is characterized by variable QRS complexes within each lead (i.e., QRS complexes may be different from beat to beat).
The course a disease typically takes from its onset, progression in time, and eventual resolution or death of the affected individual.
A functional anomaly of the mouth (which is also known as the oral cavity).
The physiological functions of the mouth include salivary gland secretory function, mastication (chewing) and preparation of food for swallowing.
Any structural anomaly of the mouth, which is also known as the oral cavity.
Abnormal appearance of material expectorated (coughed up) from the respiratory system and that is composed of mucus but may contain other substances such as pus, blood, microorganisms, and fibrin.
An anomaly of the adjacent structures (i.e., adnexa) of the eye, defined as the lacrimal apparatus, the extraocular muscles and the eyelids, eyelashes, eyebrows and the conjunctiva.
A type of infection that is regarded as a sign of a pathological susceptibility to infection. There are five general subtypes. (i) Opportunistic infection, meaning infection by a pathogen that is not normally able to cause infection in a healthy host (e.g., pneumonia by Pneumocystis jirovecii or CMV); (ii) Unusual location (focus) of an infection (e.g., an aspergillus brain abscess); (iii) a protracted course or lack of adequate response to treatment (e.g., chronic rhinosinusitis); (iv) Unusual severity or intensity of an infection; and (v) unusual recurrence of infections.
Intermittent pain, i.e., pain that occurs occasionally and at irregular intervals.
A type of abdominal pain characterized by a feeling of contractions and typically fluctuating in intensity.
An unusual infection classified by the affected body part.
An abnormal level of an analyte measured in the blood.
Abnormal circulating metabolite concentration
Any deviation from the normal concentration of a metabolite in a tissue.
Abnormal tissue metabolite concentration
Abnormal increase in blood pressure. An individual measurement of increased blood pressure does not necessarily imply hypertension. In practical terms, multiple measurements are recommended to diagnose the presence of hypertension.
Involuntary tightening of the abdominal musculature that occurs in response to touching the abdomen to avoid pain. Rigidity can occur in the presence of abdominal inflammation and usually involves only the inflamed area.
A voluntary contraction of the abdominal wall musculature to avoid pain.
Abdominal guarding tends to be generalized over the entire abdomen. In contrast to abdominal rigidity, guarding can often be overcome by having the patient purposely relax the muscles; rigidity cannot be.
Persistent blue color of the skin that surrounds the mouth.
Circumoral cyanosis may be a sign of peripheral or of central cyanosis.
A cutaneous wound is a defined as a disruption of normal anatomic structure and function of the skin that occurs owing to an injury of the skin. Wound healing is a dynamic, interactive process involving soluble mediators, blood cells, extracellularmatrix, and parenchymal cells. Wound healing has three phases: inflammation, tissue formation, and tissue remodeling, that overlap in time.
A cutaneous wound that is proceeding through an orderly and timely reparative process that results in sustained restoration of the anatomic and functional integrity of the skin.
Wound healing accors in multiple overlapping stages, with re=-eipthelialization normally beginning on day one or two. In most clinical settings, closure of acute and chronic wounds is considered the wound healing end point, but wounds can continue to undergo remodeling or tissue maturation for several months or even years.
A cutaneous wound that has failed to proceed through the orderly and timely process to produce an atomic and functional integrity, or proceeded through the repair process without establishing a sustained anatomic and functional result.
An anomaly of the musculoskeletal system, which consists of the bones of the skeleton, muscles, cartilage, tendons, ligaments, joints, and other connective tissue. The musculoskeletal system supports the weight of the body, maintains body position and produces movements of the body or of parts of the body.
Abnormality of the musculoskeletal system
Osmotic diarrhea results from the presence of osmotically active, poorly absorbed solutes in the bowel lumen that inhibit normal water and electrolyte absorption.
Osmotic diarrhea involves an unabsorbed substance that draws water from the plasma into the intestinal lumen along osmotic gradients. Secretory diarrhea results from disordered electrolyte transport and, despite the term, is more commonly caused by decreased absorption rather than net secretion. Inflammatory diseases cause diarrhea with exudative, secretory, or osmotic components.
Passage of an increased number of stools containing mucus, a thick fluid substance secreted by mucous membranes.
Any structural anomaly of a blood vessel (artery, arteriole, capillary, venule, or vein).
A sudden onset of abdominal pain with associated nausea or vomiting. The acute abdomen may be caused by an infection, inflammation, vascular occlusion, or obstruction.
Ischemia is defined as a restriction of arterial blood supply to a tissue associated with insufficient oxygenation to support the metabolis requirements of the tissue. Depending on the involved tissues, clinical manifestations may include pain, pallor, lack of pulse, coldness, paresthesia, and paralysis. Additional associated manifestations include hemodynamic parameters (reduced blood pressure distal to the site of restricted arterial supply) and angiographic evidence of arterial occclusion.
Feeding problem necessitating food and nutrient delivery via a tube.
Passage of excessive amounts of gas and the feeling of abdominal fullness and bloating.
Intermittent abdominal pain with diarrhea and/or constipation.
Acute respiratory distress syndrome (ARDS) is defined as an acute disorder that starts within seven days of the inciting event and is characterized by bilateral lung infiltrates and severe progressive hypoxemia in the absence of any evidence of cardiogenic pulmonary edema. ARDS is defined by the patient's oxygen in arterial blood (PaO2) to the fraction of the oxygen in the inspired air (FiO2). These patients have a PaO2/FiO2 ratio of less than 300.
Acute respiratory distress syndrome (ARDS) is a life-threatening condition of seriously ill patients, characterized by poor oxygenation, pulmonary infiltrates, and acuity of onset. On a microscopic level, the disorder is associated with capillary endothelial injury and diffuse alveolar damage. Once ARDS develops, patients usually have varying degrees of pulmonary artery vasoconstriction and may subsequently develop pulmonary hypertension. ARDS carries a high mortality, and few effective therapeutic modalities exist to combat this condition. ARDS can be observed as a complication of many diseases including pulmonary infection or aspiration, sepsis, trauma, massive transfusion, drowning, drug overdose, fat embolism, inhalation of toxic fumes, and pancreatitis.
Acral areas of erythema with vesicles or pustules. The lesions resemble chilblains and have purpuric areas, affecting hands and feet.
This condition is termed pseudo-chilblain because of the similar appearance of these lesions to chilblains. Pseudochilblains may be observed in persons with COVID-19 without documented exposure to cold or other risk factors for chilblains.
An increase in the amount of airway mucus. This feature may be characterized by frequent or excessive throat clearing (exhalation through tightly constricted laryngopharyngeal tissues accompanied by vibration of the palatoglossal arch and the vocal folds serving to clear mucus from the airway).
If excessive sputum production is manifested by frequent and often involuntary coughing, the HPO term Productive cough should be used.
Pleuritic chest pain is characterized by sudden and intense sharp, stabbing, or burning pain in the chest when inhaling and exhaling.
A feeling of general discomfort, weakness, or lack of health.
The condition of being unable to eat a full meal because of a feeling of fullness (satiety), or or feeling very full after eating only a small amount of food.
Inability to ingest sufficient quantities of nutrition by mouth or by tube-feeding with the corresponding requirement for intravenous administration of nutrition.
Bluish discoloration of one or more regions of the face.
Bluish discoloration of the distal extremities in the absence of cold temperature or stress. Peripheral cyanosis can involve hands, fingertips, or toes, and sometimes circumoral and periorbital areas. Mucous membranes are generally not involved.
Presence of any form of communication (e.g., verbal or non-verbal) that does not align with cultural expectations or developmental level.
The concentration of a metabolite in the liver is above or below the limits of normal.
Murphy's sign is elicited in patients with acute cholecystitis by asking the patient to take in and hold a deep breath while palpating the subcostal region. In practice, Murphy's sign is performed by palpating the subcostal region during inspiration. If pain is elicited and the patient suddenly stops their inspiratory effort, a positive Murphy's sign has been elicited.
Vomiting whereby the vomit has the color of bile, yellowish-green.
Obstipation is the inability to pass either stool or flatus (gas).
Obstipation can be a sign of an acute obstruction of the GI tract, either of the small or large bowel.
Individuals with gastroesophageal reflux disease (GERD) will frequently vomit when coughing for a non-GI reason. Vomiting occurs during these coughing spells because the intrabdominal pressure is high from the coughing and the propensity to reflux results in stomach contents emerging as vomit. This is a historical question that allows a parent to impart information suggesting GERD at an age when it is difficult to obtain a reliable GERD history from the child.
Recurrent abnormal consumption of food, liquids, or objects that could have negative consequences for the individual.
The condition of inability to eat normally treated by placement of a thin tube through the nose into the stomach that is then used to carry food.
A rare condition that is characterized by a complete loss of taste function of the tongue.
A chronic inflammatory bowel disease that includes characteristic ulcers, or open sores, in the colon. The main symptom of active disease is usually constant diarrhea mixed with blood, of gradual onset and intermittent periods of exacerbated symptoms contrasting with periods that are relatively symptom-free. In contrast to Crohn's disease this special form of colitis begins in the distal parts of the rectum, spreads continually upwards and affects only mucose and submucose tissue of the colon.
A chronic granulomatous inflammatory disease of the intestines that may affect any part of the gastrointestinal tract from mouth to anus, causing a wide variety of symptoms. It primarily causes abdominal pain, diarrhea which may be bloody, vomiting, or weight loss, but may also cause complications outside of the gastrointestinal tract such as skin rashes, arthritis, inflammation of the eye, tiredness, and lack of concentration. Crohn's disease is thought to be an autoimmune disease, in which the body's immune system attacks the gastrointestinal tract, causing inflammation.
A chronic inflammatory disease of the large intestine (colon, cecum and rectum).
Immunological states where the immune system produces harmful responses upon reexposure to sensitizing antigens.
Inflammation of the eye, parts of the eye or the periorbital region.
Abnormal cognition is characterized by deficits in thinking, reasoning, or remembering.
An individual with cognitive impairment may experience difficulties in remembering, learning new things, concentrating, or making decisions.
An abnormality of the forebrain, which has as its parts the telencephalon, diencephalon, lateral ventricles and third ventricle.
Death between the age of 16 and 40 years.
A chronic condition in which the pancreas produces little or no insulin. Type I diabetes mellitus is manifested by the sudden onset of severe hyperglycemia with rapid progression to diabetic ketoacidosis unless treated with insulin.
The onset of type 1 diabetes is typically during adolescence, but it can develop at any age.
An anomaly of the cerebral blood vessels.
Abnormality of the cerebral blood vessels
Abnormal eating habits involve excessive or insufficient consumption of food, or any other abnormal pattern of food consumption.
Please note that this HPO term refers to an abnormal eating habit but does not directly refer to an eating disorder. An eating disorder is a psychological disorder characterized by one or more abnormal eating behaviors.
An unpleasant sensation characterized by physical discomfort (such as pricking, throbbing, or aching) localized to the chest.
An anomaly of the lymphatic system, a network of lymphatic vessels that carry a clear fluid called lymph unidirectionally towards either the right lymphatic duct or the thoracic duct, which in turn drain into the right and left subclavian veins respectively.
Systemic inflammatory response to infection.
Emotions are complex psychological states that involve three distinct components: a subjective experience, a physiological response, and a behavioral or expressive response. In an abnormal emotional state, an affected individual shows altered intensity, frequency, or duration of emotional experiences.
When one is assessing whether an individual has an Abnormal emotional state, emphasis should be placed on the observed clinical phenomena and subjective perceptions of the person, without regard to interpretation of the possibility of causality or context.
A small elevation of the skin containing cloudy or purulent material usually consisting of necrotic inflammatory cells.
Any structural anomaly of the bile-secreting organ that is important for detoxification, for fat, carbohydrate, and protein metabolism, and for glycogen storage.
Onset of disease manifestations before adulthood, defined here as before the age of 16 years, but excluding neonatal or congenital onset.
A heterogeneous group of symptoms that are localized in the epigastric region. Typical dyspeptic symptoms include postprandial fullness, early satiation, epigastric pain and epigastric burning, but other upper gastrointestinal symptoms such as nausea, belching or abdominal bloating often occur.
An abnormality of carbon dioxide (CO2) in the arterial blood.
An abnormality of the partial pressure of oxygen in the arterial blood.
The presence of any atypical form of expressive language.
A repeating behavior that is either immediately unproductive or has negative long-term consequences. This includes harmful coping mechanisms such as addictive behavior and failure to control impulses and compulsions.
Repetitive air swallowing and belching and that may result in abdominal distention.
An increase in the gas content inside the bowel associated with distension of the abdomen and hydroaeric noises. The most common symptom of meteorism is a bloated sensation. It may be associated with abdominal discomfort. Some individuals may also complain of a distended stomach and excessive belching and/or passage of flatus.
Abnormal bowel sounds of an unually high frequency.
This finding is characteristic of Ogilvie syndrome.
A directive information that describes how population units will be chosen for sample/data collection in a surveillance activity.
Describe how units have been planned to be sampled Sampling at the primary sampling unit (PSU) level Describe the information used to calculate sample size at the PSU level, e.g. the number of PSU in the population (see section 6 also), (between−herd) design prevalence, desired confidence, desired power, sensitivity, specificity. If recommended parameters from international standards are used, indicate the source of such standards (e.g. OIE) Sampling at the secondary sampling unit (SSU) level Describe the information used to calculate sample size at the SSU level, e.g. the number of SSU in the population (see section 6 also), (within−herd) design prevalence, desired confidence, desired power, sensitivity, specificity.
sampling strategy
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.
2009-03-16: provenance: a term measurement unit was proposed for OBI (OBI_0000176) , edited by Chris Stoeckert and Cristian Cocos, and subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definition of this, different, term.
2009-03-16: review of this term done during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI.
PERSON: Melanie Courtot
objective specification
A directive information entity that describes an intended process endpoint. When part of a plan specification the concretization is realized in a planned process in which the bearer tries to effect the world so that the process endpoint is achieved.
2009-03-16: original definition when imported from OBI read: "objective is an non realizable information entity which can serve as that proper part of a plan towards which the realization of the plan is directed."
2014-03-31: In the example of usage ("In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction") there is a protocol which is the ChIP assay protocol. In addition to being concretized on paper, the protocol can be concretized as a realizable entity, such as a plan that inheres in a person. The objective specification is the part that says that some protein and DNA interactions are identified. This is a specification of a process endpoint: the boundary in the process before which they are not identified and after which they are. During the realization of the plan, the goal is to get to the point of having the interactions, and participants in the realization of the plan try to do that.
Answers the question, why did you do this experiment?
PERSON: Barry Smith
PERSON: Bjoern Peters
PERSON: Jennifer Fostel
goal specification
OBI Plan and Planned Process/Roles Branch
A directive information entity that describes an action the bearer will take.
OBI Plan and Planned Process branch
action specification
datum label
A label is a symbol that is part of some other datum and is used to either partially define the denotation of that datum or to provide a means for identifying the datum as a member of the set of data with the same label
GROUP: IAO
software
Software is a plan specification composed of a series of instructions that can be interpreted by or directly executed by a processing unit.
see sourceforge tracker discussion at http://sourceforge.net/tracker/index.php?func=detail&aid=1958818&group_id=177891&atid=886178
PERSON: Chris Stoeckert
GROUP: OBI
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.
a data item is an information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements.
2/2/2009 Alan and Bjoern discussing FACS run output data. This is a data item because it is about the cell population. Each element records an event and is typically further composed a set of measurment data items that record the fluorescent intensity stimulated by one of the lasers.
2009-03-16: data item deliberatly ambiguous: we merged data set and datum to be one entity, not knowing how to define singular versus plural. So data item is more general than datum.
2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym.
2014-03-31: See discussion at http://odontomachus.wordpress.com/2014/03/30/aboutness-objects-propositions/
JAR: datum -- well, this will be very tricky to define, but maybe some information-like stuff that might be put into a computer and that is meant, by someone, to denote and/or to be interpreted by some process... I would include lists, tables, sentences... I think I might defer to Barry, or to Brian Cantwell Smith JAR: A data item is an approximately justified approximately true approximate belief
data
symbol
An information content entity that is a mark(s) or character(s) used as a conventional representation of another entity.
20091104, MC: this needs work and will most probably change
2014-03-31: We would like to have a deeper analysis of 'mark' and 'sign' in the future (see https://github.com/information-artifact-ontology/IAO/issues/154).
PERSON: James A. Overton
based on Oxford English Dictionary
numeral
A symbol that denotes a number.
information content entity
A generically dependent continuant that is about some thing.
An information entity is an entity that represents information about some other entity. For example, a measurement, a clustered data set.
an information content entity is an entity that is generically dependent on some artifact and stands in relation of aboutness to some entity
2014-03-10: The use of "thing" is intended to be general enough to include universals and configurations (see https://groups.google.com/d/msg/information-ontology/GBxvYZCk1oc/-L6B5fSBBTQJ).
information_content_entity 'is_encoded_in' some digital_entity in obi before split (040907). information_content_entity 'is_encoded_in' some physical_document in obi before split (040907). Previous. An information content entity is a non-realizable information entity that 'is encoded in' some digital or physical entity.
integer numeral
A numeral that denotes an integer
scalar measurement datum
A scalar measurement datum is a measurement datum that is composed of two parts, numerals and a unit label.
2009-03-16: we decided to keep datum singular in scalar measurement datum, as in this case we explicitly refer to the singular form
Would write this as: has_part some 'measurement unit label' and has_part some numeral and has_part exactly 2, except for the fact that this won't let us take advantage of OWL reasoning over the numbers. Instead use has measurment value property to represent the same. Use has measurement unit label (subproperty of has_part) so we can easily say that there is only one of them.
An information content entity whose concretizations indicate to their bearer how to realize them in a process.
2009-03-16: provenance: a term realizable information entity was proposed for OBI (OBI_0000337) , edited by the PlanAndPlannedProcess branch. Original definition was "is the specification of a process that can be concretized and realized by an actor" with alternative term "instruction".It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term.
2013-05-30 Alan Ruttenberg: What differentiates a directive information entity from an information concretization is that it can have concretizations that are either qualities or realizable entities. The concretizations that are realizable entities are created when an individual chooses to take up the direction, i.e. has the intention to (try to) realize it.
8/6/2009 Alan Ruttenberg: Changed label from "information entity about a realizable" after discussions at ICBO
Werner pushed back on calling it realizable information entity as it isn't realizable. However this name isn't right either. An example would be a recipe. The realizable entity would be a plan, but the information entity isn't about the plan, it, once concretized, *is* the plan. -Alan
directive information entity
curation status specification
The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value.
Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting)
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.
2009/10/23 Alan Ruttenberg. The intention is that this term represent collections of like data. So this isn't for, e.g. the whole contents of a cel file, which includes parameters, metadata etc. This is more like java arrays of a certain rather specific type
2014-05-05: Data sets are aggregates and thus must include two or more data items. We have chosen not to add logical axioms to make this restriction.
person:Allyson Lister
person:Chris Stoeckert
data about an ontology part
Data about an ontology part is a data item about a part of an ontology, for example a term
plan specification
A directive information entity with action specifications and objective specifications as parts, and that may be concretized as a realizable entity that, if realized, is realized in a process in which the bearer tries to achieve the objectives by taking the actions specified.
2009-03-16: provenance: a term a plan was proposed for OBI (OBI_0000344) , edited by the PlanAndPlannedProcess branch. Original definition was " a plan is a specification of a process that is realized by an actor to achieve the objective specified as part of the plan". It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term.
2014-03-31: A plan specification can have other parts, such as conditional specifications.
2022-01-16 Updated definition to that proposed by Clint Dowloand, IAO Issue 231.
Alternative previous definition: a plan is a set of instructions that specify how an objective should be achieved
Clint Dowland
2/3/2009 Comment from OBI review. Action specification not well enough specified. Conditional specification not well enough specified. Question whether all plan specifications have objective specifications. Request that IAO either clarify these or change definitions not to use them
measurement datum
A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device.
2/2/2009 is_specified_output of some assay?
A settings datum is a datum that denotes some configuration of an instrument.
2/3/2009 Feedback from OBI This should be a "setting specification". There is a question of whether it is information about a realizable or not. Pro other specification are about realizables. Cons sometimes specifies a quality which is not a realizable.
Alan grouped these in placeholder for the moment. Name by analogy to measurement datum.
setting datum
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.
AR, (IAO call 2009-09-01): a document as a whole is not typically a textual entity, because it has pictures in it - rather there are parts of it that are textual entities. Examples: The title, paragraph 2 sentence 7, etc.
MC, 2009-09-14 (following IAO call 2009-09-01): textual entities live at the FRBR (http://en.wikipedia.org/wiki/Functional_Requirements_for_Bibliographic_Records) manifestation level. Everything is significant: line break, pdf and html versions of same document are different textual entities.
PERSON: Lawrence Hunter
text
document part
An information content entity that is part of a document.
A scalar measurement datum that is the result of measurement of length quality
length measurement datum
A scalar measurement datum that is the result of measurement of mass quality
2009/09/28 Alan Ruttenberg. Fucoidan-use-case
mass measurement datum
A scalar measurement datum that is the result of measuring a temporal interval
Damion Dooley's note: See https://www.w3.org/TR/NOTE-datetime for ISO 8601 time standards
time measurement datum
email address
Alan Ruttenberg 1/3/2012 - Provisional id, see issue at https://github.com/information-artifact-ontology/IAO/issues/130&thanks=130&ts=1325636583
Person:Chris Stoeckart
A symbol that is part of a CRID and that is sufficient to look up a record from the CRID's registry.
PERSON: Bill Hogan
Original proposal from Bjoern, discussions at IAO calls
Damion notes: Subclasses can actually have two components - the identifier, and the agency it is associated with. Under the general concept of "postal code" one can place particular national postal code systems like the US Postal code.
centrally registered identifier symbol
time stamped measurement datum
A software application is software that can be directly executed by some processing unit.
PERSON: Michel Dumontier
software application
notes section
A part of a document containing typically short notes about the document itself and/or the authors. Often the notes section contains subsections related to funding, competing interests, ethical approval, etc.
PERSON: Bill Baumgartner
notes
pregnant woman
A pathogen host role borne by an organism in virtue of the fact that its extended organism contains an infectious agent.
By this definition, vectors and other organisms that may not be infected are bearers of the infectious agent host role.
infectious agent host role
A host role borne by an organism in virtue of the fact that its extended organism contains a pathogen.
Bearing the infectious agent host role implies bearing the pathogen host role, but the reverse is not true. See comment for infectious agent host role.
pathogen host role
An infectious agent host role borne by an organism in virtue of the fact that its extended organism contains an infectious agent, the infectious agent has the infectious disposition towards the host, and the host has no symptoms of the infectious disease caused by the infectious agent.
infectious agent carrier role
A disposition that inheres in a material entity in virtue of the fact that the entity has a part (e.g. a gene product), which itself has a disposition to mitigate damage to the entity.
Examples include the following: CCR5 mutations protect T cells from HIV invasion. A tumor cell's resistance to chemotherapy protects the cell from damage by the drug (although this harms the patient). An insect's resistance to insecticide protects it from the insecticide.
The disposition is realized in a process that mitigates damage to the bearer and has the part as a participant.
protective resistance
A protective resistance that mitigates the damaging effects of a drug.
drug resistance
resistance to drug
A disposition borne by an infectious agent that is the disposition to penetrate the epithelial barriers of an organism of another Species.
invasive disposition
An infectious disease course that begins soon after infection is established and progresses rapidly to severe stages.
acute infectious disease course
A disease course that is the realization of an infectious disease.
infectious disease course
A chronic infectious disease course that does not progress to severe stages for a long period of time.
long-term non-progressing infectious disease course
A process of infectious disease realizations and for which there is a statistically significant increase in the infectious disease incidence of a population.
infectious disease outbreak
infectious disease epidemic
An infection that is clinically abnormal.
infectious disorder
An aggregate of organisms of the same Species.
The organism population may be delineated by spatio-temporal proximity or by demographic criteria such as age.
organism population
An organism population whose members have an infection.
infected population
An organism population in whose members an infectious disease is being realized.
diseased population
An organism population whose members each have an infectious disposition.
infectious agent population
An organism population whose members are not infected with an infectious agent and who lack immunity to the infectious agent.
at-risk population
susceptible population
An organism population whose members are participating in non-parasitic symbiosis with a particular host.
normal resident microflora population
normal resident microbiota population
An organism bearing a host role.
host
An organism bearing an infectious agent host role.
infectious agent host
An organism bearing a pathogen host role.
pathogen host
An organism bearing an infectious agent vector role.
infectious agent vector
A material entity bearing an infectious agent vehicle role.
vehicle of infectious agent
A biological macromolecule produced by a pathogen and that has a virulence factor disposition.
virulence factor
An infection bearing the secondary infection role.
secondary infection
An organism that is host to an infectious agent and has no symptoms of the infectious disease associated with the infectious agent.
asymptomatic host of infectious agent
An organism who is host to an infectious agent and has symptoms of the infectious disease associated with the infectious agent
symptomatic host of infectious agent
A resistance to drug that mitigates the damaging effects of an antibiotic.
antibiotic resistance
A part of an extended organism that itself has as part a population of one or more infectious agents and that (1) exists as a result of processes initiated by members of the infectious agent population and is (2) clinically abnormal in virtue of the presence of this infectious agent population, or (3) has a disposition to bring clinical abnormality to immunocompetent organisms of the same Species as the host (the organism corresponding to the extended organism) through transmission of a member or offspring of a member of the infectious agent population.
The organism corresponding to the extended organism is host to the infectious agents. By this definition, parts of the host can be considered part of the infection.
infection
An infectious disease course that unfolds over a long period of time.
persistent infectious disease course
chronic infectious disease course
An organism population whose members have acquired immunity to an infectious agent.
immune population
An organism population persisting in a site it has colonized.
colony
A colony whose members are infectious agents.
infectious agent colony
A role borne by an organism in virtue of the fact that it's extended organism contains a material entity other than the organism.
A process that is a systemic inflammatory response to infection.
sepsis
An organism that is not infected with an infectious agent and lacks protective immunity to the infectious agent.
domestic animal that bears a food production role.
Livestock refers to one or more domesticated animals raised in an agricultural setting to produce commodities such as food, fiber and labor. The term "livestock" as used in this article does not include poultry or farmed fish; however the inclusion of these, especially poultry, within the meaning of "livestock" is common. (http://en.wikipedia.org/wiki/Livestock)
data source
Database that originally provided the interaction record for exchange purposes.
Damion Dooley's note: GenEpiO is using members of this class for the first part of the hasDbXref relation. This is where we are keeping the mapping between a code and its source database. Depending on its context, hasDbXref annotations may point directly to metadata field names in the target database, and may be annotated with additional information that guides any additional specifications that impact on data conversion of these fields.
source database
The manner, procedure or technique by which a morphological or physiological state or property in a single individual or sample or a group of individuals or samples is assessed and a quantitative or qualitative value assigned.
A postmortem examination of a body to determine the cause of death or the character and extent of changes produced by disease.
tissue collection (necropsy)
A postmortem examination of the body of an animal to determine the cause of death or the character and extent of changes produced by disease.
A postmortem examination of the body of an animal to determine the cause of death or the character and extent of changes produced by disease. [database_cross_reference: Merriam-Webster:Merriam-Websters_Online_Dictionary--11th_Ed]
necropsy
A disease is a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism.
A disease involving the lower respiratory tract.
disease or disorder of lower respiratory tract
lower respiratory tract disease or disorder
A malignant neoplasm involving the respiratory system
malignant neoplasm of respiratory system
A monogenic disease that is has material basis in a mutation in a single gene on one of the non-sex chromosomes.
A hypersensitivity reaction type II disease that involves the peripheral nervous system.
peripheral nervous system autoimmune disease
peripheral nervous system hypersensitivity reaction type II disease
autoimmune disorder of peripheral nervous system
Life-threatening respiratory failure that develops rapidly. Causes include injury, sepsis, drug overdose, and pancreatitis. It manifests with dyspnea and cyanosis and may lead to cardiovascular shock.
A disorder characterized by behavioral and/or psychological abnormalities, often accompanied by physical symptoms. The symptoms may cause clinically significant distress or impairment in social and occupational areas of functioning. Representative examples include anxiety disorders, cognitive disorders, mood disorders and schizophrenia.
A non-neoplastic or neoplastic disorder that affects the pleura. Representative examples include pleural infection, pleural mesothelioma, and pleural solitary fibrous tumor.
The use of alcoholic beverages to excess, either on individual occasions ("binge drinking") or as a regular practice.
Acute or chronic inflammation of one or more lymph nodes. It is usually caused by an infectious process.
Abnormal presence of air in the pleural cavity.
A disease involving the musculoskeletal system.
disease or disorder of musculoskeletal system
musculoskeletal system disease or disorder
A group of signs, symptoms, and clinicopathological characteristics that may or may not have a genetic basis and collectively define an abnormal condition.
syndrome associated with disease or disorder
A category of psychiatric disorders which include disorders related to the taking of a drug of abuse (including alcohol, prescribed medications and recreational drugs).
A non-neoplastic or neoplastic disorder that affects the liver, bile ducts, and gallbladder. Representative examples of non-neoplastic disorders include hepatitis, cirrhosis, cholangitis, and cholecystitis. Representative examples of neoplastic disorders include hepatocellular adenoma, hepatocellular carcinoma, and cholangiocarcinoma.
disease or disorder of hepatobiliary system
hepatobiliary system disease or disorder
A primary or metastatic malignant neoplasm involving any part of the digestive system.
malignant gastrointestinal system neoplasm
A disease involving the central nervous system.
central nervous system disease or disorder
disease or disorder of central nervous system
A disorder characterized by the degeneration of the nervous system due to autoimmunity. Representative examples include multiple sclerosis, Guillain-Barre syndrome, and myasthenia gravis.
autoimmune disorders of the nervous system
nervous system hypersensitivity reaction type II disease
autoimmune disorder of the nervous system
A primary or metastatic malignant neoplasm affecting the tissues of the thorax.
malignant neoplasm of thoracic segment of trunk
malignant thoracic segment of trunk neoplasm
Vasculitis affecting the blood vessels of the brain and/or spinal cord.
A disease involving the peripheral nervous system.
PNS (peripheral nervous system) diseases
disease or disorder of peripheral nervous system
disorder of the peripheral nervous system
peripheral nervous system disease or disorder
A broad classification of disorders that affect the cell-mediated aspect of the immune response. Circulating numbers of T lymphocytes are decreased or ineffective.
A disease that is caused by genetic modifications where those modifications are inherited from a parent's genome.
Usage note: this is intended only for diseases with an inherited genetic etiology. Somatic genetic mutations are excluded. Some ontologies use the term 'genetic disease' in the sense of inherited disorders only, we are here careful to distinguish.
A disease involving the connective tissue.
disease or disorder of connective tissue
Following clinical usage of the term 'connective tissue disorder' this grouping excludes some diseases affecting tissues classically considered to be connective tissue, such as bone.
An imbalanced nutritional status resulting from excessive intake of nutrients. Generally, overnutrition generates an energy imbalance between food consumption and energy expenditure leading to disorders such as obesity.
A disease or disorder that involves the digestive system.
An autoimmune, connective tissue chronic inflammatory disorder affecting the skin, joints, kidneys, lungs, heart, and the peripheral blood cells. It is more commonly seen in women than men. Variants include discoid and systemic lupus erythematosus.
Necrosis of the myocardium, as a result of interruption of the blood supply to the area. It is characterized by a severe and rapid onset of symptoms that may include chest pain, often radiating to the left arm and left side of the neck, dyspnea, sweating, and palpitations.
A tumor composed of atypical neoplastic, often pleomorphic cells that invade other tissues. Malignant neoplasms often metastasize to distant anatomic sites and may recur after excision. The most common malignant neoplasms are carcinomas (adenocarcinomas or squamous cell carcinomas), Hodgkin and non-Hodgkin lymphomas, leukemias, melanomas, and sarcomas.
A disease involving the cardiovascular system.
cardiovascular system disease or disorder
disease of subdivision of hemolymphoid system
disease or disorder of cardiovascular system
A non-neoplastic or neoplastic disorder that affects the small or large intestine.
A brain disorder characterized by episodes of abnormally increased neuronal discharge resulting in transient episodes of sensory or motor neurological dysfunction, or psychic dysfunction. These episodes may or may not be associated with loss of consciousness or convulsions.
A disease involving the reproductive system.
disease or disorder of reproductive system
A disorder resulting from an abnormality in the immune system.
Gross necrosis of the myocardium, as a result of interruption of the blood supply to the area, as in coronary thrombosis.
A benign or malignant tissue growth resulting from uncontrolled cell proliferation. Benign neoplastic cells resemble normal cells without exhibiting significant cytologic atypia, while malignant cells exhibit overt signs such as dysplastic features, atypical mitotic figures, necrosis, nuclear pleomorphism, and anaplasia. Representative examples of benign neoplasms include papillomas, cystadenomas, and lipomas; malignant neoplasms include carcinomas, sarcomas, lymphomas, and leukemias.
A non-neoplastic or neoplastic disorder that affects the brain, spinal cord, or peripheral nerves.
'psychiatric disorder' is not classified as a 'nervous system disorder' in Mondo (though it is often as such): the hallmarks of psychiatric disorders are based in behavior and emotional state, and the relation with nervous system malfunction or damage is not always clearly determined.
A non-neoplastic or neoplastic disorder that affects the respiratory system. Representative examples include pneumonia, chronic obstructive pulmonary disease, pulmonary failure, lung adenoma, lung carcinoma, and tracheal carcinoma.
disease or disorder of respiratory system
An infection caused by the human immunodeficiency virus.
Human immunodeficiency virus caused disease or disorder
Human immunodeficiency virus disease or disorder
Human immunodeficiency virus infectious disease
An acute infectious disorder that is caused by gram positive or gram negative bacteria; representative examples include pneumococcal, streptococcal, salmonella, and meningeal infections.
Any condition related to a disturbance between proper intake and utilization of nourishment.
An excess of body weight, normally defined as an individual with a body mass index greater than 35 or a body weight greater than one hundred percent of ideal body weight.
A disease involving the endocrine system.
liver and intrahepatic bile duct disorder
A spectrum of small and large bowel inflammatory diseases of unknown etiology. It includes Crohn's disease, ulcerative colitis, and colitis of indeterminate type.
A disease involving the heart and/or pericardium.
A benign or malignant neoplasm that affects the colon or rectum. Representative examples of benign neoplasms include lipoma and leiomyoma. Representative examples of malignant neoplasms include carcinoma, lymphoma, and sarcoma. Colorectal adenomas always exhibit epithelial dysplasia and are considered premalignant neoplasms.
A general term used to describe any disease affecting blood vessels]. It includes vascular abnormalities caused by degenerative, metabolic and inflammatory conditions, embolic diseases, coagulative disorders, and functional disorders such as posteri or reversible encephalopathy syndrome.
The etiology of vasculopathy is generally unknown and the condition is frequently not pathologically proven. Vasculitis, on the other hand, is a more specific term and is defined as inflammation of the wall of a blood vessel. However, the term vasculopathy is also used for “vasculitis” that has not been pathologically established.
A medical condition characterized by long-term fatigue and other symptoms that limit a person's ability to carry out ordinary daily activities.
chronic fatigue immune dysfunction syndrome
myalgic encephalomeyelitis/chronic fatigue syndrome
A disorder directly resulting from the presence and activity of a microbial, viral, or parasitic agent in humans. It can be transmitted by direct or indirect contact.
Replaces 'infection' in disease hierarchy. OBI imported term infection is moved to pathologic process. This class is a container class for infectious diseases, not the process of infection itself.
Inflammatory and degenerative diseases of connective tissue structures, such as arthritis.
This is an umbrella term encompassing conditions causing chronic, often intermittent pain affecting the joints and/or connective tissue
A disease affecting the brain or part of the brain.
Editor note: NCIT has different classes for brain disease and encephalopathy
A disease involving the hematopoietic system.
disease of the blood and blood-forming organs
disease or disorder of haematopoietic system
disease or disorder of hematopoietic system
haematopoietic system disease or disorder
hematopoietic system disease or disorder
A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma.
colorectal cancer with chromosomal instability, somatic
colorectal cancer, autosomal dominant, somatic mutation
colorectal cancer, susceptibility to, autosomal dominant, somatic mutation
malignant neoplasm of the large intestine
Editor note: some sources make distinct classes for colorectal vs large intestine. We follow NCIT and make these equivalent
A malignant neoplasm involving the intestine
A disease involving the lymphatic part of lymphoid system.
disease of lymphatic part of lymphoid system
disease or disorder of lymphatic part of lymphoid system
disorder of lymphatic part of lymphoid system
lymphatic part of lymphoid system disease
lymphatic part of lymphoid system disease or disorder
Editor note: check alignment to anatomy, consider lymphoid system disease
Infections with viruses of the order nidovirales. The concept includes arterivirus infections and coronaviridae infections.
disease or disorder, autosomal recessive
Progressive and life-threatening pulmonary distress in the absence of an underlying pulmonary condition, usually following major trauma or surgery. Cases of neonatal respiratory distress syndrome are not included in this definition.
This disease can present as a mild ARDS (PaO2/FiO2 of 201–300 mmHg) moderate ARDS (PaO2/FiO2 of 101–200 mmHg) and severe ARDS (PaO2/FiO2 ≤100 mmHg). [PMID:30872586]
A disorder resulting from loss of function or tissue destruction of an organ or multiple organs, arising from humoral or cellular immune responses of the individual to their own tissue constituents. It may be systemic (e.g., systemic lupus erythematosus), or organ specific, (e.g., thyroiditis).
A primary or metastatic malignant neoplasm involving the breast. The vast majority of cases are carcinomas arising from the breast parenchyma or the nipple. Malignant breast neoplasms occur more frequently in females than in males.
A malignant neoplasm involving the lung.
adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation
lung cancer, protection against, autosomal dominant, somatic mutation
lung cancer, resistance to, autosomal dominant, somatic mutation
lung cancer, susceptibility to, autosomal dominant, somatic mutation
nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation
nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation
Cystic fibrosis (CF) is a genetic disorder characterized by the production of sweat with a high salt content and mucus secretions with an abnormal viscosity.
cystic fibrosis lung disease, modifier of
pseudomonas aeruginosa, susceptibility to chronic infection by, in cystic fibrosis
Infant acute respiratory distress syndrome is a lung disorder that affects premature infants caused by developmental insufficiency of surfactant production and structural immaturity of the lungs. The symptoms usually appear shortly after birth and may include tachypnea, tachycardia, chest wall retractions (recession), expiratory grunting, nasal flaring and cyanosis during breathing efforts.
respiratory distress syndrome in premature infants
A disorder resulting from inadequate blood flow in the vessels that supply the brain. Representative examples include cerebrovascular ischemia, cerebral embolism, and cerebral infarction.
A disorder involving an excessive amount of body fat.
Obesity is a complex disease that may involve multiple environmental and genetic causes. See the subclass monogenic disease for genetic subtypes
Sickle cell anemias are chronic hemolytic diseases that may induce three types of acute accidents: severe anemia, severe bacterial infections, and ischemic vasoocclusive accidents (VOA) caused by sickle-shaped red blood cells obstructing small blood vessels and capillaries. Many diverse complications can occur.
A syndrome resulting from the acquired deficiency of cellular immunity caused by the human immunodeficiency virus (HIV). It is characterized by the reduction of the Helper T-lymphocytes in the peripheral blood and the lymph nodes. Symptoms include generalized lymphadenopathy, fever, weight loss, and chronic diarrhea. Patients with AIDS are especially susceptible to opportunistic infections (usually pneumocystis carinii pneumonia, cytomegalovirus (CMV) infections, tuberculosis, candida infections, and cryptococcosis), and the development of malignant neoplasms (usually non-Hodgkin lymphoma and Kaposi sarcoma). The human immunodeficiency virus is transmitted through sexual contact, sharing of contaminated needles, or transfusion of contaminated blood.
AIDS, acquired immunodeficiency syndrome
acquired immunodeficiency syndrome, AIDS
Kawasaki disease (KD) is a febrile, systemic, self-limiting vasculitis affecting children and characterized by inflammation in the medium sized vessels associated with coronary arterial aneurysms (CAA) that may be life threatening when untreated. KD is the most common cause of acquired heart disease in children in developed countries and is a risk factor for ischemic heart disease in adulthood.
acute febrile mucocutaneous lymph node syndrome
acute febrile mucocutaneous lymph node syndrome [MCLS]
Bleeding into one or both cerebral hemispheres including the basal ganglia and the cerebral cortex. It is often associated with hypertension and craniocerebral trauma.
A condition of lung damage that is characterized by bilateral pulmonary infiltrates (pulmonary edema) rich in neutrophils, and in the absence of clinical heart failure. This can represent a spectrum of pulmonary lesions, endothelial and epithelial, due to numerous factors (physical, chemical, or biological).
A diverse group of lung diseases that affect the lung parenchyma. They are characterized by an initial inflammation of pulmonary alveoli that extends to the interstitium and beyond leading to diffuse pulmonary fibrosis. Interstitial lung diseases are classified by their etiology (known or unknown causes), and radiological-pathological features.
A spectrum of rare post-infectious neuropathies that usually occur in otherwise healthy patients. GBS is clinically heterogeneous and encompasses acute inflammatory demyelinating polyradiculoneuropathy (AIDP), acute motor axonal neuropathy (AMAN) and acute motor-sensory axonal neuropathy (AMSAN), Miller-Fisher syndrome (MFS) and some other regional variants.
A interstitial lung disease that occurs during childhood.
The terms chILD or chILD syndrome (not preferred) have been coined to memorize easily and to identify a phenotype that requires prompt and expert evaluation.
interstitial lung disease specific to childhood
primary interstitial lung disease specific to childhood
A chronic, recurrent infection caused by the bacterium Mycobacterium tuberculosis. Tuberculosis (TB) may affect almost any tissue or organ of the body with the lungs being the most common site of infection. The clinical stages of TB are primary or initial infection, latent or dormant infection, and recrudescent or adult-type TB. Ninety to 95% of primary TB infections may go unrecognized. Histopathologically, tissue lesions consist of granulomas which usually undergo central caseation necrosis. Local symptoms of TB vary according to the part affected; acute symptoms include hectic fever, sweats, and emaciation; serious complications include granulomatous erosion of pulmonary bronchi associated with hemoptysis. If untreated, progressive TB may be associated with a high degree of mortality. This infection is frequently observed in immunocompromised individuals with AIDS or a history of illicit IV drug use.
Vasculitis represents a clinically heterogenous group of diseases of multifactorial etiology characterized by inflammation of either large-sized vessels (large-vessel vasculitis, e.g. Giant-cell arteritis and Takayasu arteritis), medium-sized vessels (medium-vessel vasculitis e.g. polyarteritis nodosa and Kawasaki disease), or small-sized vessels (small-vessel vasculitis, e.g. granulomatosis with polyangiitis, microscopic polyangiitis, immunoglobulin A vasculitis, and cutaneous leukocytoclastic angiitis). Vasculitis occurs at any age, may be acute or chronic, and manifests with general symptoms such as fever, weight loss and fatigue, as well as more specific clinical signs depending on the type of vessels and organs affected. The degree of severity is variable, ranging from life or sight threatening disease (e.g. Behcet disease) to relatively minor skin disease.
An inherited disorder characterized by structural alterations of a globin chain within the hemoglobin molecule.
Any disease that impairs the functioning of the muscles, either directly, being pathologies of the voluntary muscle, or indirectly, being pathologies of nerves or neuromuscular junctions
A infectious disease that involves the nervous system.
infectious disorder of the nervous system
Infection due to organisms from the genus Mycobacteria.
A benign or malignant, primary or metastatic neoplasm involving the respiratory tract.
Disease having a short and relatively severe course.
Infectious disease causes by viruses in the subfamily Orthocoronavirinae (coronaviruses). In humans, coronaviruses cause respiratory tract infections that can be mild, such as some cases of the common cold (among other possible causes, predominantly rhinoviruses), and others that can be lethal, such as SARS, MERS, and COVID-19.
Disease in which there is a deficiency or defect in the mechanisms of immunity, either cellular or humoral.
A benign or malignant neoplasm of the breast parenchyma. It can originate from the ducts, lobules or the breast adipose tissue. Breast neoplasms are much more common in females than males.
The significant impairment of gas exchange within the lungs resulting in hypoxia, hypercarbia, or both, to the extent that organ tissue perfusion is severely compromised. Causes include chronic obstructive pulmonary disease, asthma, emphysema, acute respiratory distress syndrome, pneumonia, pulmonary edema, pneumothorax, and congestive heart failure. Treatment requires intubation and mechanical ventilation until the time the lungs recover sufficient function.
A benign or malignant, primary or metastatic neoplasm involving the lungs. Representative examples of benign neoplasms include adenoma, papilloma, chondroma, and endobronchial lipoma. Representative examples of malignant neoplasms include carcinoma, carcinoid tumor, sarcoma, and lymphoma.
A benign or malignant neoplasm involving the small or large intestine.
A disease involving a pathogenic inflammatory response in the anatomical structure.
Damage inflicted on the body as the direct or indirect result of an external force, with or without disruption of structural continuity.
A neoplasm (disease) that involves the digestive system.
A neoplasm (disease) that involves the thoracic segment of trunk.
thoracic segment of trunk neoplasm (disease)
A disorder that follows infection but is distinct from the infection itself and its usual manifestations.
A post-infectious disorder that follows viral infection but is distinct from the viral infection itself and its usual manifestations.
A Disease due to or propagated by sexual contact.
Viral diseases which are potentially transmitted or propagated by sexual conduct.
Disorders related to or resulting from abuse or mis-use of alcohol.
Virus diseases caused by the Lentivirus genus. They are multi-organ diseases characterized by long incubation periods and persistent infection.
Either an isolated neoplasm or a syndrome with neoplasm as a major feature.
An infectious process that affects the brain and/or spinal cord. Representative examples include encephalitis, poliomyelitis, arachnoiditis, and meningitis.
central nervous system infectious disease
central nervous system infectious disorder
infectious disease of central nervous system
A disease that involves the large intestine.
A disorder that affects the muscle tissue of the heart. Representative examples include myocardial infarction, myocarditis, and cardiomyopathy.
A malignant tumor that has spread from its original (primary) site of growth to another site close to or distant from the primary site.
Note that we currently treat secondary neoplasms as being neoplastic diseases that are derived from neoplasm; classes such as 'neoplasm', 'carcinoma' are implicitly primary. This may change in future.
A malignant neoplasm that arises from a pre-existing lower grade lesion, or as a result of a primary lesion that has spread to secondary sites, or due to a complication of a cancer treatment.
A neoplasm that arises from a pre-existing lower grade lesion, or as a result of a primary lesion that has spread to secondary sites, or due to a complication of a cancer treatment.
A tumor that has spread from its original (primary) site of growth to another site, close to or distant from the primary site. Metastasis is characteristic of advanced malignancies, but in rare instances can be seen in neoplasms lacking malignant morphology.
multisystem inflammatory syndrome in children and adults
A very serious type of heart attack during which one of the heart’s major arteries (one of the arteries that supplies oxygen and nutrient-rich blood to the heart muscle) is blocked. ST-segment elevation is an abnormality detected on the 12-lead ECG.
ST segment elevation myocardial infarction
acute-ST segment elevation myocardial infarction
A disorder of the nervous system related to a vascular etiology.
A disease or disorder that involves the erythrocyte.
A disease or disorder that involves the lymphoid system.
Any disorder that features disrupted cell proliferation. Includes hyperplasia, neoplastic syndrome and isolated neoplasm diseases as well as precancerous conditions.
A disease caused by infection with severe acute respiratory syndrome coronavirus 2.
severe acute respiratory syndrome coronavirus 2 infectious disease
Acute respiratory distress syndromet that occurs in pediatric patients and includes findings of new infiltrates (unilateral or bilateral) consistent with acute parenchymal disease, edema not fully explained by fluid overload or cardiac failure, and may present as new acute lung disease in setting of chronic lung disease and/or heart disease, and perinatal lung disease is excluded.
pediatric acute respiratory distress syndrome
A inflammatory syndrome in children infected by the SARS-CoV-2 with similarities to Kawasaki disease. Clinical manifestations range from fever and inflammation to myocardial injury, shock, and development of coronary artery aneurysms.
COVID-19 -related paediatric inflammatory multisystem syndrome
COVID-19 -related pediatric inflammatory multisystem syndrome
COVID-19 associated multisystem inflammatory syndrome in children
multisystem inflammatory syndrome in children
multisystem inflammatory syndrome in children associated with COVID-19
multisystem inflammatory syndrome in children associated with coronavirus disease 2019
paediatric inflammatory multisystem syndrome
paediatric inflammatory multisystem syndrome temporally associated with SARS-CoV-2
paediatric inflammatory multisystem syndrome: temporally associated with SARS-CoV-2
paediatric multi-system inflammatory syndrome potentially associated with COVID-19
paediatric multisystem inflammatory syndrome
pediatric inflammatory multisystem syndrome
pediatric inflammatory multisystem syndrome temporally associated with SARS-CoV-2
pediatric inflammatory multisystem syndrome: temporally associated with SARS-CoV-2
pediatric multi-system inflammatory syndrome potentially associated with COVID-19
pediatric multisystem inflammatory syndrome
The clinical presentation of MIS-C includes fever, severe illness, and the involvement of two or more organ systems, in combination with laboratory evidence of inflammation and laboratory or epidemiologic evidence of SARS-CoV-2 infection. Some features of MIS-C resemble Kawasaki Disease, toxic shock syndrome, and secondary hemophagocytic lymphohistiocytosis/macrophage activation syndrome.
COVID-19–associated multisystem inflammatory syndrome in children
A liver disease characterized by the liver losing or has lost all of its function.
A chronic disease triggered by acute COVID-19 infection that is characterized by persistent symptoms following the acute phase of the SARS-CoV-2 infection, which may include fatigue, coughing, dyspnea, clouding of mentation, sleep disturbances, exercise intolerance and autonomic symptoms including tachycardia upon mild exercise or standing, night sweats, temperature dysregulation, gastroparesis, constipation or loose stools, and peripheral vasoconstriction.
post-acute sequelae of SARS-CoV-2 infection
A inflammatory syndrome in adults infected by the SARS-CoV-2 with severe illness requiring hospitalization in a person aged ≥21 years; a positive test result for current or previous SARS-CoV-2 infection (nucleic acid, antigen, or antibody) during admission or in the previous 12 weeks; severe dysfunction of one or more extrapulmonary organ systems (e.g., hypotension or shock, cardiac dysfunction, arterial or venous thrombosis or thromboembolism, or acute liver injury); laboratory evidence of severe inflammation (e.g., elevated CRP, ferritin, D-dimer, or interleukin-6); and absence of severe respiratory illness (to exclude patients in which inflammation and organ dysfunction might be attributable simply to tissue hypoxia).
COVID-19–associated multisystem inflammatory syndrome in adults
A SARS-CoV-2-related disease that is caused by infection by SARS-CoV-2, and manifests after the original primary infection.
The initial viral infectious disase that causes illness.
A heterogeneous group of genetic conditions with Mendelian (autosomal dominant, recessive, or X-linked) or chromosomal etiology characterized by abnormalities in the brain, spinal cord, nerves, or muscles.
A syndrome that occurs after therapeutic infusion of antibodies into the blood and is characterized by nausea, headache, tachycardia, hypotension, rash, and shortness of breath. It is caused by the release of cytokines from the cells that are targeted by the antibodies. Most patients experience a mild to moderate reaction; however, the reaction may be severe and life-threatening.
A condition beginning in the first day of life that results from inadequate surfactant production, causing increased work of breathing and impaired gas exchange.
RDS, respiratory distress syndrome Of newborns
infant acute respiratory distress syndrome
newborns (RDS), respiratory distress syndrome Of
pulmonary hypoperfusion syndrome of newborn
respiratory distress syndrome Of newborns
respiratory distress syndrome Of newborns (RDS)
respiratory distress syndrome in the newborn
respiratory distress syndrome of newborn
syndrome Of newborns (RDS), respiratory distress
Phenotypic observation of the presence or absence of a pathological entity.
Lesions leading to or consequent on failure of, or atypical movement of, blood throughout the body.
A syndrome consequent to uncontrolled activation of blood clotting factors leading to disseminated platelet lysis, and fibrin deposition, ultimately leading to bleeding and necrosis as a consequence of inhibition of fibrin polymerisation by degradation products.
Diagnosed by microthrombi in many organs.
Anatomically located instance of pathological response or entity.
the observable morphological, physiological, behavioral and other characteristics of mammalian organisms that are manifested through development and lifespan
any anomaly in the cessation of function at the cellular level
pathologic death of cells, usually from irreversible damage
deviation from the normal function of the immune system
immune system: response/ function abnormalities
aberrant reaction of the microcirculation characterized by movement of fluid and leukocytes from the blood into extravascular tissues
greater than expected response to injury, infection, or insult
local accumulation of fluid, plasma proteins, and leukocytes in the proximal portion of the respiratory passages
inflammation of the mucous membrane of the nose
any functional anomaly of the pulmonary system; inability or reduced ability to intake and exchange oxygen and carbon dioxide with the environment
respiratory system physiology abnormalities
respiratory system: respiratory distress/failure/functional anomalies
local accumulation of fluid, plasma proteins, and leukocytes in the respiratory system
the observable morphological and physiological characteristics of the basic structural and functional unit of all mammalian organisms that are manifested through development and lifespan
the observable morphological and physiological characteristics of the mammalian system that protects the body from foreign substances, cells, and tissues by producing the immune response and that includes especially the thymus, spleen, lymphoid tissue, lymphocytes including the B cells and T cells, and antibodies that are manifested through development and lifespan
the observable morphological and physiological characteristics of the mammalian system responsible for the exchange of oxygen and carbon dioxide with the environment that are manifested through development and lifespan
any functional anomaly of the vital processes of the cell
necrosis or death of soft tissue due to lack of blood flow resulting from injury, infection or other conditions that affect blood circulation
a form of coagulative necrosis that develops in ischemic tissue, where the blood supply is inadequate to keep tissue viable, in the absence of superimposed microbial infection; can be due to peripheral artery disease or acute limb ischemia; the affected body part is dry, shrunken, and dark reddish-black and can fall off (autoamputate) if not removed surgically
The term dry is used only when referring to a limb or to the gut; in other locations, this same type of necrosis is called an infarction, such as myocardial infarction
"The action, reaction, or performance of an organism in response to external or internal stimuli." [GO:GO\:0007610]
Behavior related to the intake of substances.
consumption behavior
Consumption behavior that involves burning a substance and inhaling the particulate and gas suspension emitted.
smoking behavior
Salmonella enterica subsp. enterica serovar Newport
Mus musculus domesticus x M. m. molossinus
Salmonella enterica subsp. enterica serovar Hadar
Salmonella enterica subsp. enterica serovar Enteritidis
Salmonella enterica subsp. enterica serovar Stanley
The Archaea constitute a domain and kingdom of single-celled microorganisms
Severe acute respiratory syndrome coronavirus 2
Salmonella enterica subsp. enterica serovar Javiana
Mus musculus musculus x M. m. domesticus
Mus musculus musculus x Mus musculus castaneus
Salmonella enterica subsp. enterica serovar Virchow
Salmonella enterica subsp. enterica serovar Infantis
Salmonella enterica subsp. enterica serovar Heidelberg
clam, squid, octopus
Severe acute respiratory syndrome-related coronavirus
Salmonella enterica subsp. enterica serovar Typhimurium
whales, hippos, ruminants, pigs, camels etc.
subspecies
A method to determine microbial susceptibility to antibiotics wherein bacteria are inoculated onto agar plates and the antimicrobial agent diffused onto the agar plate from a filter paper disk. An approximate, but not exact, MIC is determined by the diameter of growth inhibition zones. This method has been found to have good correlation between in-vivo data and in-vitro data.
A method to determine microbial susceptibility to antibiotics in which a plastic strip impregnated with the antibiotic of interest is placed on an agar plate that has been inoculated with bacteria. The antibiotic diffuses from the strip producing a concentration gradient of drug on the agar. The point at which the elliptical shaped area of growth inhibition meets the strip is the minimum inhibitory concentration of the drug of interest.
A method to determine the minimum inhibitory concentration (MIC) of antibiotics in which growth media is pipetted into a multi-well plate. Each well contains a known concentration of drug which is inoculated with a known quantity of bacteria. The plate is incubated for a specified period of time and each well is assessed for bacterial cell growth. The drug concentration in the first well showing no growth is known as the MIC for that antibiotic. Minimum 2 mL total broth dilution volume.
A person that is associated with another person in some manner or action.
An individual who provides support to a pregnant individual.
A person with whom one has had sexual relations.
A statement that defines conventions, guidelines, characteristics or methods for consistent data handling to facilitate exchange or processing of the data. This set of criteria are reviewed by and agreed upon by the user community or a governing body before they are released and adopted for use.
A vial used to store specimens in a cryopreservative at very low temperatures.
The RNA component of the small (30S) subunit of prokaryotic ribosomes.
Damion Dooley's note: this term was mistakenly placed in a list of GenEpiO diagnostic tests; in fact it references a material entity
The fluid which runs through a dialysis machine and captures, for discard or analysis, the excess water and waste from the blood stream through diffusion and ultrafiltration.
An indicator as to whether the female subject is pregnant during the study period.
Unexpected death of an infant less than one year of age, whose cause of death is not immediately obvious prior to investigation.
Unexpected death of a child over one year of age, which remains unexplained when all known and possible causes of death have been ruled out.
Death resulting from conditions or complications which are unique to pregnancy and occur during the antepartum, intrapartum, or postpartum period.
Death resulting from previously existing disease or a disease developing during pregnancy which was not associated with gestation, but which was aggravated by the unique physiologic changes of pregnancy. Examples of indirect deaths include those associated with epilepsy, diabetes, cardiac disease and hormone-dependent malignancies.
The death of a woman while pregnant or within 42 days of the end of the pregnancy, irrespective of the duration or anatomic site of the pregnancy, due to any cause related to or aggravated by the pregnancy or its management, but not from accidental or incidental causes.
A test tube, capillary tube, or other tube designed for the collection of blood.
A blood collection tube that contains a vacuum, allowing it to draw blood through a needle to fill the tube.
Evacuated Blood Specimen Collection Tube
A person who shares a house with another person.
Hepatic necrosis, inflammation, or scarring due to any cause that persists for more than 6 months. Manifestations may include signs and symptoms of cholestasis, portal hypertension, and/or abnormal liver function tests.
An identifying designation assigned to an individual that corresponds with their function.
A title that describes the function of a designated group, governing body, or institution.
A fetus of 16-20 weeks gestational age that shows signs of life at birth but dies after delivery.
Post-Natal Death at 16-20 Weeks Gestation
An age group comprised of infants delivered after full 37 weeks gestation whose 5 minute Apgar score was above 7, has no major congenital anomalies and was discharged home with mother without any additional diagnoses except for physiologic hyperbilirubinemia.
An age group comprised of healthy newborns whose only diagnoses are those related to prematurity.
An age group comprised of infants greater than or equal to 34 weeks, 0 days and less than 37 weeks, 0 days gestational age.
An age group comprised of infants less than 28 weeks, 0 days gestational age.
An age group comprised of infants greater than or equal to 42 weeks, 0 days gestational age.
healthy
Having no significant health-related issues.
A laboratory test to determine the concentration of a substance that will inhibit a biological or biochemical function, such as microorganism growth or enzymatic activity.
Irreversible absence of cortical and brain stem functioning.
Interventions or procedures not otherwise categorized.
Death of a live newborn during the first 7 days of life.
Death of live newborn between 7and 27 days after birth.
Symptoms, physical examination results, and/or laboratory test results related to the female reproductive system.
Fetal or infant death during the period of time that includes the antepartum, intrapartum, and neonatal stages.
An age group comprised of infants greater than 28 weeks, 0 days and less than 34 weeks, 0 days.
Death of a live newborn during the first 24 hours of life
Death between 28 days and 1 year of life.
A response indicating that a person has lost their ability for fine movement: cannot button, write, eat, etc., or minor loss of sensitivity.
A human biological structure, fluid or other substance; excludes single molecular entities.
Anatomic Structure, System, or Substance
A bacterial toxin produced by Shigella dysenteriae and by some strains of E. coli that inhibits protein synthesis by blocking the interaction of ribosomal RNA with peptide elongation factors. The non-catalytic beta subunit of Shiga toxin may be useful as a fusion vector for induction of antigen-specific cytotoxic T lymphocyte responses.
The physical sexual characteristics of the neonate at birth.
A death of the embryo occurring inside the uterus.
A death of the fetus occurring inside the uterus.
A general term comprising tissue that is not hardened or calcified; including muscle, fat, blood vessels, nerves, tendons, ligaments and fascia.
Death due to complications following an organ transplant.
Any individual with whom the subject attends or attended the same school.
An anatomical structure consisting of similarly specialized cells and intercellular matrix, aggregated according to genetically determined spatial relationships, performing a specific function.
An age group comprised of infants born alive with a gestational age between 32 to less than 37 weeks.
A laboratory test to determine the lowest concentration of a substance that will inhibit a biological or biochemical function, such as microorganism growth or enzymatic activity.
NCIT offers this alternate definition which GenEpiO intends: "A measurement that specifies the minimum concentration of the agent at which organism growth was inhibited."
Clinical and Laboratory Standards Institute MIC antimicrobial testing standards at http://em100.edaptivedocs.info/GetDoc.aspx?doc=CLSI%20M100%20S27:2017&scope=user
The supporting connective tissue of an organ.
An individual who is receiving a transplant of a solid organ.
An individual receiving a bone marrow transplant.
A body part, organ or organ component that is formed during the embryonic stage of life of an organism.
An unborn or unhatched vertebrate in the later stages of development showing the main recognizable features of the mature being.
A female who is married to a spouse with children whom are not biologically related to her.
Pertaining to, affecting, or associated with the liver.
Fluid withdrawn from a body cavity, organ, cyst, or tumor.
An adjectival term used to specify a region of the body or other concepts associated with the body.
An indication that death occurred on or within 90 days of a patient's initial admission to a hospital.
Death During, or within 90 Days of, Index Hospital Admission
Death Less than 90 Days or During Index Hospital Admission
A loss of any arm of immune functions, resulting in potential or actual increase in infections. This state may be reached secondary to specific genetic lesions, syndromes with unidentified or polygenic causes, acquired deficits from other disease states, or as result of therapy for other diseases or conditions.
A population or type of organisms that is genetically different from others of the same species and possessing a set of defined characteristics.
Any agent that can alter hormone levels or modulate hormone effects.
A plan of action intended to accomplish a specific goal.
A heterogeneous and variable aggregate of body fluids, tissues, cells, microorganisms, and other materials that are collected from a swab biospecimen collection procedure.
The removal of tissue specimens or fluid from the living body for microscopic examination, performed to establish a diagnosis.
A procedure to remove toxic substances from the blood that is used in patients with end-stage chronic kidney disease or acute kidney failure. This includes hemodialysis and peritoneal dialysis.
A therapeutic procedure used in patients with kidney failure. It involves the extracorporeal removal of harmful wastes and fluids from the blood using a dialysis machine. Following the dialysis, the blood is returned to the body.
Inoculating an individual with either killed or live agents to prevent contraction of a disease.
Prevention of disease or mental disorders in susceptible individuals or populations through promotion of health, including mental health, and specific protection, as in immunization, as distinguished from the prevention of complications or after-effects of existing disease.
The removal of excess fluid via needle puncture from any body cavity.
An invasive procedure in which a hollow needle is introduced through an intervertebral space in the lower back to access the subarachnoid space in order to sample cerebrospinal fluid or to administer medication.
A diagnostic or treatment procedure performed by manual and/or instrumental means, often involving an incision and the removal or replacement of a diseased organ or tissue; of or relating to or involving or used in surgery or requiring or amenable to treatment by surgery.
Administration of vaccines to stimulate the host's immune response. This includes any preparation intended for active immunological prophylaxis or treatment.
Chemotherapy that is administered subsequent to the main treatment plan to minimize or prevent disease recurrence.
An intentional cut made to an individual's body with the intent of performing a diagnostic or therapeutic intervention.
The removal of excess fluid via needle puncture from the thoracic cavity.
Puncture of Pleural Cavity for Aspiration
Deliberate stimulation of a host's immune response via administration of antigens or immunologic adjuvants.
A male that is related to a child or children through marriage to their biological parent.
Treat infections with antibacterial, antifungal, antiparasite or antiviral drugs
Infectious Diseases / Treatment, General
Procedure using suction, usually with a thin needle and syringe, to remove bodily fluid or tissue.
The use of synthetic or naturally-occurring chemicals for the treatment of diseases.
A death attributed to the progression of a cancer-related pathologic condition.
A death attributed to any cause other than the progression of a cancer-related pathologic condition.
Any surgery performed inside the thoracic cavity.
General term for hemodialysis, plasmapheresis, blood transfusions, and related procedures involving autologous removal, alteration, and replacement of patients' blood or blood components.
Therapeutic Procedures Hematopoietic System
A non-neoplastic or neoplastic disorder that affects the genitourinary system.
Any therapy that is administered to augment or stimulate other treatment modalities or to minimize or prevent disease recurrence subsequent to the main treatment plan.
An individual who is receiving or has received a transplant of a kidney.
Surgical procedures targeted at minimizing or eliminating a neoplastic process.
Therapeutic, nutritional, environmental, social and/or behavioral interventions at the societal, community, organizational or individual levels to reduce, modify or stop the course of a disease.
Treatment of disease through the use of drugs.
Treatment of human immunodeficiency virus (HIV) infections with medications that target the virus directly, limiting the ability of infected cells to produce new HIV particles.
Treatment of viral infections with agents that prevent viral replication in infected cells without impairing the host cell function.
A population group that is characterized by a common descriptive factor such as age, sex, race, education, etc.
The determination of the amount of nitrate present in a sample.
Any individual related biologically to another individual and considered immediate family as in the case of a parent, sibling or child.
A facility where items can be deposited for storage or safekeeping.
A categorization of surgical procedures by type or purpose.
Any specific activity undertaken during the course of a clinical study or research protocol.
The actions of prevention, treatment, and management of illness and the preservation of mental and physical well-being through the services offered by the medical and allied health professions.
Any intervention for management of a malignant neoplasm.
An age group comprised of individuals 65 years of age and older.
The actions or reactions of an object or organism, usually in relation to the environment or surrounding world of stimuli.
Synthetically made hormones possessing the steroid ring system; e.g., androgens, estrogens, and adrenocortical hormones.
An age group comprised of individuals who are not yet an adult. The specific cut-off age will vary by purpose.
A sample containing a mixture of multiple individual specimens of interest that were collected in a study.
A person who belongs to the sex that normally produces ova. The term is used to indicate biological sex distinctions, or cultural gender role distinctions, or both.
The biological father of the offspring of the female subject.
The biological mother of the offspring of the male subject.
The male who supplied the sperm or the female who supplied the egg which resulted in one's conception.
A non-biological parent through current or prior marriage to the subject's biological or legal parent.
A parent in the parent-child relationship established by a legal adoption proceeding.
A male parent in the parent-child relationship established by a legal adoption proceeding.
A female parent in the parent-child relationship established by a legal adoption proceeding.
A death that is considered to be causally linked to a treatment.
Any demarcated area of the Earth; may be determined by both natural and human boundaries.
Any disease or condition resulting in postnatal death before age 1 yr. (NCI)
An age group comprised of infants during the first month after birth.
Any object, or item of electrical or electronic equipment, which is designed to carry out a specific function or set of functions.
Any physical object that is useful for prevention, diagnosis, monitoring, or treatment of disease or other conditions.
A difficulty or problem that occurs at or just after delivery of an infant that can jeopardize the health of the infant.
A representation of something, often idealized or modified to make it conceptually easier to understand.
An indication that the mortality of the individual was related to the stem cell treatment.
Mortality related to Stem Cell Treatment
An indication that the subject has died due to the progression of their disease.
A person who receives medical attention, care, or treatment, or who is registered with medical professional or institution with the purpose to receive medical care when necessary.
A group of individuals united by a common factor (e.g., geographic location, ethnicity, disease, age, gender)
A word or phrase that imparts a distinctive characteristic or attribute to the word or phrase it is modifying.
A manufactured object designed for non-medical use.
Pneumonia caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). It is characterized by the presence of ground glass opacities on CT scan images.
Acute respiratory distress syndrome caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2).
COVID-19-Associated Acute Respiratory Distress Syndrome
SARS-CoV-2-Associated Acute Respiratory Distress Syndrome
Coagulation disorder caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2).
COVID-19-Associated Coagulation Disorder
SARS-CoV-2-Associated Coagulation Disorder
Characteristics of people that are socially constructed, including norms, behaviors, and roles based on sex. As a social construct, gender varies from society to society and can change over time. (Adapted from WHO.)
Inhaling the vapor produced by an electronic cigarette or similar device.
A biospecimen collected from the rectum by swabbing.
A plan used to minimize the effects of a deleterious phenomenon.
A method used by an individual to be kept apart in seclusion from others for a period of time in an attempt to minimize the risk of transmission of an infectious disease.
The primary person in charge of the care of a patient, usually a family member or a designated health care professional.
The time of life between childhood and maturity. This period overlaps with adolescence.
A device which is an artificial substitute for a missing body part or function; used for functional or cosmetic reasons, or both.
An age group comprised of humans who have reached reproductive age.
A portion of an absorbent material attached to one end of a small stick for the purpose of applying or collecting material.
A tuft of material on the end of a stick for applying solutions and suspensions
Population groups with an increased likelihood of a disease or other health issue, eg smoking, drug use, teen pregnancy.
An activity occurring within an organism, between organisms or among organisms and the mechanisms underlying such events.
Any procedure or test to diagnose a disease or disorder.
The name or names between a person's first name and their surname (last name, family name).
infant death due to causes other than AIDS
A disease or disorder that occurs during the course of, or because of COVID-19 infection or treatment.
The population of retired people, generally over 62
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
Any natural, endogenously-derived, synthetic or semi-synthetic compound with pharmacologic activity. A pharmacologic substance has one or more specific mechanism of action(s) through which it exerts one or more effect(s) on the human or animal body. They can be used to potentially prevent, diagnose, treat or relieve symptoms of a disease. Formulation specific agents and some combination agents are also classified as pharmacologic substances.
Death attributable to heart disease during acute SARS-CoV-2 infection.
Cardiovascular Mortality During Acute COVID-19
Cardiovascular Mortality During Acute SARS-CoV-2 Infection
Ventilatory or circulatory support given to patients to assist with pulmonary or cardiac function.
Death related to hemorrhage such as a non-stroke intracranial hemorrhage, non-procedural or non-traumatic vascular rupture, or hemorrhage causing cardiac tamponade in a patient with probable or confirmed acute COVID-19.
Death due to Cardiovascular Hemorrhage Related to COVID-19
Death caused by complications of a cardiovascular procedure in a patient with probable or confirmed acute COVID-19.
Death due to Cardiovascular Procedure Related to COVID-19
Death from a cardiovascular cause not otherwise noted but with a specific, known cause in a patient with probable or confirmed acute COVID-19.
Death due to Other Cardiovascular Cause Related to COVID-19
Death due to other cardiovascular causes
Death by any cardiovascular mechanism (e.g., arrhythmia, sudden death, heart failure (HF), stroke, pulmonary embolus, peripheral arterial disease) less than or equal to 30 days after a myocardial infarction (MI), related to the immediate consequences of the MI, such as progressive HF or recalcitrant arrhythmia in a patient with probable or confirmed acute COVID-19.
Death due to Acute Myocardial Infarction Related to COVID-19
Death in association with clinically worsening symptoms or signs of heart failure regardless of etiology in a patient with probable or confirmed acute COVID-19.
Death due to Heart Failure Related to COVID-19
Death as a consequence of pulmonary embolism in a patient with probable or confirmed acute COVID-19.
Death due to Pulmonary Embolus Related to COVID-19
Death following a stroke that is either a direct consequence of the stroke or a complication of the stroke in a patient with probable or confirmed acute COVID-19.
A part of a thing, or of several things, taken to demonstrate or to determine the character of the whole, e.g. a substance, or portion of material obtained for use in testing, examination, or study; particularly, a preparation of tissue or bodily fluid taken for examination or diagnosis.
A grouping of occupations and fields of study.
Sudden cardiac death in a patient with probable or confirmed acute COVID-19.
Sudden Cardiac Death Related to COVID-19
Unexpected death caused by sudden cardiac arrest with asystole, pulseless electrical activity, sustained ventricular tachycardia, or ventricular fibrillation in a patient with probable or confirmed acute COVID-19 despite successful return of spontaneous circulation (ROSC).
Sudden Cardiac Death with Return of Spontaneous Circulation Related to COVID-19
A manufactured object that is used to perform diagnostic, therapeutic or research activities.
Diagnostic, Therapeutic, and Research Equipment
Diagnostic, Therapeutic, or Research Equipment
The postal code of the facility where the encounter occurred.
The postal code of the facility where the interventional procedure was performed.
The postal code of the patient's residence.
Occupations within the field of medicine.
A chemical that influences the properties of another chemical or biological function. (NCI)
The distinguishing qualities or prominent aspects of an individual person.
personal attribute
A physical object, or electronic counterpart, that is characterized by containing writing which is meant to be human-readable.
An individual who is classified by their work type.
A person described by their relationship with another person.
A person described by an activity with which they are engaged.
A person described by the circumstances in which they are currently living.
A person described by a medical or psychological condition.
Groups that have a focus on health issues.
An indication that a subject died during treatment but had not achieved remission.
A biologic function, activity, or process involving either specialized organ functions, individual organs, organ systems, body parts, or whole organisms.
A container designed for the collection of a specimen.
An alphanumeric system designed to identify countries. The ISO 3166 standard includes a two letter representation, a three letter representation, and a 3 number representation. The last two are identical to the UN system. The US State Department system maintains a separate two letter representation code set.
An organizational header for concepts representing mostly abstract entities.
A distinguishing quality or prominent aspect of a person, object, action, process, or substance.
A biospecimen that consists of a body fluid.
The male or female designation that doctors ascribe to a newborn infant, usually based on the appearance of the child's external genitalia, and that is marked on their birth records.
A Reproductive System Process involves a function of cellular, cell, or tissue components of the organ system involved in generation of offspring that includes the ovaries, fallopian tubes, uterus, cervix, and vagina in women or the prostate, testes, and penis in men.
Any relative who is one meiosis away from a particular individual in a family; a relative with whom one half of an individual's genes is shared (i.e., parent, sibling, offspring) (from Genetics Home Reference glossary)
Terms used to indicate units of time or other terms associated with time.
Pharmacological agents which affect the function of the adrenal glands.
A large and densely populated urban area; a city specified in an address.
A symbol or combination of symbols which is assigned to the members of a collection.
The particular day, month and year an event has happened or will happen.
The condition of being treated as a patient in a hospital.
A patient who is residing in the hospital where he is being treated.
A word or group of words indicating the identity of a person usually consisting of a first (personal) name and a last (family) name with an optional middle name. In some cultural traditions the family name comes first.
The principal activity that a person does to earn money.
Anything (e.g., a document) providing permanent evidence of or information about past events.
An activity that produces an effect, or that is intended to alter the course of a disease in a patient or population. This is a general term that encompasses the medical, social, behavioral, and environmental acts that can have preventive, therapeutic, or palliative effects.
Occurring first in time or sequence; original; of greatest rank or importance or value.
Exhibiting the symptoms of a particular disease.
Any procedure that involves testing or manipulating a sample of blood, urine, or other body substance in a laboratory setting.
A numeral or string of numerals expressing value, quantity, or identification.
A position, site, or point in space where something can be found.
A person, enterprise, or entity that produces finished goods.
Manufacturer
A standardized representation of the location of a person, business, building, or organization.
Pertaining to a portion of the whole; any one of two or more samples of something, of the same volume or weight.
The distinguishing qualities or prominent aspect of a person, object, action, process, or substance.
A collective generic term that refers here to a wide variety of dependencies, areas of special sovereignty, uninhabited islands, and other entities in addition to the traditional countries or independent states.
Something that happens at a given place and time.
diseased
Caused by or altered by or manifesting disease or pathology.
sick
Any system designed to expedite the sorting and delivery of mail by assigning a series of alphanumeric codes to each delivery area. Also used to refer to any individual delivery area code.
A region, district or division of a country; a tract; a portion a state, especially one remote from the capital.
Derived as a result of a primary condition; not direct or immediate; of second rank or importance or value.
The spatial arrangement of something as distinct from its substance.
The street name and building number where a person or organization is located.
A named quantity in terms of which other quantities are measured or specified, used as a standard measurement of like kinds.
The state or condition of being living or deceased; also includes the case where the vital status is unknown.
A system designed to expedite the sorting and delivery of mail by assigning a series of numbers to each delivery area in the United States. Also used to refer to any individual delivery area code.
A doctor; a person who has been educated, trained, and licensed to practice the art and science of medicine; a practitioner of medicine, as contrasted with a surgeon.
The state or condition of having a developing embryo or fetus in the body (uterus), after union of an ovum and spermatozoon, during the period from conception to birth.
A non-neoplastic or neoplastic disorder that arises from the hematopoietic and lymphoid cells. Representative examples include disorders that affect the synthesis of hemoglobin, coagulation disorders, leukemias, and lymphomas.
Hematopoietic and Lymphoid Cell Disorder
A non-neoplastic disorder that arises from hematopoietic and lymphoid cells. It is characterized by the absence of a clonal cellular component. It rarely progresses to a malignant neoplasm.
Non-Malignant Hematologic and Lymphocytic Disorder
Non-Neoplastic Hematologic and Lymphocytic Disorder
Non-Neoplastic Hematologic and Lymphoid Cell Disorder
Non-Neoplastic Hematopoietic and Lymphoid Cell Disorder
A protein, RNA or a complex that contains proteins and/or RNA.
The product of so-called RNA genes; a functional RNA represents the final product of a gene rather than a transient molecule that will be translated into protein.
A disorder resulting from the presence and activity of a microbial, viral, fungal, or parasitic agent. It can be transmitted by direct or indirect contact.
Acute inflammation of the lung parenchyma caused by viruses, bacteria, fungi, radiation treatment, or exposure to chemicals. Signs and symptoms include cough, shortness of breath, fevers, chills, chest pain, headache, sweating, and weakness.
A non-neoplastic disorder that affects the gastrointestinal tract, anus, liver, biliary system, and pancreas. Representative examples include infections, ulcers, cirrhosis, and diverticulosis.
Non-Neoplastic Digestive System Disorder
Non-Neoplastic Gastrointestinal Disorder
Non-Neoplastic Gastrointestinal System Disorder
A term that refers to the classification of a disorder according to the anatomic site that is involved in the pathologic process.
A lung disorder not caused by a neoplasm. Representative examples include chronic obstructive pulmonary disease, atelectasis, lung infections, pulmonary fibrosis, and pneumoconiosis.
A non-neoplastic or neoplastic disorder that affects the respiratory system or the thoracic organs.
Respiratory, Thoracic, and Mediastinal Disease
Respiratory, Thoracic, and Mediastinal Disorder
An age group comprised of juveniles between the onset of puberty and maturity; in the state of development between puberty and maturity.
An age group comprised of individuals between one month and two years of age.
An adjectival term used to specify and describe a disease appearance or processes.
A term that helps define and render another concept unique.
An organism in its initial stage of development following fertilization. The human embryonic period lasts approximately eight weeks, during which time organogenesis takes place.
The collection of blood from a vein, most commonly via needle venipuncture.
A patient who comes to a healthcare facility for diagnosis or treatment but is not admitted for an overnight stay.
The assemblage of physical properties or qualities by which male is distinguished from female; the physical difference between male and female; the distinguishing peculiarity of male or female.
deceased
A condition in which there is a deviation from or interruption of the normal coagulation properties of the blood.
A non-neoplastic or neoplastic disorder affecting the heart or the vessels (arteries, veins and lymph vessels). Representative examples of non-neoplastic cardiovascular disorders are endocarditis and hypertension. Representative examples of neoplastic cardiovascular disorders are endocardial myxoma and angiosarcoma.
Unspecified disorder of circulatory system
Any disease or disorder that occurs during the course of, or because of, another disease, treatment, or procedure.
A non-neoplastic or neoplastic disorder that affects the gastrointestinal tract, anus, liver, biliary system, and pancreas.
Any abnormal condition of the body or mind that causes discomfort, dysfunction, or distress to the person affected or those in contact with the person. The term is often used broadly to include injuries, disabilities, syndromes, symptoms, deviant behaviors, and atypical variations of structure and function.
Subject to little fluctuation; showing little if any change.
A non-neoplastic or neoplastic disorder that affects the heart and/or the pericardium. Representative examples include endocarditis, pericarditis, atrial myxoma, cardiac myeloid sarcoma, and pericardial malignant mesothelioma.
Any substance that induces, enhances, restores or suppresses the host's immune system, or an agent that utilizes or is derived from a component of the immune system.
A neoplastic or non-neoplastic condition affecting the kidney. Representative examples of non-neoplastic conditions include glomerulonephritis and nephrotic syndrome. Representative examples of neoplastic conditions include benign processes (e.g., renal lipoma and renal fibroma) and malignant processes (e.g., renal cell carcinoma and renal lymphoma).
A non-neoplastic or neoplastic disorder that affects the liver parenchyma and intrahepatic bile ducts. Representative examples of non-neoplastic disorders include hepatitis, cirrhosis, cholangitis, and polycystic liver disease. Representative examples of neoplastic disorders include hepatocellular adenoma, hepatocellular carcinoma, intrahepatic cholangiocarcinoma, lymphoma, and angiosarcoma.
A non-neoplastic or neoplastic disorder affecting the lung. Representative examples of non-neoplastic disorders include chronic obstructive pulmonary disease and pneumonia. Representative examples of neoplastic disorders include benign processes (e.g., respiratory papilloma) and malignant processes (e.g., lung carcinoma and metastatic cancer to the lung).
An acute, acute and chronic, or chronic inflammation focally or diffusely affecting the lung parenchyma, due to infections (viruses, fungi, mycoplasma, or bacteria), treatment (e.g. radiation), or exposure (inhalation) to chemicals. Symptoms include cough, shortness of breath, fevers, chills, chest pain, headache, sweating, and weakness.
The presence of pathogenic microorganisms in the blood stream causing a rapidly progressing systemic reaction that may lead to shock. Symptoms include fever, chills, tachycardia, and increased respiratory rate. It is a medical emergency that requires urgent medical attention.
Clinical, laboratory or molecular evidence, or absence of evidence of disease.
Body tissue, region, surface, cavity, fluid, organ, or collection of organs present in, or associated with, an embryo.
A circumscribed inflammatory and often suppurating lesion on the skin or an internal mucous surface resulting in necrosis of tissue.
A non-neoplastic or neoplastic disorder affecting the urinary system.
A non-neoplastic or neoplastic disorder that affects the bone marrow.
A life-threatening condition that requires immediate medical intervention. It is characterized by reduced blood flow that may result in damage of multiple organs. Types of shock include cardiogenic, hemorrhagic, septic, anaphylactic, and traumatic shock.
A state of acute circulatory failure characterized by persistent arterial hypotension despite adequate fluid resuscitation or by tissue hypoperfusion unexplained by other causes.
A term that refers to the nature and/or clinical outcome of a disease (e.g., acute or chronic disease, aggressive or indolent disease, recurrent disease, etc.).
Symptoms, physical examination results, and/or laboratory test results related to the cardiovascular system.
Accumulated material from the secretions of an organ. It is solid and representative examples include gallbladder stones, kidney stones, and salivary gland stones.
A non-neoplastic or neoplastic disorder that affects the thorax and/or the organs of the thoracic cavity. Representative examples include pleural infection, mediastinitis, thymoma, mediastinal lymphoma, and pleural mesothelioma.
A non-neoplastic disorder that affects the thorax and/or the organs of the thoracic cavity. Representative examples include pleural infection, mediastinitis, pneumonia, and chronic obstructive pulmonary disease.
A non-neoplastic disorder that affects the respiratory system. Representative examples include pneumonia, chronic obstructive pulmonary disease, pulmonary failure, tracheitis, and tracheal agenesis.
Non-Neoplastic Respiratory System Disorder
A non-neoplastic or neoplastic disorder that affects the hematopoietic and lymphatic system.
Hematopoietic and Lymphatic System Disorder
Hematopoietic and Lymphoid System Disorder
A term that refers to the classification of a clinical or laboratory finding according to the anatomic site or system that is involved.
Symptoms, physical examination results, and/or laboratory test results related to the reproductive system.
Symptoms, physical examination results, and/or laboratory test results related to the connective and soft tissue.
A facility equipped and competent to conduct scientific experiments, observations, tests, investigations, and/or to manufacture chemicals or medical products.
Showing characteristics of life; displaying signs of life.
Without clinical signs or indications that raise the possibility of a particular disorder or dysfunction.
A word or group of words indicating a person's first (personal or given) name; the name that precedes the surname.
A word or group of words indicating a person's last (family) name.
phone
A sequence of decimal digits (0-9) that is used for identifying a destination telephone line or other device in a telephone network.
A term that helps define and render a concept unique.
A prosthesis placed permanently in tissue.
Information regarding the person who is acting as a channel for communication between groups.
Any of the individuals who are descended from a common progenitor, related by marriage or other legal tie, or by a feeling of closeness.
A small, often stoppered glass or plastic bottle for holding fluids.
A hollow cylinder, especially one for holding or conveying liquids.
A hollow cylinder, especially one for holding or conveying liquids; anything shaped like such a hollow cylinder, e.g. an organic structure having the shape or function of a tube such as channel within a plant or animal body (e.g. fallopian tube).
An indication of the type of unit of measure being used to express a mass.
The words or language units by which a thing is known.
The account name used by a person to access a computer system.
A mother or a father; an immediate progenitor.
A text string identifier for a location to which e-mail can be delivered.
Damion Dooley's note: It can also be used as an authorization token in some identification processes.
A soft flexible, absorbent pad usually made from natural material such as gauze or cotton, used to absorb blood and other fluids, as in surgery or the dressing of a wound. The term also refers to a small absorbent contraceptive pad that contains a spermicide and is placed against the cervix of the uterus before sexual intercourse.
Kinds of packages that bulk drug substances and final drug dosage forms are contained in, including both the immediate (or primary) and secondary containers.
A vessel with a narrow neck designed to accept a specific closure.
An object that can be used to hold things.
A glass container designed for use with parenteral drug products.
A plastic container designed for use with parenteral drug products.
Any number of entities (members) considered as a unit.
An active process; excludes processes and mechanisms which fulfill biological functions.
A physical structure or device capable of holding objects or samples.
Refers to an individual who was born with genitalia and/or secondary sexual characteristics of indeterminate sex, or which combine features of both sexes.
A mix of specimens from multiple individuals representing multiple sex groups.
Damion Dooley's note: here "sample" means more than one specimen merged together.
pooled
The cultural, social, psychological, and behavior norms that are associated with being a man.
The cultural, social, psychological, and behavior norms that are associated with being a woman.
A way of doing something; how a result is obtained or an end is achieved.
The tangible substance that goes into the makeup of a physical object.
Knowledge derived from study, experience, or instruction that has been gathered or received by communication.
An established procedure to be followed in carrying out a given operation or in a given situation.
The basic quantity or increment used to describe the strength of a product or amount of product in a package.
The traditional unit of mass. The avoirdupois ounce is equal to 1/16 pound, or 28.349 5 grams, or 0.911 457 troy ounce.
The traditional unit of mass. By international agreement, one avoirdupois pound is equal to exactly 0.453 592 37 kilogram, 16 ounces, or 1.215 28 troy pounds.
A specific reason explaining why a meaningful value is not available. A meaningful value answers the question posed by a Data Element Concept. In contrast, a Missing Value Reason answers the implicit question "Why is there no 'meaningful' value?", when there is none.
The usual or expected function of something; the part something plays in an action or event.
A categorization of surgical procedures based on surgical techniques.
A laboratory procedure to detect microorganisms in a sample.
An action or administration of therapeutic agents to produce an effect that is intended to alter or stop a pathologic process.
A laboratory test designed for the quantification of an organic or inorganic chemical within a biological specimen.
One of the possible results of an adverse event outcome that indicates that the event has improved or recuperated.
The period of time during which the embryo or fetus is present in the uterus of the female. Also describes the location of the embryo or fetus as being in the uterus in contrast to outside the uterus (ex utero).
An age group comprised of infants less than 37 weeks, 0 days gestational age.
An age group comprised of individuals between 28 days to 23 months of age.
Infant And Toddler (28 Days to 23 Months)
An age group comprised of individuals between 2 to 11 years of age.
An age group comprised of individuals from 18 years to 65 years of age.
A physical object that is a device or a component or accessory of a device.
A device consisting of a narrow loop of material moving over shafts or pulleys.
An unexpected natural death from a cardiac cause within a short time period from the onset of symptoms.
A prenatal diagnostic procedure in which a small sample of amniotic fluid is removed from the uterus by a needle inserted into the abdomen. This procedure is used to detect various genetic abnormalities in the fetus and/or the sex of the fetus.
A person qualified to be engaged in activity directed at preservation of mental and physical health by diseases prevention and treatment as a source of livelihood.
A specific individual microbe and its genetically identical progeny separated on a single occasion from a sample taken from a host or culture system.
Any disorder other than abnormal tissue growth resulting from uncontrolled cell proliferation.
Non-Neoplastic Disease by Special Category
Non-Neoplastic Disorder by Special Category
A non-neoplastic disorder that affects the liver parenchyma and the intrahepatic bile ducts. Representative examples include hepatitis, cirrhosis, and cholangitis.
Non-Neoplastic Liver and Intrahepatic Bile Duct Disorder
A female individual who has had her ovaries removed.
The cessation of life due to heart abnormalities or disease.
An expected natural death from a cardiac cause. This condition usually occurs in persons with pre-existing cardiac abnormalities or disease.
The numeric, three-digit country codes specified by the ISO 3166-1 country code standard.
The two-letter country codes specified by the ISO 3166-1 country code standard.
The three-letter country codes specified by the ISO 3166-1 country code standard.
Any synthetic or animal-derived agent that is chemically identical or similar to an endogenous hormone with therapeutic application.
Information regarding the means of contacting a person or group.
Death of a fetus, neonate, or patient 20 years or younger.
An object contrived for a specific purpose.
The degree of differences in identifying features among the members of a purposefully defined group.
Variety; quality, state, fact, or instance of being different.
diversitet
diversity
Services and space and equipment provided for a particular purpose; a building or place that provides a particular service or is used for a particular industry.
A brand of of test tube specifically designed for venipuncture; the tube contains a vacuum allowing it to suck blood though a needle and fill itself. The tube may contain additives to facilitate downstream processing and testing of the blood samples; the tube cap is color-coded to indicate the type of additive present.
A quantitative measurement of the amount of nitrite present in a sample.
The withdrawal of fluid via a needle for microscopic examination for the purpose of diagnosing a disease/disorder.
The calendar date on which a person was born.
A condition that is relevant to human neoplasms and non-neoplastic disorders. This includes observations, test results, history and other concepts relevant to the characterization of human pathologic conditions.
Any material sample taken from a biological entity for testing, diagnostic, propagation, treatment or research purposes, including a sample obtained from a living organism or taken from the biological object after halting of all its life functions. Biospecimen can contain one or more components including but not limited to cellular molecules, cells, tissues, organs, body fluids, embryos, and body excretory products.
The value for a particular telecommunication address used as the contact telecommunication information for a person or organization.
A method to mechanically assist or replace spontaneous breathing in patients by use of a powered device that forces oxygenated air into the lungs.
An animal that is amenable to experimentation and whose physiological or pathologic mechanisms are sufficiently similar to those of a human for the animal to serve as a model.
A person related by descent rather than by marriage or law.
Family members related by secondary marriage or other legal arrangement.
Unrelated persons who are part of the same foster family.
A family relation established by a legal proceeding that creates a parent-child relation between persons not related by blood.
A family relation established through a subsequent marriage of your parent.
brand name
The part of the name or logo associated with a specific product or service identifying and distinguishing it from varieties of the same product or service marketed by competing companies.
A term used to indicate an object's position in space or it's relationship in space to another object.
The determination of the opacity of a sample.
A laboratory procedure that involves the examination of blood, urine, other fluids, and stool for diagnostic or research purposes.
A laboratory procedure that is performed in more than one of these laboratory specializations: anatomic pathology, clinical pathology, or molecular pathology.
The anatomic site of a cut made during surgery. The term may also refer to the resultant scar from the surgical procedure.
Cancer Diagnostic or Therapeutic Procedure
An entity, either biologic or otherwise, of interest in an investigation. [def-source: NCI]
NCIT Thesaurus
investigative subject
Death of a live newborn during the first 28 days of life.
A political unit, such as a city, town, or village, incorporated for local self-government.
A fictitious name used when the person performs a particular social role.
Systems designed to elucidate facts about complex biological phenomena, usually in a less complex or theoretical test environment.
The inability of the bone marrow to produce hematopoietic elements.
An RNA molecule that does not contain protein-coding sequence information and constitutes the majority of the cellular RNA (~80%). This nucleic acid associates with multiple proteins to form ribosomes, which are the organelles that drive mRNA-directed protein synthesis.
A document, established by consensus and approved by a recognized body, that provides, for common and repeated use, rules, guidelines or characteristics for activities or their results.
Death that is attributed to the progression of a disease or pre-existing condition, and which is not attributable to any outside action or force.
A situation that imperils the existence of an entity.
A refrigerated cabinet or room for preserving materials at or below 32F (0C).
Unexpected death in infancy which remains unexplained following autopsy, review of the medical history, and investigation of the death circumstances and death scene.
An age group comprised of individuals between 5 and 12 years of age.
antimicrobial resistance testing method
A method to determine whether microbial growth is affected by an antimicrobial compound.
A method to determine microbial susceptibility to antibiotics in which test bacteria is inoculated onto agar plates with serial dilutions of know quantities of antibiotics. The minimum inhibitory concentration of antibiotic is assessed.
E-test (Epsilometry)
A method to determine the minimum inhibitory concentration (MIC) of antibiotics in which growth media is pipetted into a test tube. Each tube contains a known concentration of drug and is inoculated with a known quantity of bacteria. The tubes are incubated for a specified period of time and each is assessed for bacterial cell growth. The drug concentration in the first tube showing no growth is known as the MIC for that antibiotic.
A constituent administrative district of a nation.
A site where a microbiology specimen is collected.
A term referring to the lack of definitive clinical or pathologic criteria for a tumor to predict its clinical course or to classify it as benign or malignant.
An age group comprised of infants greater than or equal to 37 weeks, 0 days and less than or equal to 41 weeks, 6 days gestational age.
An age group comprised of individuals between 12 and 18 months of age.
A chemical, physical, or biological agent that causes disease or some alteration of the normal structure and function of an organism. Usually refers to poisonous substance produced during the metabolism and growth of certain microorganisms and some higher plant and animal species, or any poisonous isomer, homolog, or derivative of such a substance. It causes either permanent or reversible injury to the health of a living thing on contact or absorption, typically by interacting with biological macromolecules such as enzymes and receptors. Onset of effects may be immediate or delayed, and impairments may be slight or severe. (NCI)
A geographical area under the jurisdiction of a sovereign state and marked off for administrative or other purposes.
An indication that the subject's death was due to a mishap.
The cessation of life at an unplanned time.
A statement (either spoken or written) that is made in reply to a clinical research assessment question.
Clinical or Research Assessment Question Response
Clinical or Research Assessment Response
An age group comprised of individuals who have reached sexual maturity but whose character and personality are still developing. In psychology this generally covers the age range of 20-40.
An age group comprised of individuals between young adult and elderly, approximately 40-60 years of age.
Symptoms, signs, diagnostic examinations or a test results in a pregnant mother.
Uterine contractions resulting in cervical change (dilation and/or effacement). (reVITALize)
An infectious or non infectious disorder characterized by signs and symptoms derived from focal or extensive tissue infiltration by acute (e.g., polymorphonuclear) or chronic (e.g., lymphocytic-plasmacytic) inflammatory cells. Representative examples of infectious disorders include viral infections, bacterial infections, and parasitic infections. Representative examples of non-infectious inflammatory disorders include inflammatory bowel disease and inflammatory polyps.
A local name for an individual's occupation.
organization name
A textual identifier for an organization.
NCI Thesaurus
Treatment of retroviral infections with medications that target the virus directly, limiting the ability of infected cells to produce new virus particles.
A male who contributes to the genetic makeup of his offspring through the fertilization of an ovum by his sperm.
A female who contributes to the genetic makeup of her offspring from the fertilization of her ovum.
A non-neoplastic disorder that affects the liver, bile ducts, and gallbladder. Representative examples include hepatitis, cirrhosis, cholangitis, and cholecystitis.
Non-Neoplastic Liver and Biliary Disorder
Non-Neoplastic Liver and Biliary System Disorder
A physical object created by hand or machine.
Creations of the mind, such as those created by musicians, authors, artists, and inventors.
Damage inflicted on the soft tissues and their supporting structures as the direct or indirect result of an external force, with or without disruption of structural continuity.
The patient died while in a medical center such as a hospital, skilled nursing facility (SNF), intermediate care facility (ICF), or a freestanding hospice center. (ACC)
antibiotic treatment
fetal death (miscarriage/still birth)
The age at which Alzheimer disease manifestations first appear.
The age at which asthma manifestations first appear.
The age at which urinary bladder carcinoma manifestations first appear.
age at onset of urinary bladder carcinoma
age urinary bladder carcinoma symptoms begin
age of onset of urinary bladder carcinoma
The age at which cataract manifestations first appear.
The age at which hyperlipidemia manifestations first appear.
The age at which osteoarthritis manifestations first appear.
The age at which Parkinson disease manifestations first appear.
The age at which essential hypertension manifestations first appear.
age essential hypertension symptoms begin
The age at which schizophrenia manifestations first appear.
The age at which type 1 diabetes mellitus manifestations first appear.
age at onset of type 1 diabetes mellitus
age type 1 diabetes mellitus symptoms begin
age of onset of type 1 diabetes mellitus
The age at which type 2 diabetes mellitus manifestations first appear.
age at onset of type 2 diabetes mellitus
age type 2 diabetes mellitus symptoms begin
age of onset of type 2 diabetes mellitus
The age at which childhood onset asthma manifestations first appear.
age childhood onset asthma symptoms begin
The age at which alcohol dependence manifestations first appear.
The age at which allergic disease manifestations first appear.
The age at which amyotrophic lateral sclerosis manifestations first appear.
age amyotrophic lateral sclerosis symptoms begin
age at onset of amyotrophic lateral sclerosis
age of onset of amyotrophic lateral sclerosis
The age at which bipolar disorder manifestations first appear.
The age at which Buruli ulcer disease manifestations first appear.
The age at which frontotemporal dementia manifestations first appear.
age frontotemporal dementia symptoms begin
The age at which Huntington disease manifestations first appear.
The age at which migraine disorder manifestations first appear.
The age at which migraine with aura manifestations first appear.
The age at which migraine without aura manifestations first appear.
age migraine without aura symptoms begin
The age at which multiple sclerosis manifestations first appear.
The age at which myopia manifestations first appear.
The age at which refractive error manifestations first appear.
The age at which narcolepsy-cataplexy syndrome manifestations first appear.
age at onset of narcolepsy-cataplexy syndrome
age narcolepsy-cataplexy syndrome symptoms begin
age of onset of narcolepsy-cataplexy syndrome
The age at which coronary atherosclerosis manifestations first appear.
age at onset of coronary atherosclerosis
age coronary atherosclerosis symptoms begin
age of onset of coronary atherosclerosis
The age at which disease manifestations first appear.
The age at which cancer manifestations first appear.
The age at which glaucoma manifestations first appear.
The age at which stroke disorder manifestations first appear.
The age at which coronary stenosis manifestations first appear.
The age at which glioblastoma manifestations first appear.
The age at which systemic lupus erythematosus manifestations first appear.
age at onset of systemic lupus erythematosus
age systemic lupus erythematosus symptoms begin
age of onset of systemic lupus erythematosus
The age at which hypertensive disorder manifestations first appear.
age hypertensive disorder symptoms begin
The age at which Machado-Joseph disease manifestations first appear.
age Machado-Joseph disease symptoms begin
The age at which major depressive disorder manifestations first appear.
age at onset of major depressive disorder
age major depressive disorder symptoms begin
age of onset of major depressive disorder
The age at which cognitive disorder manifestations first appear.
The age at which depressive disorder manifestations first appear.
The age at which cervical dystonia manifestations first appear.
The age at which anorexia nervosa manifestations first appear.
The age at which colorectal cancer manifestations first appear.
The age at which pancreatic ductal adenocarcinoma manifestations first appear.
age at onset of pancreatic ductal adenocarcinoma
age pancreatic ductal adenocarcinoma symptoms begin
age of onset of pancreatic ductal adenocarcinoma
The age at which diverticulitis manifestations first appear.
The age at which isolated dystonia manifestations first appear.
The morphology of a integumental system.
A setting datum that specifies the temperature inside a container participating in a storage process.
Examples: -18 °C to -35 °C, -60 °C to -85 °C, Liquid nitrogen, Room temperature etc
storage temperature setting
planned process
Injecting mice with a vaccine in order to test its efficacy
A process that realizes a plan which is the concretization of a plan specification.
A processual entity that realizes a plan which is the concretization of a plan specification.
'Plan' includes a future direction sense. That can be problematic if plans are changed during their execution. There are however implicit contingencies for protocols that an agent has in his mind that can be considered part of the plan, even if the agent didn't have them in mind before. Therefore, a planned process can diverge from what the agent would have said the plan was before executing it, by adjusting to problems encountered during execution (e.g. choosing another reagent with equivalent properties, if the originally planned one has run out.)
We are only considering successfully completed planned processes. A plan may be modified, and details added during execution. For a given planned process, the associated realized plan specification is the one encompassing all changes made during execution. This means that all processes in which an agent acts towards achieving some objectives is a planned process.
6/11/9: Edited at workshop. Used to include: is initiated by an agent
This class merges the previously separated objective driven process and planned process, as they the separation proved hard to maintain. (1/22/09, branch call)
Jackson Labs is an organization which provide mice as experimental material
a role realized through the process of supplying materials such as animal subjects, reagents or other materials used in an investigation.
Supplier role is a special kind of service, e.g. biobank
PERSON:Jennifer Fostel
material supplier role
processed material
Examples include gel matrices, filter paper, parafilm and buffer solutions, mass spectrometer, tissue samples
Is a material entity that is created or changed during material processing.
investigation
Lung cancer investigation using expression profiling, a stem cell transplant investigation, biobanking is not an investigation, though it may be part of an investigation
a planned process that consists of parts: planning, study design execution, documentation and which produce conclusion(s).
Bjoern Peters
OBI branch derived
Could add specific objective specification
Following OBI call November 2012,26th: it was decided there was no need for adding "achieves objective of drawing conclusion" as existing relations were providing equivalent ability. this note closes the issue and validates the class definition to be part of the OBI core editor = PRS
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.
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.
Discussion on OBI call 2023-05-01 resulted in an agreement to revise the textual definition of 'assay'. https://github.com/obi-ontology/obi/issues/1683.
PlanAndPlannedProcess Branch
measuring
scientific observation
A growth medium or culture medium is a substance in which microorganisms or cells can grow. Wikipedia, growth medium, Feb 29, 2008
a processed material that provides the needed nourishment for microorganisms or cells grown in vitro.
changed from a role to a processed material based on on Aug 22, 2011 dev call. Details see the tracker item: http://sourceforge.net/tracker/?func=detail&aid=3325270&group_id=177891&atid=886178 Modification made by JZ.
Person: Jennifer Fostel, Jie Zheng
OBI
culture medium
a hospitalized person; a person with controlled diabetes; the patient's role http://www.fertilityjourney.com/testingAndDiagnosis/theRightDoctor/thePatientsRole/index.asp?C=55245395146924652778
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
GROUP:Role Branch
OBI, CDISC
CDISC definition: patient. Person under a physician's care for a particular disease or condition. NOTE: A subject in a clinical trial is not necessarily a patient, but a patient in a clinical trial is a subject. See also subject, trial subject, healthy volunteer. Often used interchangeably
patient role
A planned process which results in physical changes in a specified input material.
Incubators are used in microbiology for culturing (growing) bacteria and other microorganisms. Incubators in tissue culture rooms are used for culturing stem cells, lymphocytes, skin fibroblasts and other types of cells
A device in which environmental conditions (light, photoperiod, temperature, humidity, etc.) can be controlled
population
PMID12564891. Environ Sci Technol. 2003 Jan 15;37(2):223-8. Effects of historic PCB exposures on the reproductive success of the Hudson River striped bass 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
1/28/2013, BP, on the call it was raised that we may want to switch to an external ontology for all populatin terms: http://code.google.com/p/popcomm-ontology/
PERSON: Philippe Rocca-Serra
adapted from Oxford English Dictionnary
rem1: collection somehow always involve a selection process
organization
PMID: 16353909.AAPS J. 2005 Sep 22;7(2):E274-80. Review. The joint food and agriculture organization of the United Nations/World Health Organization Expert Committee on Food Additives and its role in the evaluation of the safety of veterinary drug residues in foods.
An entity that can bear roles, has members, and has a set of organization rules. Members of organizations are either organizations themselves or individual people. Members can bear specific organization member roles that are determined in the organization rules. The organization rules also determine how decisions are made on behalf of the organization by the organization members.
BP: The definition summarizes long email discussions on the OBI developer, roles, biomaterial and denrie branches. It leaves open if an organization is a material entity or a dependent continuant, as no consensus was reached on that. The current placement as material is therefore temporary, in order to move forward with development. Here is the entire email summary, on which the definition is based: 1) there are organization_member_roles (president, treasurer, branch editor), with individual persons as bearers 2) there are organization_roles (employer, owner, vendor, patent holder) 3) an organization has a charter / rules / bylaws, which specify what roles there are, how they should be realized, and how to modify the charter/rules/bylaws themselves. It is debatable what the organization itself is (some kind of dependent continuant or an aggregate of people). This also determines who/what the bearer of organization_roles' are. My personal favorite is still to define organization as a kind of 'legal entity', but thinking it through leads to all kinds of questions that are clearly outside the scope of OBI. Interestingly enough, it does not seem to matter much where we place organization itself, as long as we can subclass it (University, Corporation, Government Agency, Hospital), instantiate it (Affymetrix, NCBI, NIH, ISO, W3C, University of Oklahoma), and have it play roles. This leads to my proposal: We define organization through the statements 1 - 3 above, but without an 'is a' statement for now. We can leave it in its current place in the is_a hierarchy (material entity) or move it up to 'continuant'. We leave further clarifications to BFO, and close this issue for now.
DNA extraction
A DNA extraction is a nucleic acid extraction where the desired output material is DNA.
enzyme
(protein or rna) or has_part (protein or rna) and has_function some GO:0003824 (catalytic activity)
MC: known issue: enzyme doesn't classify under material entity for now as it isn't stated that anything that has_part some material entity is a material entity. If we add as equivalent classes to material entity has_part some material entity and part_of some material entity (each one in his own necessary and sufficient block) Pellet in P3 doesn't classify any more.
plasmid
plasmid = DNA and has_quality circular and has_function (is_realized_as some gene expression) GO:0010467
Ovarian carcinoma presenting with axillary lymph node metastasis: A case diagnosed by fine-needle aspiration and brief review of the literature. Diagn Cytopathol. 2008 Oct 16. PMID: 18925569
A needle is a sharp, hollow device used to penetrate tissue or soft material. When attached to a syringe. it allows delivery of a specific volume of liquid or gaseous mixture.
With respect to The Accuri C6 Flow Cytometer System, the organization Accuri bears the role manufacturer role. With respect to a transformed line of tissue culture cells derived by a specific lab, the lab whose personnel isolated the cll line bears the role manufacturer role. With respect to a specific antibody produced by an individual scientist, the scientist who purifies, characterizes and distributes the anitbody bears the role manufacturer role.
Manufacturer role is a role which inheres in a person or organization and which is realized by a manufacturing process.
Illumina (Solexa) sequencing is an example of DNA sequencing
A sequencing assay which determines information on the sequence of a DNA molecule.
A data set that is produced as the output of a class discovery data transformation and consists of a data set with assigned discovered class labels.
data set with assigned discovered class labels
clustered data set
The Cytoscape application is commonly used to visualize data representational models about biological entities. It can read and write several serializations of data representational models, including BioPAX.
An information content entity representing the relationships between data items.
2009-02-28: work on this term has been finalized during the OBI workshop winter 2009
drawing blood from a patient for analysis, collecting a piece of a plant for depositing in a herbarium, buying meat from a butcher in order to measure its protein content in an investigation, collecting a stone from a site
A planned process with the objective to obtain a material entity for potential use as an input upon which measurements or observations are performed.
Definition updated following discussion on 2024-10-07 OBI dev call.
Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation.
Philly2013: A specimen collection can have as part a material entity acquisition, such as ordering from a bank. The distinction is that specimen collection necessarily involves the creation of a specimen role. However ordering cell lines cells from ATCC for use in an investigation is NOT a specimen collection, because the cell lines already have a specimen role.
Philly2013: The specimen_role for the specimen is created during the specimen collection process.
label changed to 'specimen collection process' on 10/27/2014, details see tracker: http://sourceforge.net/p/obi/obi-terms/716/
5/31/2012: This process is not necessarily an acquisition, as specimens may be collected from materials already in posession
A data item that is produced as the output of an averaging data transformation and represents the average value of the input data.
average value
PMID: 18946007.Pyrosequencing analysis of the oral microflora of healthy adults. Keijser BJ, Zaura E, Huse SM, van der Vossen JM, Schuren FH, Montijn RC, ten Cate JM, Crielaard W. J Dent Res. 2008 Nov;87(11):1016-20.
is a DNA sequencer first manufactured by 454 Life Science Corporation in 2005, and enables pyrosequencing to be performed. It comprises both optics and fluidics subsystems, which are controlled by a computer subsystem. The fluidics subsystem ensures accurate reagent dispensing. It consists of a reagents cassette (which holds the reagent containers), a sipper manifold, pumps, valves, and debubblers. The fluidics subsystem flows the sequencing reagents across the wells of the PicoTiterPlate device, and moves the spent reagents from the PicoTiterPlate device to the waste receptacle. The optics subsystem consists of a CCD camera and a camera controller. The camera captures the light emitted in the wells of the PicoTiterPlate device during each step of the sequencing cycle, and sends the digital images to the computer subsystem for processing. The computer controls the other Sequencer subsystems, and processes the digital images sent by the camera to extract the DNA sequence information.
is a DNA sequencer which is manufactured by Applied Biosystems corporation (formerly Perkin-Elmer). It allows automated chain termination DNA sequencing. It has part polyacrylamide gel electrophoresis system and a laser -based detection system to detect fluorescence intensity emitted by the dyes attached to the dideoxyterminator nucleotides or to the primers.
PMID: 19336255. RNA-Seq-quantitative measurement of expression through massively parallel RNA-sequencing. Wilhelm BT, Landry JR. Methods. 2009 Jul;48(3):249-57.
is a DNA sequencer which is manufactured by Applied Biosystems and which enable DNA sequencing by ligation
PMID: 18388294. Single-molecule DNA sequencing of a viral genome.
A DNA sequencing by synthesis assay that identifiies the sequnece of billions of DNA molecules immobilized to a surface using DNA polymerase and fluorescently labeled nucleotides added one at a time. The sequencing process does not require an amplification step and is typically able to produce reads of 25 base pair length.
PMID: 18616967. The Genome Sequencer FLX System--longer reads, more applications, straight forward bioinformatics and more complete data sets. Droege M, Hill B. J Biotechnol. 2008 Aug 31;136(1-2):3-10.
is a DNA sequencer which was first manufactured by 454 Life Science Corporation in 2008 and enables pyrosequencing to be performed. It comprises both optics and fluidics subsystems, which are controlled by a computer subsystem. The fluidics subsystem ensures accurate reagent dispensing. It consists of a reagents cassette (which holds the reagent containers), a sipper manifold, pumps, valves, and debubblers. The fluidics subsystem flows the sequencing reagents across the wells of the PicoTiterPlate device, and moves the spent reagents from the PicoTiterPlate device to the waste receptacle. The optics subsystem consists of a CCD camera and a camera controller. The camera captures the light emitted in the wells of the PicoTiterPlate device during each step of the sequencing cycle, and sends the digital images to the computer subsystem for processing. The computer controls the other Sequencer subsystems, and processes the digital images sent by the camera to extract the DNA sequence information. It has the ability to sequence 400-600 million base pairs per run with 400-500 base pair read lengths.
adapted from https://www.roche-applied-science.com/servlet/RCProductDisplay?langId=-1&storeId=10202&productId=3.8.8.1.1.3&catalogId=10202&krypto=mgV8a0Sdps6%2BCXU8IoddmzNEyGgjde9j8MOFCiMzRsduELeenAlVZ%2FE1QR%2BxLpzNlqMZPLRHqaI%3D&ddkey=https:RCProductDisplay
PMID: 19336255. RNA-Seq-quantitative measurement of expression through massively parallel RNA-sequencing. Wilhelm BT, Landry JR.Methods. 2009 Jul;48(3):249-57.
is a DNA sequence which is manufactured by Illumina (Solexa) corporation. it support sequencing of single or paired end clone libraries relying on sequencing by synthesis technology
PMID: 19119315. High-resolution analysis of the 5'-end transcriptome using a next generation DNA sequencer. Hashimoto S, Qu W, Ahsan B, Ogoshi K, Sasaki A, Nakatani Y, Lee Y, Ogawa M, Ametani A, Suzuki Y, Sugano S, Lee CC, Nutter RC, Morishita S, Matsushima K. PLoS One. 2009;4(1):e4108.
A DNA sequencing by ligation assay that identifies sequence information using primers to hybridize to the P1 adapter sequence within the library template, fluorescently labeled di-base probes to compete for ligation to the sequencing primer, multiple cycles of ligation, detection and cleavage to determine the eventual read length, following a series of ligation cycles, the extension product is removed and the template is reset with a primer complementary to the n-1 position for a second round of ligation cycles.
is a DNA sequencer which is manufactured by Li-Cor corporation and enable automated chain termination based DNA sequencing
is a DNA sequencer manufacturer by Helicos Corporation to carry out Single Molecule sequencing using reversible termination chemistry
Pathogen: An agent of disease. A disease producer. The term pathogen most commonly is used to refer to infectious organisms. These include bacteria (such as staph), viruses (such as HIV), and fungi (such as yeast). Less commonly, pathogen refers to a noninfectious agent of disease such as a chemical. http://www.medterms.com/script/main/art.asp?articlekey=6383
pathogen role is a role which inheres in an organism and realized in the process of disease course in the organism bearing host role caused by the organism bearing pathogen role
6 April 2009: from the Vaccine Community
The enzyme EcoR1 cuts DNA at the canonical cleavage site CAATTG
an enzyme that has a specific target cleavage sites within nucleic acids
5/22 Need to explore if there are GO / other classes exist that capture this. We need it now for cloning experiments
a role borne by a portion of blood taken to represent all the blood in an organism; the role borne by a population of humans with HIV enrolled in a study taken to represent patients with HIV in general.
A material sample role is a specimen role borne by a material entity that is the output of a material sampling process.
7/13/09: Note that this is a relational role: between the sample taken and the 'sampled' material of which the sample is thought to be representative off.
A rate that represents the percentage of people or animals in a study or treatment group who are alive for a given period of time after diagnosis or initiation of monitoring.
adapted from wikipedia http://en.wikipedia.org/wiki/Survival_rate
survival rate
A ruler, a microarray scanner, a Geiger counter.
A device in which a measure function inheres.
Preparation of polyA RNA by cellulose-bound oligo-dT (Aviv, H., Leder, P. 1972. Purification of biologically active globin messenger RNA by chromatography on oligothymidylic acid-cellulose. Proc. Nat. Acad. Sci. USA 69, 1408-1412.)
A RNA extract that is the output of an extraction process in which RNA molecules with poly A tail at its 3' end are purified.
real time polymerase chain reaction assay
An assay, based on the PCR, that amplifies and simultaneously quantifies a specific DNA molecule based on the use of complementary probes/primers. It enables both detection and quantification (as absolute number of copies or relative amount when normalized to DNA input or additional normalizing genes) of one or more specific sequences in a DNA sample.
quantitative real time polymerase chain reaction
Extraction of total RNA from cells with Qiagen mini RNeasy kit
A RNA extract that is the output of an extraction process in which total celluar and organelle RNA molecules are isolated from a specimen.
is a material entity bearing the disposition to infect an organism
IEDB
Note: testing use of 'transmitted by' relation; issue to be resolved is whether appropriate domain and range are involved. This use would place 'transmitted by' as a subclass of 'participates in'
infectious agent
A measurement datum that is reported on a categorical scale.
The labels 'positive' vs. 'negative', or 'left handed', 'right handed', 'ambidexterous', or 'strongly binding', 'weakly binding' , 'not binding', or '+++', '++', '+', '-' etc. form scales of categorical labels.
A label that is part of a categorical datum and that indicates the value of the data item on the categorical scale.
A voltmeter is a measurement device which is intended to perform some measure function.
An autoclave is a device that sterlizes instruments or contaminated waste by applying high temperature and pressure.
A material entity that is designed to perform a function in a scientific investigation, but is not a reagent.
2012-12-17 JAO: In common lab usage, there is a distinction made between devices and reagents that is difficult to model. Therefore we have chosen to specifically exclude reagents from the definition of "device", and are enumerating the types of roles that a reagent can perform. 2013-6-5 MHB: The following clarifications are outcomes of the May 2013 Philly Workshop. Reagents are distinguished from devices that also participate in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in some chemical interaction or reaction during the realization of their experimental role. By contrast, devices do not participate in such chemical reactions/interactions. Note that there are cases where devices use reagent components during their operation, where the reagent-device distinction is less clear. For example: (1) An HPLC machine is considered a device, but has a column that holds a stationary phase resin as an operational component. This resin qualifies as a device if it participates purely in size exclusion, but bears a reagent role that is realized in the running of a column if it interacts electrostatically or chemically with the evaluant. The container the resin is in (“the column”) considered alone is a device. So the entire column as well as the entire HPLC machine are devices that have a reagent as an operating part. (2) A pH meter is a device, but its electrode component bears a reagent role in virtue of its interacting directly with the evaluant in execution of an assay. (3) A gel running box is a device that has a metallic lead as a component that participates in a chemical reaction with the running buffer when a charge is passed through it. This metallic lead is considered to have a reagent role as a component of this device realized in the running of a gel. In the examples above, a reagent is an operational component of a device, but the device itself does not realize a reagent role (as bearing a reagent role is not transitive across the part_of relation). In this way, the asserted disjointness between a reagent and device holds, as both roles are never realized in the same bearer during execution of an assay.
example of usage: the representation of a nucleotide sequence in FASTA format used for a sequence similarity search.
A measurement datum that representing the primary structure of a macromolecule(it's sequence) sometimes associated with an indicator of confidence of that measurement.
sequence data
A DNA sequencing process provided as a service - which is the realization of some DNA sequencing in which the service provider role is realized.
Eagle-i will supply better English definition
A microinjection device that is used to measure very small volumes of liquids.
individual organism identifier
a CRID symbol used to distinguish one individual organism from another.
MO_169 Individual
age measurement datum
A time measurement datum that is the result of measurement of age of an organism
note that we are currently defining subtypes of age measurement datum that specify when the age is relative to, e.g. planting, as we don't have adequate temporal predicates yet. life of bearer doesn't imply organism this assay measures time not developmental stage. we recognize that development can take different time periods under different conditions such as media / temperature age as a quality is dubious; we plan to revisit stages in development are currently handled with controlled vocabulary, such as 2-somite stage.
PERSON: Alan Ruttenberg, Chris Stoeckert, Jie Zheng
In MageTab file, we use initialTimePoint (a process) + age (a number expected) + TimeUnit (definied in UO, such as year, hour, day, etc.) Now we use the term label indicating the start time point of measuring the age, (number + TimeUnit) are expected instances of the class
discussed on Nov 15, dev call All subtype will be defined by textual definition now.
age since birth measurement datum
An age measurement datum that is the result of the measurement of the age of an organism since birth, the process of emergence and separation of offspring from the mother.
providing a training course for UCSD employees how to run a DNA sequencer; sequencing a DNA sample provided by a service consumer restricted to non-human samples; giving access to tissue samples in a biobank within OHSU; JAX shipping mice from their colony.
A planned process in which a service provider performs a task (i.e. a planned process) for a service consumer.
An assay that determines the sequence of an RNA molecule.
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).
sampling time measurement datum
A time measurement datum when an observation is made or a sample is taken from a material as measured from some reference point.
Person: Chris Stoeckert
time point
MO_738 timepoint
A service that offers liquid nitrogen stroage.
A storage service in which a service consumer provides some material as input which a service provider stores and returns as output.
GenBank ID
A CRID symbol uniquely indentifies the submitted GeneBank sequence record.
Person: Chris Stoeckert, Jie Zheng
investigation description
A textual entity that describes an investigation.
project description
Project Description
specimen identifier
A CRID symbol denotes a specimen and used to distinguish one specimen from another in an investigation.
specimen ID
sample identifier
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
specimen collection date
specimen collection time measurement datum
A time measurement datum that is the measure of the time when the specimens are collected.
collection date
help:Latitude should not be abstracted to the centre of a city, province/state or country as this may falsely implicate an existing location.
latitude coordinate measurement datum
A measurement datum that is the measure of the latitude coordinate of a site.
Damion Dooley's note: IAO lat/long can't be made a subclass of "angular coordinate" or disjoint contradiction arises.
latitude
See http://www.csgnetwork.com/gpscoordconv.html See http://www.geomidpoint.com/latlon.html See http://www.ontobee.org/browser/rdf.php?o=OBI&iri=http://purl.obolibrary.org/obo/OBI_0001621 See http://www.w3.org/2003/01/geo/wgs84_pos
longitude coordinate measurement datum
A measurement datum that is the measure of the longitude coordinate of a site.
longitude
Specimen Collection Location - Longitude
investigation title
A textual entity that denotes an investigation.
Person:Chris Stoeckert, Jie Zheng
project title
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
Damion Dooley's note: A 'sovereign state' entity should have attribute or relationships to measurables - population, size, name, etc. So e.g. " 'country name' inheres in some 'sovereign state/country'". Also note historical name issue (Myanmar vs Burma) and diplomatic name issue (Taiwan vs "Republic of China"). Both point to needing a single entity with multiple names.
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
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.
Discussed on May 7, 2012 dev call propose:contact role, type of organization role, and create shortcut relation between 'organization role' and 'organization' ? Whether it works for communicating author in manuscript or not? Tracker: https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891&atid=886178
A cultured cell that has been passaged or derives from a cell that has been passaged in culture.
A secondary cultured cell has been passaged in culture or is a descendant of such a cell that is derived through propagation in culture.
reagent
A biological or chemical entity that bears a reagent role in virtue of it being intended for application in a scientific technique to participate in (or have molecular parts that participate in) a chemical reaction that facilitates the generation of data about some distinct entity, or the generation of some distinct material specified output.
2013-6-5 MHB: Clarifications regarding the distinction between reagetns and devices were made at the May 2013 Philly Workshop. Reagents are distinguished from devices that also participate in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in some chemical interaction or reaction during the realization of their experimental role. By contrast, devices do not participate in such chemical reactions/interactions. Note that there are cases where devices use reagent components during their operation, where the reagent-device distinction is less clear. For examples, see editor note on OBI:device.
(copied from ReO) Reagents are distinguished from devices/instruments that also serve as facilitators in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in or have parts that participate in some chemical interaction or reaction during their intended participation in some technique. By contrast, devices do not participate in a chemical reaction/interaction during the technique. Reagents are distinguished from study subjects/evaluants in that study subjects and evaluants are that about which conclusions are drawn and knowledge is sought in an investigation - while reagents, by definition, are not. It should be noted, however, that reagent and study subject/evaluant roles can be borne by instances of the same type of material entity - but a given instance can only realize one of these roles in the execution of a given assay. For example, taq polymerase can bear a reagent role or an evaluant role. In a DNA sequencing assay aimed at generating sequence data about some plasmid, the reagent role of the taq polymerase is realized. In an assay to evaluate the quality of the taq polymerase itself, the evaluant/study subject role of the taq is realized, but not the reagent role since the taq is the subject about which data is generated. In regard to the statement that reagents are 'distinct' from the specified outputs of a technique: note that a reagent may be incorporated into a material output of a technique, as long as the IDENTITY of this output is distinct from that of the bearer of the reagent role. For example, dNTPs input into a PCR are reagents that become part of the material output of this technique, but this output has a new identity (ie that of a 'nucleic acid molecule') that is distinct from the identity of the dNTPs that comprise it. Similarly, a biotin molecule input into a cell labeling technique are reagents that become part of the specified output, but the identity of the output is that of some modified cell specimen which shares identity with the input unmodified cell specimen, and not with the biotin label. Thus, we see that an important criteria of 'reagent-ness' is that it is a facilitator, and not the primary focus of an investigation or material processing technique (ie not the specified subject/evaluant about which knowledge is sought, or the specified output material of the technique).
specimen provider PI organization
organization of specimen provider principal investigator
An organization that is the affiliation of the principal investigator providing the specimens for the investigation
target material
target material in specimen specification
Some examples of target material are Genome, Purified chromosome, Transcriptome, Phenotype, Proteome.
A plan specification which specifies the type of material that will be assayed in an investigation.
Used in NCBI BioProject specifcation
specimen sample scope
specimen-based scope of investigation specification
Some examples of specimen scope are Monoisolate, Multiisolate, Multi-species, Environment, or Synthetic.
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
sequencing facility contact person
A person who is the contact representative at the sequencing facility
specimen provider principal investigator
A person who is a principal investigator and provides the specimen
Sample Provider Principal Investigator (PI) Name
sequencing facility
sequencing facility organization
An organization that provides sequence determination service
project objective
specification of data to be generated in an investigation
Some examples of Project Objectives are Raw sequence reads, Sequence, Analysis, Assembly, Annotation, Variation, Epigenetic markers, expression, maps, phenotype
An objective specification which indicates the type of data that will be generated and submitted to a database.
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
project method
investigation assay specification
Some examples of Project Method are Sequence, Array, Mass Spectrometry
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
target capture specification
Some examples of target capture are Whole, CloneEnds, Exome, TargetedLocusLoci, RandomSurvey
A plan specification which specifies how the material enrichment procedure will influence the scale, or type of material that will be assayed in the specimen.
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
specimen provider PI email
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.
A cultured cell population that is derived through one or more passages in culture.
The concept of a 'secondary cultured cell population' covers cell lines as well as cultured cell populations more immediately derived from a primary culture which have yet to achieve adequate genetic stability and compositional homogeneity to be considered a cell line. The extent of the collection of cells in a 'secondary cultured cell population' is restricted only in that all cell members must share a propagation history (ie be derived through a common lineage of passages from an initial culture). Secondary cultured cell populations can be under active culture, stored in a quiescent state for future use, or applied experimentally.
categorical
A value specification that is specifies one category out of a fixed number of nominal categories
scalar
A value specification that consists of two parts: a numeral and a unit label
The value of 'positive' in a classification scheme of "positive or negative"; the value of '20g' on the quantitative scale of mass.
An information content entity that specifies a value within a classification scheme or on a quantitative scale.
This term is currently a descendant of 'information content entity', which requires that it 'is about' something. A value specification of '20g' for a measurement data item of the mass of a particular mouse 'is about' the mass of that mouse. However there are cases where a value specification is not clearly about any particular. In the future we may change 'value specification' to remove the 'is about' requirement.
Damion Dooley's note: Often a value specification may need to allow for a "data item state" that indicates that a given datum doesn't have a recorded or observed or retrievable value, and the general reason for this state.
N50
Gigascience. 2012 Dec 27;1(1):18. doi: 10.1186/2047-217X-1-18. PMID: 23587118. "Here, the contig and scaffold N50 of the YH genome were ~20.9 kbp and ~22 Mbp"
the weighted median item size or N50 is a weighted median of the lengths of items, equal to the length of the longest item i such that the sum of the lengths of items greater than or equal in length to i is greater than or equal to half the length of all of the items. With regard to assemblies the items are typically contigs or scaffolds. It therefore denotes the ability of the software to create contigs and provides information about the resulting sequence assembly
Alejandra Gonzalez-Beltran
Philippe Rocca-Serra
weighted median item size
adapted from: "http://genome.cshlp.org/content/21/12/2224.full?sid=74019122-f944-4ccc-bffe-d16fdd0e7d6c" (from table 7) and from "http://www.nature.com/nrg/journal/v14/n3/full/nrg3367.html"
contig N50
N50 statistic computed for the contigs produced by the assembly process. A contig N50 is calculated by first ordering every contig by length from longest to shortest. Next, starting from the longest contig, the lengths of each contig are summed, until this running sum equals one-half of the total length of all contigs in the assembly. The contig N50 of the assembly is the length of the shortest contig in this list.
adapted from: nature:http://www.nature.com/nrg/journal/v13/n5/box/nrg3174_BX1.html
grant agency
An organization that provides funding support for projects such as investigations.
'funding organization' http://vivoweb.org/ontology/core#FundingOrganization
Gravina, Michael T., Jenny H. Lin, and Stuart S. Levine. "Lane-by-lane sequencing using Illumina's Genome Analyzer II." BioTechniques 54.5 (2013): 265-269. PMID: 23662897
An Illumina Genome Analyzer II which is manufactured by the Illumina corporation. It supports sequencing of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology. The Genome Analyzer IIx is the most widely adopted next-generation sequencing platform and proven and published across the broadest range of research applications.
PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg
Wang J, Qi J, Zhao H, He S, Zhang Y, Wei S, Zhao F. Metagenomic sequencing reveals microbiota and its functional potential associated with periodontal disease. Sci Rep. 2013 May;3:1843. PMID:23673380
A DNA sequencer which is manufactured by the Illumina corporation, with two flow cells and a throughput of up to 55 Gb per day. Built upon sequencing by synthesis technology, the machine is optimized for generation of data for multiple samples in a single run.
PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng
Spaethling, Jennifer M., and James H. Eberwine. "Single-cell transcriptomics for drug target discovery." Current opinion in pharmacology (2013). pmid:23725882
A DNA sequencer which is manufactured by the Illumina corporation, with two flow cells and a throughput of up to 160 Gb per day. Built upon sequencing by synthesis technology, the machine is optimized for generation of data for batching multiple samples or rapid results on a few samples.
Rutvisuttinunt W, Chinnawirotpisan P, Simasathien S, Shrestha SK, Yoon IK, Klungthong C, Fernandez S. Simultaneous and complete genome sequencing of influenza A and B with high coverage by Illumina MiSeq Platform. J Virol Methods. 2013 Nov;193(2):394-404. [PMID:23856301]
A DNA sequencer which is manufactured by the Illumina corporation. Built upon sequencing by synthesis technology, the machine provides an end-to-end solution (cluster generation, amplification, sequencing, and data analysis) in a single machine.
Vissers, Lisenka ELM, et al. "A de novo paradigm for mental retardation." Nature genetics 42.12 (2010): 1109-1112. PMID:21076407
A DNA sequencer which is manufacted by the Applied Biosystems corporation. Built upon SOLiD sequencing technology, the machine generates greater than 1 billion mappable reads per run.
A DNA sequencer which is manufactured by the Pacific Biosciences corporation. Built upon single molecule real-time sequencing technology, the machine is optimized for generation with long reads and high consensus accuracy.
A DNA sequencer which is a desktop sequencer ideal for smaller-scale studies manufactured by the Illumina corporation. It supports sequencing of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology.
A DNA sequencer which is manufactured by the Illumina corporation, with a single flow cell and a throughput of up to 35 Gb per day. It supports sequencing of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology.
An AB SOLid System which is manufacted by the Applied Biosystems corporation. Built upon SOLiD sequencing technology, the machine generates greater than 1 billion mappable reads per run.
An Illumina Genome Analyzer II which is manufactured by the Illumina corporation. It supports sequencing of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology. The Genome Analyzer IIe makes industry-leading next-generation sequencing technology accessible to more laboratories.
A DNA sequencer manufactured by Illumina corporation, with a single flow cell and a throughput of more than 200 Gb per day.
A DNA sequencer manufactured by Illumina corporation, with two flow cell and a throughput of more than 400 Gb per day.
COPAN eSwab, CPT vacutainer, PAXgene Blood DNA tube
A container with the function of containing a specimen.
For details see tracker item: http://sourceforge.net/p/obi/obi-terms/792/
Person: Chris Stoeckert, Jason Hilton, Sagar Jain, Richard Scheuermann
A data transformation in which adapter sequences at the end of a molecular sequence are cut (removed).
A specimen collection process that uses a swab as the collection device. A swab is an absorbent material (e.g. cotton) on a rod (e.g., wooden stick).
Looking at the reads for each ribosomal RNA-depleted RNA extract, the vast majority align to protein coding genes based on the ENSEMBL annotation.
An extract of RNA which is produced through rRNA (ribosomal RNA) depletion (the removal of highly abundant rRNA species).
Genomic DNA of Xenophilus sp. E41 was extracted and sequenced using an Illumina NovaSeq 6000 system.
The cDNAs were sequenced on the PacBio Sequel platform.
The cDNAs were sequenced on the PacBio Sequel II platform.
A specimen collection that obtains a sample of tissue or cell from a living multicellular organism body for diagnostic purposes by means intended to be minimally invasive.
Image-guided needle biopsy allows a doctor to biopsy suspicious areas that aren't readily seen or felt through skin, such as in a prostate gland.
A biopsy which uses an imaging procedure to guide a needle biopsy.
Approaches to Whole Mitochondrial Genome Sequencing on the Oxford Nanopore MinION
Nineteen libraries were constructed and sequenced on nineteen different R9.4 FlowCells using the GridION X5 sequencer
A DNA sequencer that is manufactured by the Oxford Nanopore Technologies corporation, that can run and analyze up to five individual flow cells producing up to 150 Gb of data per run. The sequencer produces real-time results and utilizes nanopore technology with the option of running the flow cells concurrently or individually.
Structural variants identified by Oxford Nanopore PromethION sequencing of the human genome.
cDNA library
cDNA library lacks the non-coding and regulatory elements found in genomic DNA
A collection of DNA molecules with sequences complementary to a specified set of mRNA molecules and commonly developed by enzymatic reverse transcription.
Dan Berrios
modified from Wikipedia
A specimen that is collected with a suctioning tube from the trachea.
Examples of PPE include respirators, gloves, aprons, fall protection, and full body suits, as well as head, eye and foot protection.
PPE is equipment worn by a worker to minimize exposure to specific hazards.
A device which is a wearable garment designed to protect the wearer's body from injury or infection.
A systematic review on the efficacy of face coverings against respiratory viruses analyzed 19 randomized trials and concluded that use of face masks and respirators appeared to be protective in both health care and community settings
A personal protective device worn over the nose and mouth as a respiratory filter to inhibit the flow of particles.
Adapted from https://dictionary.cambridge.org/dictionary/english/face-mask
A non-medical mask may contain fabrics that are not regulated for use in surgical masks or respirators, or may not be designed to form a seal around the nose and mouth.
A face mask not manufactured according to medical equipment standards.
The finding of a much higher rate of infection in the cloth mask arm could be interpreted as harm caused by cloth masks, efficacy of medical masks, or most likely a combination of both.
A face mask manufactured according to a recognized medical equipment standard.
A face mask that meets the U.S. National Institute for Occupational Safety and Health (NIOSH) N95 classification of air filtration, meaning that it filters at least 95% of incoming airborne particles.
A personal protective device used to protect the wearer's entire face (or part of it) from hazards such as flying objects and road debris, chemical splashes, or alternately potentially infectious materials.
A personal protective clothing item which is a gown designed for use by a patient to facilitate caregiving by medical staff.
Examples consist of a short-sleeve V-necked shirt and drawstring pants or a short-sleeve calf-length dress, a tie-back or bouffant-style cap, a mask, a surgical gown, latex gloves, and supportive closed-toe shoes.
A personal protective clothing item which is sterilized and which is worn by a health care professional. It can reference a shirt and pants or dress, and depending on medical protocol, may include a medical cap.
A patient gown intended to be reused after being laundered.
A patient gown intended for a single period of continuous use and then disposed of.
A personal protective clothing item which is a gown worn by a medical professional in order to provide a barrier between patient and professional.
A medical gown which is subjected to a sterilization process and which is intended to be worn by a medical professional during surgical procedures.
A personal protective device which is a glove.
A personal protective device which consists of a garment that serves in place of or in addition to regular body clothing.
A personal protective clothing item which is an overcoat worn by medical or laboratory professionals.
A personal protective glove which is disposable and is used during medical examinations and procedures to help prevent cross-contamination between caregivers and patients.
A personal protective glove which is made out of nitrile rubber.
A personal protective device which is an impermiable material which covers a shoe or boot in order to prevent spread of specific environmental contaminants.
A footwear cover which is designed for a single period of continuous use and then disposed of.
A footwear cover which is designed for repeated use.
A N95 respirator which has been approved by the FDA as a surgical mask.
A personal protective clothing item which is a loose fitting coverall for ease of movement, with sleeves, full leggings and often a hood to cover the head. These can also include overshoe pieces to cover footwear and protect against contamination.
A protective sleeve can be designed to provide protection from heat, welding spatter or hot metal, chemicals, sharp objects, paint or other liquids.
A personal protective clothing item which is a protective cover worn over the arm.
A personal protective clothing item which is an apron.
A personal protective device which is worn on the head that helps prevent transmission of contaminants contained in hair and scalp.
A device used to collect a specimen.
An absorbent pad and its accompanying container are designed to provide safe storage and transport to various degrees for diagnostic and clinical samples, infectious and hazardous materials, chemicals, pharmaceuticals and environmental samples.
A sample collection device consisting of a soft flexible, absorbent pad usually made from natural material such as gauze or cotton, used to absorb specimen fluid or particulate matter.
A swab stick allows a worker to collect samples without touching the inside of the bag
A specimen collection device which is a specimen pad attached to a long handle used to collect specimen material.
A specimen collection device consisting of a specimen pad made of sterile gauze which is aseptically attached to a pole by clips or to a string
A specimen collection swab stick that is pre-moistened with liquid prior to sampling.
Surface sampling procedures involved the use of polyester wipes, swabs, contact slides (two types), and adhesive tapes; a gelatin filter was used to sample the air.
A sample collection device consisting of a thin, less absorbent sheet, used to collect material from surfaces.
Whole genome sequencing of Klebsiella pneumoniae ST11 was performed using an Illumina Miniseq Sequencing System. PMID:31493526
A small benchtop DNA sequencer which is manufactured by the Illumina corporation with integrated cluster generation, sequencing and data analysis. The sequencer accommodates various flow cell configurations and can produce up to 25M single reads or 50M paired-end reads per run.
A DNA sequencer which is manufactured by the Illumina corporation, with a single flow cell. Built upon sequencing by synthesis technology, the machine employs dual surface imaging and offers two high-output options and one rapid-run option.
A DNA sequencer manufactured by the Illumina corporation, which provides the increased flexibility of microarray scanning in addition to sequencing.
plant
virus
A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs.
10/21/09: This is a placeholder term, that should ideally be imported from the NCBI taxonomy, but the high level hierarchy there does not suit our needs (includes plasmids and 'other organisms')
13-02-2009: OBI doesn't take position as to when an organism starts or ends being an organism - e.g. sperm, foetus. This issue is outside the scope of OBI.
WEB: http://en.wikipedia.org/wiki/Organism
specimen
Biobanking of blood taken and stored in a freezer for potential future investigations stores specimen; collecting a stone from a site.
A material entity that is collected for potential use as an input upon which measurements or observations are performed.
GROUP: OBI Biomaterial Branch
sample
A processed material comprised of a collection of cultured cells that has been continuously maintained together in culture and shares a common propagation history.
The extent of a 'cultured cell population' is restricted only in that all cell members must share a propagation history (ie be derived through a common lineage of passages from an initial culture). In being defined in this way, this class can be used to refer to the populations that researchers actually use in the practice of science - ie are the inputs to culturing, experimentation, and sharing. The cells in such populations will be a relatively uniform population as they have experienced similar selective pressures due to their continuous co-propagation. And this population will also have a single passage number, again owing to their common passaging history. Cultured cell populations represent only a collection of cells (ie do not include media, culture dishes, etc), and include populations of cultured unicellular organisms or cultured multicellular organism cells. They can exist under active culture, stored in a quiescent state for future use, or applied experimentally.
PMID: 18524968.Filtration of CSF improves isolation of Mycobacteria.J Clin Microbiol. 2008 Jun 4.
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
ABI 377 DNA Sequencer, ABI 310 DNA Sequencer
A DNA sequencer is an instrument that determines the order of deoxynucleotides in deoxyribonucleic acid sequences.
study design
a matched pairs study design describes criteria by which subjects are identified as pairs which then undergo the same protocols, and the data generated is analyzed by comparing the differences between the paired subjects, which constitute the results of the executed study design.
A plan specification comprised of protocols (which may specify how and what kinds of data will be gathered) that are executed as part of an investigation and is realized during a study design execution.
Editor note: there is at least an implicit restriction on the kind of data transformations that can be done based on the measured data available.
experimental design
rediscussed at length (MC/JF/BP). 12/9/08). The definition was clarified to differentiate it from protocol.
collecting specimen from organism
taking a sputum sample from a cancer patient, taking the spleen from a killed mouse, collecting a urine sample from a patient
a process with the objective to obtain a material entity that was part of an organism for potential future use in an investigation
PERSON:Bjoern Peters
environmental material collection
Taking 1 liter of surface ocean water from the San Diego Mission Bay Jetty. Capturing mice living in rural Arkansas
environmental_material_collection is an acquisition where an object is taken from an environment and put into a storage container. Roles include, environment, thing collected, container, acquirer.
relabel the term and add axiom connecting to EnVO:'environmental material' discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/obi-terms/779/
Bjoern Peters, Alan Ruttenberg
the researcher is very interested in the location
environmental material collection process
http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=104564; Combining spleens of 20 mice, Combining supernatant from a cell culture obtained at different time points
physical combination of several instances of like material
sample pooling
like' is one of the things that you should be controling for in a well-designed experiment. The instances of material need to have the same class.
pooling specimens
lavage
the collection of bronchoalveolar lavage fluid (BAL) from the lungs of mice in order to study the cytokines present
A protocol application to separate cells and/or cellular secretions from an anatomical space by the introduction and removal of fluid
This is not washing, in which case the material of interest is not the resulting fluid
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
A material entity that has the antigen role.
antigen
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
disease (OGMS)
A disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism.
A material entity which is clinically abnormal and part of an extended organism. Disorders are the physical basis of disease.
The totality of all processes through which a given disease instance is realized.
The representation of a conclusion of a diagnostic process.
diagnosis
An object aggregate consisting of an organism and all material entities located within the organism, overlapping the organism, or occupying sites formed in part by the organism.
extended organism
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 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 that involves the interpretation of a clinical picture from a given patient (input) and the assertion to the effect that the patient has a disease, disorder, or syndrome of a certain type, or none of these (output).
A diagnosis that is the outcome of a diagnostic process targeting a second or additional health problem.
amended from http://en.wikipedia.org/wiki/Comorbidity
comorbidity
Analytical,Diagnostic and Therapeutic Techniques and Equipment Category
population density
Pathological Conditions, Signs and Symptoms
Vital signs are unstable and not within normal limits. Patient may be unconscious. Indicators are unfavorable.
A type of Shiga toxin found in E. coli
Shiga toxin 1
A type of Shiga toxin found in E. coli which is antigenically distinct from Shiga toxin 1
Shiga toxin 2
MLST typing
A microbial phenotype that is distinguished by the presence a specific surface antigen.
A social role inhering in a human being.
human social role
A role in human social processes that is realized by health care processes such as seeking or providing treatment for disease and injury, diagnosing disease and injury, or undergoing diagnosis.
health care role
human health care role
A role borne by an organism and that is realized by presenting to a health care provider in a clinical encounter.
Amanda Hicks
patient
CAFE domain expert working group.
In order to avoid the presumption of the formal structures and institutions of Western civilization, bearing a patient role does not entail that the organism presents at an official place of business, with an organization formally and legally registered with various gov't entities, with a person endowed by the gov't with certain certifications.
A human health care role inhering in an organization or human being that is realized by a process of providing health care services to an organism.
health care provider role
A health care role borne by a human being and realized by promoting, maintaining or restoring human health through the study, diagnosis, and treatment of disease, injury and other physical and mental impairments.
physician role
A health care role borne by a human being and realized by the care of individuals, families, and communities so they may attain, maintain, or recover optimal health and quality of life.
nurse
based on: http://en.wikipedia.org/wiki/Nursing
nurse role
A role in human social processes that inheres in an organism.
William R. Hogan Mathias Brochhausen
Defined class that we will ultimately move to an application ontology. We are leaving here for now until we determine which application ontology: it is likely going to be an ontology that does not currently (2012-06-05) exist. Ditto for its current descendants.
Includes animals as well as humans. For example, pet, assistance animal, animal grown for food, work animal, domesticated animal, K-9, etc. Human roles include gender role, party to legal entities, health care provider roles like doctor, nurse, etc.
Previous definition: A role in human social processes played by an organism.
organism social role
A patient role that inheres in a human being.
human patient role
material entity role
Homo sapiens role
A human social role that, if realized, is realized by the process of formal education that the bearer undergoes.
student role
A role that inheres in some entity that is realized in a social act.
Previous definition: A role played by an entity in human social processes.
role in human social processes
A time quality inhering in a bearer by virtue of how long the bearer has existed.
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 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.
TODO: define this or obsolete it and move children somewhere else.
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.
This term was originally named "presence". It has been renamed to reduce ambiguity. Consider annotating with the reciprocal relation,PATO:0001555, has_number_of. For example, rather than E=fin ray Q=count in organism C=10, say E=organism Q=has number of E2= fin ray C=10.
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.
Length often refers to the longer or longest dimension of an object, however, this is not always true. See https://github.com/pato-ontology/pato/issues/337 for full discussion.
A physical quality of the thermal energy of a system.
Damion's Note: Future use might prefer: CMO_0000015 body temperature.
A quality in which events occur in sequence.
A biological sex quality inhering in an individual or a population that only produces gametes that can be fertilised by male gametes.
NCBI BioSample: female
A biological sex quality inhering in an individual or a population whose sex organs contain only male gametes.
A quality denoting the lack of an entity.
We recommend using the new absent terms (physical absence, absent anatomical entity, or absent process) instead of this class. This is a legacy term and will ultimately be obsoleted. See https://github.com/pato-ontology/pato/issues/331.
A quality inhering in a bearer by virtue of the bearer's existence.
A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities.
A physical quality which inheres in a bearer by virtue of some influence is exerted by the bearer's mass per unit size.
A quality inhering in a bearer by virtue of the bearer's power or force.
A quality which inheres in a continuant.
multiply inhering quality of a physical entity
Relational qualities are qualities that hold between multiple entities. Normal (monadic) qualities such as the shape of a eyeball exist purely as a quality of that eyeball. A relational quality such as sensitivity to light is a quality of that eyeball (and connecting nervous system) as it relates to incoming light waves/particles.
A 2-D extent quality inhering in a bearer by virtue of the bearer's two dimensional extent.
A biological sex quality inhering in an organism or a population with both male and female sexual organs in one individual.
A quality inhering in a bearer by virtue of the bearer's magnitude in proportion to the magnitude of another entity.
Examples: height to weight; brain size to body size; root to shoot ratio; urinary sodium to potassium ratio. waist-hip ratio.
A molecular quality that inheres in a molecular entity by virtue of the bearer's disposition to dissolve in a liquid.
A solubility quality inhering in a substance by virtue of the bearer's disposition to dissolve in a liquid.
A physical quality inhering in a bearer by virtue of the bearer's disposition to transmit of an entity through a medium.
Examples could be heat or electricity or sound.
A 1-D extent quality inhering in a bearer by virtue of the bearer's downward or backward or inward dimension.
A size quality inhering in an bearer by virtue of the bearer's extension in one dimension.
A size quality inhering in an bearer by virtue of the bearer's extension in two dimensions.
A 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.
This value is not present in NCBI BioSample host 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.
An organismal quality inhering in a bearer by virtue of the bearer's physical expression of sexual characteristics.
Phenotypic sex refers to an individual's sex as determined by their internal and external genitalia, expression of secondary sex characteristics, and behavior.
Note that NCBI Biosample has these values allowed: male | female | pooled male and female | neuter | hermaphrodite | intersex | not determined | missing | not applicable | not collected
NCBI: http://www.ncbi.nlm.nih.gov/books/NBK10943/
A quality inhering in a bearer by virtue of the bearer's passing into solution.
A quality that inheres in an entire organism or part of an organism.
A quality which inheres in a molecular entity, a single molecule, atom, ion, radical etc.
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.
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 length quality which is equal to the length of any straight line segment that passes from the center of a circle to any endpoint on the circular boundary. The radius is half of the diameter.
Damion Dooley's note: We can't say radius is a subclass of "linear coordinate" because length is considered a quality/specifically dependent continuant, which is disjoint with immaterial entity/independent continuant . I.e. "length" as quality unfortunately can't pertain to abstract entities, only "real" ones.
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
The term intersex is popular in use, but may be considered offensive when applied to humans. DSD can be expanded multiple ways to 'disorders/differences of sexual development/differentiation'.
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 hermaphroditic quality that inheres in a population or organism where an organism changes is a different sexes during different life stages.
Sequential hermaphrodity is generally characterized by an organism producing female gametes and male gametes during different life stages.
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.
May be of the same or different species.
collection of organisms
A material entity that is one or more organisms, viruses or viroids.
organismal entity
social gathering
A type of social behavior in which a collection of humans intentionally gathers together on a temporary basis to engage socially.
GenEpiO curators
human social gathering activity
A human social event in which humans living in the same area or neighborhood gather to carry out activiites relevent to the people living in the area.
GenEpio curators
human community event
A human social gathering in which the intention is to have a good time. Often the intention is to celebrate something like a birthday, anniversary, or holiday, but there is not always a purpose.
party
A human social gathering at which each participant is expected to bring food to share. A potluck also can be party, a social meal, or some other type of social gathering.
potluck
A human social gathering at which two people are married. May include a legal or social ceremony.
wedding
A human social gathering at which the key participant is an expectant parent and other guests bring presents for the soon to be born baby.
baby shower
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.
An amino acid chain that is produced de novo by ribosome-mediated translation of a genetically-encoded mRNA, and any derivatives thereof.
The definition above excludes protein complexes, which some also consider a protein. Those who wish to refer to a class representing both senses of the word are directed to CHEBI:36080. Note that the definition allows for experimentally-manipulated genes, and allows for artifically-produced derivatives that mimic those found naturally. Proteins (in the sense defined here) that descended from a common ancestor can be classified into families and superfamilies composed of products of evolutionarily-related genes. The domain architecture of a protein is described by the order of its constituent domains. Proteins with the same domains in the same order are defined as homeomorphic [PRO:WCB).
Radiation classified by where the exposure to the radiation is occurring.
That part of the Earth exposed to the Earth atmosphere.
A process occurring within or in the vicinity of an organism that exerts some causal influence on the organism via the interaction between an exposure stimulus and an exposure receptor. The exposure stimulus may be a process, material entity or condition (for example, lack of nutrients). The exposure receptor can be an organism, organism population or a part of an organism.
A material entity consisting of multiple components that are causally integrated.
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.
Any extent of continuous biological sequence.
A region of known length which may be used to manufacture a longer region.
A contiguous sequence derived from sequence assembly. Has no gaps, but may contain N's from unavailable bases.
sequence assembly
A sequence of nucleotides that has been algorithmically derived from an alignment of two or more different sequences.
A genome is the sum of genetic material within a cell or virion.
A genotype is a variant genome, complete or incomplete.
Incompatibility in the sequence due to some experimental problem.
Different sources report differing sequences.
A region of the genome of known length that is composed by ordering and aligning two or more different regions.
A collection of discontinuous sequences.
A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer.
A collection of sequences (often chromosomes) taken as the standard for a given organism and genome assembly.
A collection of one or more sequences of an individual.
A Cartesian coordinate system is a coordinate system that specifies each point uniquely in a plane by a pair of numerical coordinates, which are the signed distances from the point to two fixed perpendicular directed lines, measured in the same unit of length.
cartesian coordinate system
n-dimensional coordinate system
In geometry, a coordinate system is a system which uses one or more numbers, or coordinates, to uniquely determine the position of a point or other geometric element on a manifold such as Euclidean space.
Damion Dooley's note:Damion Dooley's note: Outstanding issue: How to attach units to each dimension? This depends on the instance of the problem involving a dimension? Linear offset can be decimal or integer or complex, or a count. - Can have a unit: meter, kilometer, foot, light-year, oranges, apples, fruit Angular offset can be radians or degrees.
coordinate system
a 2 dimensional cartesian coordinate system is a cartesian coordinate system which defines 2 orthogonal one dimensional axes and which may be used to describe a 2 dimensional spatial region.
two dimensional cartesian coordinate system
In mathematics, a spherical coordinate system is a coordinate system for three-dimensional space where the position of a point is specified by three numbers: the radial distance of that point from a fixed origin, its polar angle measured from a fixed zenith direction, and the azimuth angle of its orthogonal projection on a reference plane that passes through the origin and is orthogonal to the zenith, measured from a fixed reference direction on that plane.
spherical coordinate system
A cylindrical coordinate system is a three-dimensional coordinate system that specifies point positions by the distance from a chosen reference axis, the direction from the axis relative to a chosen reference direction, and the distance from a chosen reference plane perpendicular to the axis. The latter distance is given as a positive or negative number depending on which side of the reference plane faces the point.
cylindrical coordinate system
In mathematics, the polar coordinate system is a two-dimensional coordinate system in which each point on a plane is determined by a distance from a fixed point and an angle from a fixed direction.
polar coordinate system
A one dimensional cartesian coordinate system is a cartesian coordinate system which defines a one dimensional axis and which may be used to describe a one dimensional spatial region, i.e. a straight line. It is defined by a point O, the origin, a unit of length and the orientation for the one dimensional space.
one dimensional cartesian coordinate system
a three dimensional cartesian coordinate system is a cartesian coordinate system which defines 3 orthogonal one dimensional axes and which may be used to describe a 3 dimensional spatial region.
three dimensional cartesian coordinate system
a statistic is a measurement datum to describe a dataset or a variable. It is generated by a calculation on set of observed data.
STATO, adapted from wikipedia (http://en.wikipedia.org/wiki/Statistic).
statistic
a count is a data item denoted by an integer and representing the number of instances or occurences of an entity
Damion Dooley's note: Unfortunately an IAO "count" cannot be a subclass of immaterial entity "linear coordinate" as this leads to disjoint conflict.
STATO
Damion Dooley's note: A count datum often implicity carries a date range for which the count is ascertained, or estimated, or simulated for.
Damion Dooley's note: The result of the act of counting is a scalar number whose unit is a description of the thing being counted. One can count 10 oranges and compare that to a count of 5 oranges. One can generalize that a count of 5 oranges is a count of pieces of fruit. One can then compare 5 oranges and 5 apples, fruitfully!
signal to noise ratio is a measurement datum comparing the amount of meaningful, useful or interesting data (the signal) to the amount of irrelevant or false data (the noise). Depending on the field and domain of application, different variables will be used to determinate a 'signal to noise ratio'. In statistics, the definition of signal to noise ratio is the ratio of the mean of a measurement to its standard deviation. It thus corresponds to the inverse of the coefficient of variation
adapted from Wikipedia: http://en.wikipedia.org/wiki/Signal-to-noise_ratio#Alternative_definition last accessed: 2013-10-18
signal to noise ratio
a false positive rate is a data item which accounts for the proportion of incorrect rejection of a true null hypothesis.
PRS,AGB adapted from wikipedia and wolfram alpha
false positive rate
chromosome coordinate system is a genomic coordinate which uses chromosome of a particular assembly build process to define start and end positions. This coordinate system is unstable and will change with each new genome sequence assembly build.
chromosome coordinate system
sequence read count is a data item determining how many sequence reads have been generated by a DNA sequencing assay for a given stretch of DNA
sequence read count
The number degree of freedom is a count evaluating the number of values in a calculation that can vary. In statistics, the number of degrees of freedom ν is equal to N-1 in the case of the direct measurement of a quantity estimated by the arithmetic mean of N independent observations.
the rank of the quadratic form (mathematical definition)
number of degrees of freedom
reaction rate is a measurement datum which represents the speed of a chemical reaction turning reactive species into product species of event (i.e the number of such conversions)s occuring over a time interval
reaction rate
effect size estimate is a data item about the direction and strength of the consequences of a causative agent as explored by statistical methods. Those methods produce estimates of the effect size, e.g. confidence interval
AGB,PRS
effect size estimate
a polychotomous variable is a categorical variable which is defined to have minimally 2 categories or possible values
polychotomous variable
a dichotomous variable is a categorical variable which is defined to have only 2 categories or possible values
AGB-PRS
'has part' exactly 1 ('categorical measurement datum' and ('has category label' exactly 2 'categorical label'))
dichotomous variable
log signal intensity ratio is a data item which corresponding the logarithmitic base 2 of the ratio between 2 signal intensity, each corresponding to a condition.
Orlaith Burke
adapted from wikipedia: http://en.wikipedia.org/wiki/MA_plot last accessed: 2014-03-13
log signal intensity ratio
specificity is a measurement datum qualifying a binary classification test and is computed by substracting the false positive rate to the integral numeral 1
specificity
true negative rate
The correlation coefficient of two variables in a data sample is their covariance divided by the product of their individual standard deviations. It is a normalized measurement of how the two are linearly related.
correlation coefficient
Fold change is a number describing how much a quantity changes going from an initial to a final value or one condition to another condition
fold change
Odds ratio is a ratio that measures effect size, that is the strength of association between 2 dichotomous variables, one describing an exposure and one describing an outcome. It represents the odds that an outcome will occur given a particular exposure, compared to the odds of the outcome occurring in the absence of that exposure ( the probability of the event occuring divided by the probability of an event not occurring). The odds ratio is a ratio of describing the strength of association or non-independence between two binary data values by forming the ratio of the odds for the first group and the odds for the second group. Odds ratio are used when one wants to compare the odds of something occurring to two different groups.
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2938757/ http://www.stats.org/stories/2008/odds_ratios_april4_2008.html
A ratio is a data item which is formed with two numbers r and s is written r/s, where r is the numerator and s is the denominator. The ratio of r to s is equivalent to the quotient r/s.
adapted from Wolfram Alpha: https://www.wolframalpha.com/share/clip?f=d41d8cd98f00b204e9800998ecf8427efdcsig76g7
Threshold cycle (or Ct or Cq) is a count which is defined as the fractional PCR cycle number at which the reporter fluorescence is greater than the threshold in the context of the RT-qPCR assay. The Ct is a basic principle of real time PCR and is an essential component in producing accurate and reproducible data.
threshold cycle
a genomic coordinate system is a coordinate system to describe position of sequence on a genomic scaffold (assembly of chromosome, contig....)
ensembl, ucsc
genomic coordinate system
is a data item formed by dividing the fluorescence intensity obtained in one channel to that obtained in the other channel, typically the case when considering 2-color microarray data when imaging is done for Cy3 and Cy5 dyes.
channel1/channel2 fluorescence intensity ratio
the false negative rate is a data item which denotes the proportion of missed detection of elements known to be meeting the detection criteria
false negative rate
a random variable (or aleatory variable or stochastic variable) in probability and statistics, is a variable whose value is subject to variations due to chance (i.e. randomness, in a mathematical sense)
aleatory variable
stochastic variable
wikipedia: http://en.wikipedia.org/wiki/Random_variable
random variable
ordinal variable is a categorical variable where the discrete possible values are ordered or correspond to an implicit ranking
Alejandra Gonzalez-Beltan
ranked variable
ordinal variable
number of PCR cycle is a count which enumerates how many iterations of 'annealing, renaturation, amplification,' rounds (or cycles) are performed during a polymerase chain reaction (PCR) or an assay relying on PCR.
adapted from various sources including: http://www.ncbi.nlm.nih.gov/genome/probe/doc/TechQPCR.shtml
number of PCR cycle
sensitivity is a measurement datum qualifying a binary classification test and is computed by substracting the false negative rate to the integral numeral 1
recall
sensitivity
adapted from: http://en.wikipedia.org/wiki/Sensitivity_and_specificity and http://mathworld.wolfram.com/Sensitivity.html
true positive rate
Relative risk is a measurement datum which denotes the risk of an 'event' relative to an 'exposure'. Relative risk is calculated by forming the ratio of the probability of the event occurring in the exposed group versus the probability of this event occurring in the non-exposed group.
A continuous variable is one for which, within the limits the variable ranges, any value is possible.
continuous variable
a categorical variable is a variable which that can only assume a finite number of value and cast observation in a small number of categories
discrete variable
nominal variable
categorical variable
The allele frequency is a data item which denotes the incidence of a gene variant in a population. It is calculated as a ratio, by dividing the number of copies of a particular allele by the number of copies of all alleles at the genetic place (locus) in a population.
variable type
a variable is a data item which can assume any of a set of values, either as determined by an agent or as randomly occuring through observation.
adapted from wolfram-alpha (http://www.wolframalpha.com/input/?i=variable) definition 2. and from Oxford English Dictionary: http://www.oed.com/view/Entry/221514?redirectedFrom=variable#eid, definition B,1
variable
Bayes factor is a ratio between 2 probabilities of observing data according 2 distinct models. It is used in Bayes model selection to evaluate which model best explains the data. if K<0, the model used in the denominator term is supported, if K>1, the model used in the numerator term is supported. The Bayes factor is about the plausibility of 2 different models
adapted from Wikipedia last accessed 2013-11-13
Bayes factor
A ratio where the numerator and denominator are expressed in the same unit.
the likelihood ratio is a ratio which is formed by dividing the post-test odds with the pre-test odds in the context of a Bayesian formulation
likelihood ratio
the likelihood ratio of negative results is a ratio which is formed by dividing the difference between 1 and sensitivity of the test by the specificity value of a test. This can be expressed also as dividing the probability of a person who has the disease testing negative by the probability of a person who does not have the disease testing negative.
likelihood ratio for negative results
adapted from Wikipedia: https://en.wikipedia.org/wiki/Likelihood_ratios_in_diagnostic_testing last accessed: May 2016
negative likelihood ratio
the likelihood ratio of positive results is a ratio which is form by dividing the sensitivity value of a test by the difference between 1 and specificity of the test. This can be expressed also as dividing the probability of the test giving a positive result when testing an affected subject versus the probability of the test giving a positive result when a subject is not affected.
likelihood ratio for positive results
positive likelihood ratio
A proportion in which the numerator represents all events of interest (for example, both new and preexisting cases of a disease) in the population, which is represented by the denominator.
Brian S. Alper, Muhammad Afzal, Joanne Dehnbostel, Janice Tufte, Kenneth Wilkins, Harold Lehmann
adapted from: https://www.health.ny.gov/diseases/chronic/basicstat.htm
prevalence
A proportion in which the numerator represents new events.
Brian S. Alper, Muhammad Afzal, Joanne Dehnbostel, Janice Tufte
incidence
mortality is a ratio formed by the number of deaths due to a disease divided by the total population size.
mortality
in the context of binary classification, accuracy is defined as the proportion of true results (both true positives and true negatives) to the total number of cases examined (the sum of true positive, true negative, false positive and false negative). It can be understood as a measure of the proximity of measurement results to the true value. Accuracy is a metric used in the context of classification tasks to evaluate the proportion of correctly predicted instances among the total instances. Key Points: Use Case: Classification performance evaluation. Metric: Measures the proportion of correct predictions. Interpretation: Higher values indicate better classification performance.
adapted from wikipedia: https://en.wikipedia.org/wiki/Accuracy_and_precision#In_binary_classification last accessed: May 2016 adapted from ChatGPT using the following prompt: [what is the difference between "Rand Index" and "Accuracy" in statistics] last accessed: July 2024
accuracy
precision or positive predictive value is defined as the proportion of the true positives against all the positive results (both true positives and false positives) A proportion in which the numerator represents the correctly detected items within the denominator that represents all items detected.
positive predictive value
adapted from wikipedia: https://en.wikipedia.org/wiki/Accuracy_and_precision#In_binary_classification last accessed: May 2016
precision
The probability of a patient having the target disorder before a diagnostic test result is known
pretest probability
the proportion of individuals in a population with the outcome of interest
adapted from: http://handbook.cochrane.org/chapter_9/9_2_2_4_measure_of_absolute_effect_the_risk_difference.htm
observed risk
a estimate is a data item which is computed from a dataset to provide an approximated value (an estimator) for a 'statistical parameter' (a 'characteristics/parameter' of the true underlying distribution) of a real population.
Tom Nichols
Matthews Correlation Coefficient (or MCC) is a correlation coefficient which is a measure of the quality of binary (two-class) classifications, introduced by biochemist Brian W. Matthews in 1975.
adapted from wikipedia: https://en.wikipedia.org/wiki/Matthews_correlation_coefficient and from: https://doi.org/10.1016/0005-2795(75)90109-9
In a planned experiment where to covariance (genotype x environment) can be controlled and held at 0, the heritability is defined as the ratio of the variance of the genotypic variables to the variance of the phenotypic variables. H2 = Var(G)/Var(P) H2 is the broad-sense heritability. This reflects all the genetic contributions to a population's phenotypic variance including additive, dominant, and epistatic (multi-genic interactions), as well as maternal and paternal effects, where individuals are directly affected by their parents' phenotype, for example, milk production in mammals.
A particularly important component of the genetic variance is the additive variance, Var(A), which is the variance due to the average effects (additive effects) of the alleles. Since each parent passes a single allele per locus to each offspring, parent-offspring resemblance depends upon the average effect of single alleles. Additive variance represents, therefore, the genetic component of variance responsible for parent-offspring resemblance. The additive genetic portion of the phenotypic variance is known as Narrow-sense heritability and is defined as: h2 = Var(A)/Var(P)
the frequency (i.e., the proportion) of possible confidence intervals that contain the true value of their corresponding parameter. In other words, if confidence intervals are constructed using a given confidence level in an infinite number of independent experiments, the proportion of those intervals that contain the true value of the parameter will match the confidence level. A probability measure of the reliability of an inferential statistical test that has been applied to sample data and which is provided along with the confidence interval for the output statistic.
adapted from wikipedia: https://en.wikipedia.org/wiki/Confidence_interval and from: http://www.oxfordreference.com/view/10.1093/acref/9780191792236.001.0001/acref-9780191792236-e-103?rskey=tQCMI6&result=1
The selectivity ratio (SR) is defined as the ratio of explained vexpl,i to residual variance vres,i for the variable i on the target projection (TP) component in the context of Partial Least Squares Analysis.
the percentage of variance is an output of principal component analysis (PCRA), which is obtained by forming the ratio of an eigen-value divided by the sum of all eigen-values. This produces a "percentage of variance" for each eigen-vector.
adapted from: https://stats.stackexchange.com/questions/31908/what-is-percentage-of-variance-in-pca
the Rand index is a ratio, related to the notion of accuracy (STATO_0000415), which is used to compare the similarity of two clustering outcomes.
Rand, W.M. 1971. Objective criteria for the evaluation of clustering methods. Journal of the American Statistical Association 66: 846--850. Hubert, L. and Arabie, P. 1985. Comparing partitions. Journal of Classification. 2: 193--218.
Rand index
the adjusted Rand index is a measure which rescales the Rand index, taking into account that random chance will cause some objects to occupy the same clusters, so the Rand Index will never actually be zero.
ARI
adjusted Rand index
a proportion is a ratio which corresponds to the fraction of the total presenting a particular feature
measure of association is a statistic which quantitatively represents a relationship between two or more variables
Brian S. Alper, Joanne Dehnbostel, Kenneth Wilkins, Muhammad Afzal, Neeraj Ojha
COKA group
measure of association
measure of correlation is a measure of association between ordinal or continuous variables. A value of 0 means no association. A positive value means a positive association (as one variable increases, the other variable increases). A negative value means a negative association (as one variable increases, the other variable decreases). For correlation coefficients, the possible values range from +1 (perfect positive association) to -1 (perfect negative association)
Brian S. Alper, Joanne Dehnbostel, Muhammad Afzal, Yuan Gao, Kenneth Wilkins, Harold Lehmann
measure of correlation
A proportion in which the numerator represents the correctly non-detected items within the denominator that represents all items not detected.
Harold Lehmann, Ken Wilkins, Philippe Rocca-Serra, Joanne Dehnbostel
A proportion in which the numerator represents the cases in which an event or characteristic occurs and the denominator represents all possible cases.
Brian S. Alper, Harold Lehmann, Joanne Dehnbostel, Muhammad Afzal, Janice Tufte
diagnostic yield is a proportion in which the numerator represents the correctly detected items within the denominator that represents all items tested.
Brian S. Alper, Harold Lehmann, Joanne Dehnbostel, Kenneth Wilkins
"Diagnostic yield was defined as the number of participants with positive findings for advanced neoplasia relative to all participants" in https://pubs.rsna.org/doi/10.1148/radiol.12112486 Other 'definitions' found include synonymous use with sensitivity, and 'diagnostic yield' describing the statistic array of TP, FP, TN, and FN data.
ratio-based measure of association is a measure of association which relies on a quotient of 2 quantities to indicate the strength of the association.
ratio-based measure of association
odds correspond to a ratio in which the numerator represents the probability that an event will occur and the denominator represents the probability that an event will not occur. 'Odds' and 'Odds ratio' are different terms. 'Odds' is a ratio of probabilities. 'Odds ratio' is a ratio of two different odds. Odds are calculated as p / (1-p) where p is the probability of event occurrence. When p = 0, the odds = 0. When p = 1, the odds may be expressed as not calculable or as "odds against = 0". Odds may be expressed as p:(1-p). Odds may be expressed as p:q where q = 1-p. Odds may be expressed as a:b where a and b are multiples of p and (1-p). Examples of different expressions of the same odds include 3:2, 3/2, 0.6:0.4, 0.6/0.4, and 1.5. Odds may be expressed as "odds for" or "odds in favor" (e.g. 1:5 for a "3" on a 6-sided die) or "odds against" (e.g. 5:1 against a "3" on a 6-sided die). The term "betting odds" used in gambling that involves financial amounts in the formulation is not an "Odds" in the definition of the Scientific Evidence Code System.
Brian S. Alper, Harold Lehmann, Joanne Dehnbostel, Khalid Shahin, Kenneth Wilkins, Muhammad Afzal
A ratio formed between a numerator and a denominator (both described by the same unit), and that is multiplied by 100.
Brian S. Alper, Harold Lehmann, Joanne Dehnbostel, Kenneth Wilkins, Janice Tufte, Muhammad Afzal, Khalid Shahin, Philippe Rocca-Serra
A ratio in which the numerator represents any quantity and the denominator represents an interval of time.
Brian S. Alper, Harold Lehmann, Joanne Dehnbostel, Kenneth Wilkins, Muhammad Afzal
COKA/SEVCO Group
rate
A skin and integumentary tissue symptom that is characterized by a fluid-filled elevation of the epidermis.
A skin and integumentary tissue symptom that is characterized by an abnormal change in structure of the skin that is especially circumscribed and well defined due to injury or disease.
A symptom is a perceived change in function, sensation, loss, disturbance or appearance reported by a patient indicative of a disease.
A skin and integumentary tissue symptom that is characterized by the outer layer of the skin starting to replace itself. Often, this happens when skin is damaged, either by disease or injury.
A type of historical information or metadata about the origin, location or the source of something, or the history of the ownership or location of an object or resource including digital objects. For example, information about the Principal Investigator who recorded the data, and the information concerning its storage, handling, and migration.
Peter McQuilton
provenance
data stewardship technical concept
A process that is the means during which the pathogen is transmitted directly or indirectly from its natural reservoir, a susceptible host or source to a new host.
TRANS follows the CDC Epidemiology model of transmission between two hosts, a reservoir and host or other non-host, non-reservoir entities (e.g), a needle and a host.
transmission of infection
Direct and essentially immediate transfer of infectious agents to a receptive portal of entry through which human or animal infection may take place. This may be by direct contact such as touching, kissing, biting, or sexual intercourse or by the direct projection (droplet spread) of droplet spray onto the conjunctiva or the mucous membranes of the eyes, nose, or mouth. It may also be by direct exposure of susceptible tissue to an agent in soil, compost, or decaying vegetable matter or by the bite of a rabid animal. Transplacental transmission is another form of direct transmission.
Direct transmission is a transmission process that is the means during which the pathogen is transmitted immediately from a reservoir, source or host to another host.
direct transmission
Indirect transmission is a transmission process during which the pathogen is indirectly transferred from a reservoir, source or host to another host by intermediary vehicles, vectors or as airborne dust particles.
indirect transmission
Congenital transmission is a direct transmission process during which the pathogen is transmitted directly from mother to child at or around the time of birth.
congenital
contact transmission
Contact transmission is a direct transmission process during which the pathogen is transmitted from a reservoir, source or host to another host by kissing, skin-to-skin contact, sexual intercourse, or by contact with soil or vegetation containing the pathogen.
contact
Droplet spread transmission is a direct transmission process during which the pathogen is transmitted from a reservoir, source or host to another host by spray of aerosols over a short distance, spray from sneezing, coughing or talking.
droplet spread
Vehicle-borne ingestion transmission is an indirect vehicle-borne transmission process during which the pathogen is indirectly transferred from a reservoir, source or host to another host by ingestion of fluids or foods or food products including: food, water, milk, or meat products.
vehicle-born ingestion
Lower, narrow portion of the uterus where it joins with the top end of the vagina.
Orifice of the olfactory system. The naris is the route by which odorants enter the olfactory system[MAH].
An organ that is capable of transducing sensory stimulus to the nervous system.
Anatomical projection that protrudes from the skin. Examples: hair, nail, feather, claw, hoof, horn, wattle, spur, beak, antler, bristle and some scales.
One of the epidermal growths that form the distinctive outer covering, or plumage, on birds. Feathers are formed in tiny follicles in the epidermis, or outer skin layer, that produce keratin proteins.
Any hollow cylindrical anatomical structure containing a lumen through which substances are transported.
Any of the rounded masses of lymphoid tissue that are surrounded by a capsule of connective tissue, are distributed along the lymphatic vessels, and contain numerous lymphocytes which filter the flow of lymph.
The fibromuscular tubular canal through which urine is discharged from the bladder to the exterior via the external urinary meatus; in males, the urethra is joined by the ejaculatory ducts and serves as a passageway for semen during ejaculation, as well as a canal for urine during voiding; in females, the urethra is shorter and emerges above the vaginal opening.
A subdivision of the digestive tract that connects the small intestine to the cloaca or anus. Lacks or has few villi[Kardong].
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.
Anatomical structure that is part of the respiratory system. In mammals consists of upper and lower tracts.
A life cycle stage that starts with fertilization and ends with the fully formed embryo.
A distinct juvenile stage many animals undergo before metamorphosis into adults. Animals with indirect development such as insects, amphibians, or cnidarians typically have a larval phase of their life cycle.
proximo-distal subdivision of respiratory tract
Anatomical cluster consisting of the skeletal elements and articular elements that are part of an individual subdivision of the organism.
A spatiotemporal region encompassing some part of the life cycle of an organism.
A tube in the respiratory system. Examples: bronchus, bronchiole, trachea.
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.
Anatomical conduit that connects two adjacent body spaces (or a body space with the space surrounding the organism)[FMA,modified].
Common chamber into which the intestines and excretory system opens. Arises during development in all vertebrates, but in many it becomes subdivided, lost or incorporated into other structures.
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 section dividing a colon along a proximal-distal axis.
Organ that functions in gaseous exchange between an organism and its environment. In plants, microorganisms, and many small animals, air or water makes direct contact with the organism's cells or tissue fluids, and the processes of diffusion supply the organism with dioxygen (O2) and remove carbon dioxide (CO2). In larger animals the efficiency of gaseous exchange is improved by specialized respiratory organs, such as lungs and gills, which are ventilated by breathing mechanisms.
Amniotic fluid is a bodily fluid consisting of watery liquid surrounding and cushioning a growing fetus within the amnion. It allows the fetus to move freely without the walls of the uterus being too tight against its body. Buoyancy is also provided. The composition of the fluid changes over the course of gestation. Initially, amniotic fluid is similar to maternal plasma, mainly water with electrolytes. As the fetus develops, proteins, carbohydrates, lipids, phospholipids originating from the lungs, fetal cells, and urea are deposited in the fluid.
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 lining of mostly endodermal origin, covered in epithelium, which is involved in absorption and secretion. They line various body cavities that are exposed to the external environment and internal organs. It is at several places continuous with skin: at the nostrils, the lips, the ears, the genital area, and the anus. The sticky, thick fluid secreted by the mucous membranes and gland is termed mucus. The term mucous membrane refers to where they are found in the body and not every mucous membrane secretes mucus[WP].
A portion of organism substance that is produced by exocrine glands.
organism body product
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.
Non-material anatomical entity of three dimensions, that is generated by morphogenetic or other physiologic processes; is surrounded by one or more anatomical structures; contains one or more organism substances or anatomical structures.
Multicellular, connected anatomical structure that has multiple organs as parts and whose parts work together to achieve some shared function.
Anatomical structure that is an individual member of a species and consists of more than one cell.
Anatomical structure which is a subdivision of a whole organism, consisting of components of multiple anatomical systems, largely surrounded by a contiguous region of integument.
Anatomical structure that consists of cell parts and cell substances and together does not constitute a cell or a tissue.
Anatomical group whose component anatomical structures lie in close proximity to each other.
Multicellular anatomical structure that consists of many cells of one or a few types, arranged in an extracellular matrix such that their long-range organisation is at least partly a repetition of their short-range organisation.
Portion of tissue, that consists of one or more layers of epithelial cells connected to each other by cell junctions and which is underlain by a basal lamina. Examples: simple squamous epithelium, glandular cuboidal epithelium, transitional epithelium, myoepithelium[CARO].
Editor note: surface epithelium may contain non-epithelial cells, such as melanocytes, lymphocytes and dendritic cells, within the sheet of epithelial cells. Do we consider these part of the epithelium, or located-in it?
Unilaminar epithelium, which consists of a single layer of columnar cells. Examples: ciliated columnar epithelium, gastric epithelium, microvillus columnar epithelium.[FMA].
Compound organ that contains one or more macroscopic anatomical spaces.
Epithelium which consists of a single layer of epithelial cells. Examples: endothelium, mesothelium, glandular squamous epithelium.[FMA].
The ileocecal valve is a sphincter muscle situated at the junction of the small intestine (ileum) and the large intestine. Its critical function is to limit the reflux of colonic contents into the ileum.
Mucus is a bodily fluid consisting of a slippery secretion of the lining of the mucous membranes in the body. It is a viscous colloid containing antiseptic enzymes (such as lysozyme) and immunoglobulins. Mucus is produced by goblet cells in the mucous membranes that cover the surfaces of the membranes. It is made up of mucins and inorganic salts suspended in water.
Anatomical entity that comprises the organism in the early stages of growth and differentiation that are characterized by cleavage, the laying down of fundamental tissues, and the formation of primitive organs and organ systems. For example, for mammals, the process would begin with zygote formation and end with birth. For insects, the process would begin at zygote formation and end with larval hatching. For plant zygotic embryos, this would be from zygote formation to the end of seed dormancy. For plant vegetative embryos, this would be from the initial determination of the cell or group of cells to form an embryo until the point when the embryo becomes independent of the parent plant.
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.
A myogenic muscular circulatory organ found in the vertebrate cardiovascular system composed of chambers of cardiac muscle. It is the primary circulatory organ.
Taxon notes:" the ascidian tube-like heart lacks chambers....The ascidian heart is formed after metamorphosis as a simple tube-like structure with a single-layered myoepithelium that is continuous with a single-layered pericar- dial wall. It lacks chambers and endocardium.... The innovation of the chambered heart was a key event in vertebrate evolution, because the chambered heart generates one-way blood flow with high pressure, a critical requirement for the efficient blood supply of large-body vertebrates... all extant vertebrates have hearts with two or more chambers (Moorman and Christoffels 2003)" DOI:10.1101/gad.1485706
Anatomical structure that consists of two or more adjacent skeletal structures, which may be interconnected by various types of tissue[VSAO].
Reproductive organ that produces and releases eggs (ovary) or sperm (testis).
The gonad of a female organism which contains germ cells.
female organism reproductive system gonad
female organism reproductive system gonada
gonad of female organism reproductive system
gonad of reproductive system of female organism
gonada of female organism reproductive system
gonada of reproductive system of female organism
reproductive system of female organism gonad
reproductive system of female organism gonada
The outer epithelial layer of the skin that is superficial to the dermis.
Functional system which consists of structures involved in respiration.
An airway through which respiratory air passes in organisms.
Anterior subdivision of a digestive tract.
A portion of the respiratory and digestive tracts; its distal limit is the superior part of the esophagus and it connects the nasal and oral cavities with the esophagus and larynx; it contains the valleculae and the pyriform recesses; its upper limits are the nasal cavity and cranial base.[FEED].
Consider generalizing to deuterostome pharynx
Tube that connects the pharynx to the stomach. In mammals, the oesophagus connects the buccal cavity with the stomach. The stratified squamous non-keratinised epithelium lining the buccal cavity is continued through the pharynx down into the oesophagus. The lowest part of the oesophagus (ca. 2 cm) is lined with gastric mucosa and covered by peritoneum. The main body of the oesophagus is lined with small, simple mucous glands. Each gland opens into the lumen by a long duct which pierces the muscularis mucosae (Wilson and Washington, 1989). A sphincter is situated at the point where the oesophagus enters the stomach to prevent gastro-oesophageal reflux, i.e. to prevent acidic gastric contents from reaching stratified epithelia of the oesophagus, where they can cause inflammation and irritation (Wilson and Washington, 1989; Brown et al., 1993).
Middle subdivision of a digestive tract[CJM]. In vertebrates: The middle part of the alimentary canal from the stomach, or entrance of the bile duct, to, or including, the large intestine[GO].
The caudalmost subdivision of a digestive tract.
The terminal portion of the intestinal tube, terminating with the anus.
rectal
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.
Transudate contained in the pleural cavity.
Excretion that is the output of a kidney.
Joint fluid is a transudate of plasma that is actively secreted by synovial cells.
The lymph nodes located around the axillary vein that receive lymphatic drainage from the upper or forelimb, scapular region and pectoral region.
Subdivision of skeletal system that consists of all the vertebra and associated skeletal elements and joints in the body[modified from VSAO].
A pouch in the digestive tract that connects the ileum with the ascending colon of the large intestine. It is separated from the ileum by the ileocecal valve, and is the beginning of the large intestine. It is also separated from the colon by the cecocolic junction.
Taxon notes: in some herbivorous lizards, a cecum is present between small and large intestines[Kardong]
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.
Section of colon which is distal to the cecum and proximal to the transversecolon.[FMA,modified].
The proximal-distal subdivision of colon that runs transversely across the upper part of the abdomen, from the right to the left colic flexure. Continuous with the descending colon[BTO,modified].
The portion of the colon between the left colic flexure and the sigmoid colon at the pelvic brim; the portion of the descending colon lying in the left iliac fossa is sometimes called the iliac colon.
The part of the large intestine that is closest to the rectum and anus. It forms a loop that averages about 40 cm. in length, and normally lies within the pelvis, but on account of its freedom of movement it is liable to be displaced into the abdominal cavity.
The fundus is the portion of the stomach that lies above the cardiac notch, and contains the fundic glands[GO, Kardong].
The body of stomach is the part of the stomach that lies between the fundus above and the pyloric antrum below; its boundaries are poorly defined[GO].
The part of the stomach attached to the esophagus. The cardia begins immediately distal to the z-line of the gastroeosphageal junction, where the squamous epithelium of the esophagus gives way to the columnar epithelium of the gastrointestinal tract[WP].
The lesser curvature of the stomach, extending between the cardiac and pyloric orifices, forms the right or posterior border of the stomach. It descends as a continuation of the right margin of the esophagus in front of the fibers of the right crus of the diaphragm, and then, turning to the right, it crosses the first lumbar vertebra and ends at the pylorus. Nearer its pyloric than its cardiac end is a well-marked notch, the incisura angularis, which varies somewhat in position with the state of distension of the viscus; it serves to separate the stomach into a right and a left portion. The lesser curvature gives attachment to the two layers of the hepatogastric ligament, and between these two layers are the left gastric artery and the right gastric branch of the hepatic artery. [WP,unvetted].
The greater curvature of the stomach is directed mainly forward, and is four or five times as long as the lesser curvature. [WP,unvetted].
The area at the bottom of the stomach on the caudal side of the pyloric canal that contains gastrin-producing G cells, which stimulate acid production, and the luminal pH-sensitive population of somatostatin-producing D cells.
The stomach tissue region surrounding and controlling the distal outlet of the stomach, which opens into the duodenum.
Orifice at the opposite end of an animal's digestive tract from the mouth. Its function is to expel feces, unwanted semi-solid matter produced during digestion, which, depending on the type of animal, may be one or more of: matter which the animal cannot digest, such as bones; food material after all the nutrients have been extracted, for example cellulose or lignin; ingested matter which would be toxic if it remained in the digestive tract; and dead or excess gut bacteria and other endosymbionts.
opening of terminal part of digestive tract
Distensible musculomembranous organ situated in the anterior part of the pelvic cavity in which urine collects before excretion[MP].
Transudate contained in the peritoneal cavity.
cerebrospinal fluid (CSF)
A clear, colorless, bodily fluid, that occupies the subarachnoid space and the ventricular system around and inside the brain and spinal cord.
Skeletal element that is composed of bone tissue.
A joint that connects the hindlimb autopod and zeugopod skeletons.
The lymph nodes located in the groin area.
The lymph nodes which drain the legs; contained in the popliteal fossa.
A tube extending from the mouth to the anus.
The segment of the respiratory tract that starts proximally with the nose and ends distally with the cricoid cartilage, before continuing to the trachea.
The segment of the respiratory tract that starts proximally with the trachea and includes all distal structures including the lungs[WP,modified].
Organ consisting of a tissue made up of various elongated cells that are specialized to contract and thus to produce movement and mechanical work[GO].
An anatomical cavity that is part of the olfactory apparatus. This includes the space bounded anteriorly by the nares and posteriorly by the choanae, when these structures are present.
The section of the pharynx that lies above the soft palate.
The portion of the pharynx that lies between the soft palate and the upper edge of the epiglottis.
The small curved bones that extends horizontally along the lateral wall of the nasal passage.
The paired air-filled cavities surrounded by the bones of the face that are lined by mucous membranes and are continuous with the nasal cavity.
Aqueous substance secreted by the lacrimal gland.
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.
The thin, yellow, serous fluid secreted by the mammary glands during pregnancy and immediately postpartum before lactation begins. It consists of immunologically active substances, white blood cells, water, protein, fat, and carbohydrates.
The liquid component of blood, in which erythrocytes are suspended.
The portion of blood plasma that excludes clotting factors.
Portion of semisolid bodily waste discharged through the anus[MW,modified].
Respiration organ that develops as an outpocketing of the esophagus.
Snakes and limbless lizards typically possess only the right lung as a major respiratory organ; the left lung is greatly reduced, or even absent. Amphisbaenians, however, have the opposite arrangement, with a major left lung, and a reduced or absent right lung [WP]
Anatomical structure that is part of an embryo.
An organ that is located within the body cavity (or in its extension, in the scrotum); it consists of organ parts that are embryologically derived from endoderm, splanchnic mesoderm or intermediate mesoderm; together with other organs, the viscus constitutes the respiratory, gastrointestinal, urinary, reproductive and immune systems, or is the central organ of the cardiovascular system. Examples: heart, lung, esophagus, kidney, ovary, spleen.
The organ that functions to filter blood and to store red corpuscles and platelets.
An exocrine gland which secretes bile and functions in metabolism of protein and carbohydrate and fat, synthesizes substances involved in the clotting of the blood, synthesizes vitamin A, detoxifies poisonous substances, stores glycogen, and breaks down worn-out erythrocytes[GO].
Subdivision of digestive tract that connects the stomach to the large intestine and is where much of the digestion and absorption of food takes place (with the exception of ruminants). The mammalian small intestine is long and coiled and can be differentiated histologically into: duodenum, jejunem, ileum[WP,cjm,Kardong].
An organ that aids digestion and stores bile produced by the liver[WP].
Rats do not have a gallbladder, but produce bile. The bile flows directly from the liver through the (hepatic) bile duct into the small intestine (Hebel and Stromberg, 1988)
A paired organ of the urinary tract that produces urine and maintains bodily fluid homeostasis, blood pressure, pH levels, red blood cell production and skeleton mineralization.
The first part of the small intestine. At the junction of the stomach and the duodenum the alimentary canal is inflected. The duodenum first goes anteriorly for a short distance, turns dorsally, and eventually caudally, thus it is a U-shaped structure with two horizontal sections (a ventral and a dorsal one).
The portion of the small intestine that extends from the duodenum to the ileum.
The portion of the small intestine that extends from the jejunum to the colon.
Lung which consists of the right upper lobe, middle lobe and right lower lobe.[FMA].
The small terminal dilation of the alveolar ducts around which the alveoli form pocket-like clusters.
The upper conducting airways of the lung; these airways arise from the terminus of the trachea.
The conducting airway of the lungs found terminal to the bronchi; these structures contain neither cartilage nor mucous-secreting glands; the epithelium of the bronchioles becomes thinner with each branching.
In some texts/references/ontologies, bronchiole has been used as an exact synonym of 'lobular bronchiole'. However, a 'lobular bronchiole' is a segment of a bronchiole.
Joint in which the articulating bones or cartilages are connected by an articular capsule which encloses a synovial membrane and a synovial cavity. Examples: Temporomandibular joint, knee joint.[FMA].
The lower segment of the trunk, inferioposterior to the abdomen proper, in the transition area between the trunk and the lower limbs.
A gland that secretes products (excluding hormones and other chemical messengers) into ducts (duct glands) which lead directly into the external environment[WP]. Typical exocrine glands include sweat glands, salivary glands, mammary glands, stomach, liver, pancreas.
Endocrine glands are glands of the endocrine system that secrete their products directly into the circulatory system rather than through a duct.[WP, modified].
The soft tissue that fills the cavities of bones.
Tissue with cells that deposit non-polarized extracellular matrix including connective tissue fibers and ground substance.
Muscle tissue is a contractile tissue made up of actin and myosin fibers[GO].
Vertebrate muscle is categorized into three major muscle types defined by their structural and functional properties: skeletal, cardiac and smooth. In Dmel the counterparts are somatic, heart/cardiac and visceral. Here we take a cell type based approach.
Lymph is the fluid that is formed when interstitial fluid enters the conduits of the lymphatic system through lymph capillaries[WP].
Distal segment of the fore limb, including carpal region, metacarpal region and digits.
The double layer of peritoneum that extends from the liver to the lesser curvature of the stomach and the start of the duodenum. [WP,unvetted].
EDITOR_NOTE exact part of and develops from relationships need to be established
The fluid-filled cavity that lies between the visceral and parietal pleurae.
Transudate contained in the pericardial cavity.[FMA].
An epithelium that is part of the mouth and lines the oral cavity, typically stratified squamous, and may be para-, ortho- or non- keratinized. Primary barrier between oral environment and deeper tissues.
Cervical lymph nodes are lymph nodes found in the neck. [WP,unvetted].
The evaginations of the mucous membrane of the nasal cavity into the ethmoidal bony labyrinth, forming multiple small paranasal sinuses.
Terminal segment of free limb, immediately distal to the zeugopod region. The fully developed autopod consists of the autopod skeleton plus associated structures such as integument, muscle tissue, vasculature etc. The autopod is divided into mesopodial, metapodiual, and acropodial segments. Examples: human hand, mouse paw, human foot.
A lymph node that is part of an abdomen [Automatically generated definition].
The visceral glands that are associated with the branches of the celiac artery, including the gastric, hepatic, and pancreaticolienal (splenic) lymph nodes.
The lymph nodes located in the mesentery, of which there are 3 classes: ileocolic, juxtaintestinal mesenteric, and central superior group.
Replacement bone that forms within cartilage.
The submandibular lymph nodes (submaxillary glands in older texts), three to six in number, are placed beneath the body of the mandible in the submaxillary triangle, and rest on the superficial surface of the submaxillary salivary gland. One gland, the middle gland of Stahr, which lies on the external maxillary artery as it turns over the mandible, is the most constant of the series; small lymph glands are sometimes found on the deep surface of the submaxillary salivary glands. The afferents of the submaxillary glands drain the medial palpebral commissure, the cheek, the side of the nose, the upper lip, the lateral part of the lower lip, the gums, and the anterior part of the margin of the tongue. Efferent vessels from the facial and submental glands also enter the submaxillary glands. Their efferent vessels pass to the superior deep cervical glands. [WP,unvetted].
A lymph node that is part of a mediastinum. Each consists of several lymph node groups, especially along the trachea (5 groups), along the esophagus and between the lung and the diaphragm. In the mediastinal lymph nodes arises lymphatic ducts, which draines the lymph to the left subclavian vein (to the venous angle in the confluence of the subclavian and deep jugular veins). The mediastinal lymph nodes along the esophagus are in tight connection with the abdominal lymph nodes along the esophagus and the stomach. That fact facilitates spreading of tumors cells through these lymphatics in cases of cancers of the stomach and particularly of the esophagus. Through the mediastinum, the main lymphatic drainage from the abdominal organs goes via the thoracic duct (ductus thoracicus), which drains majority of the lymph from the abdomen to the above mentioned left venous angle.
The lymph nodes located along the brachial vein that receive drainage from most of the free upper limb and send efferent vessels to the central axillary lymph nodes.
The lumbar lymph nodes (paraaortic nodes) are a group of lymph nodes residing in the lumbar region. They consist of the following groups: right and left lateral aortic lymph nodes preaortic lymph nodes retroaortic lymph nodes (or 'postaortic').
A lymph node that is part of a pancreas [Automatically generated definition].
A lymph node located in the sacral region.
A major subdivision of a mature or developing limb, including both skeletal elements (or the mesenchyme that gives rise to the skeletal elements) and associated tissues, such as muscle, connective tissue, integument. Examples: autopod region, zeugopod region, stylopod region, metapodial region, arm region. Excludes the limb girdles.
An organ that functions as a secretory or excretory organ.
Anatomical space which contains portions of one or more body substances and is bounded by the internal surface of one maximally connected anatomical structure. Examples: cranial cavity, pharyngeal recess space, nasal cavity, tooth socket, cavity of serous sac, lumen of stomach, lumen of artery, fornix of vagina.
Anatomical structure that overlaps the outer epithelial layer and is adjacent to the space surrounding the organism.
Anatomical structure that has as its parts two or more multi-tissue structures of at least two different types and which through specific morphogenetic processes forms a single distinct structural unit demarcated by bona fide boundaries from other distinct anatomical structures of different types.
The trachea is the portion of the airway that attaches to the bronchi as it branches [GO:dph].
A female organ involved in reproduction.
female organism reproductive system organ
reproductive structure of female organism
reproductive system organ of female organism
reproductive system organ of male organism
A layer of epithelial cells on the surface of the mucosa.
A lymph node that is located in a kidney [Automatically generated definition].
A bone that is part of a head [Automatically generated definition].
Different sources vary regarding which bones are craniofacial; e.g. hyoid bone
A bone that is part of a facial skeleton [Automatically generated definition].
Any joint that is part of a (free) limb.
Most limb joints are synovial, but a few such as the tibiofibular joints are syndesmoses
A small fluid-filled sac lined by synovial membrane with an inner capillary layer of slimy fluid. It provides a cushion between bones and tendons and/or muscles around a joint. This helps to reduce friction between the bones and allows free movement. Bursae are filled with synovial fluid and are found around most major joints of the body.
A collection of teeth arranged in some pattern in the mouth or other part of the body. The arrangement may be a simple row, a collection of rows, or a more elaborate structure, such as a toooth whorl.
A fold of peritoneum originating at the stomach and supporting the viscera.
A limb joint that is part of a hindlimb [Automatically generated definition].
Epithelial tubes transport gases, liquids and cells from one site to another and form the basic structure of many organs and tissues, with tube shape and organization varying from the single-celled excretory organ in Caenorhabditis elegans to the branching trees of the mammalian kidney and insect tracheal system.
An epithelium that lines the lumen of the digestive tract.
The lymph nodes located outside the thoracic and abdominal cavities, such as the submandibular, prescapular, axillary, inguinal and popliteal lymph nodes.
One of the conchae of the ethmoid bone, which occupy the caudal part of the nasal fossae and form the lateral and superior portions of the turbinate bones in mammals[MP]. The ethmoturbinals are associated with the cribiform plate. They are covered with olfactory epithelium. Primarily, they serve to increase the surface area over which olfactory receptor neurons can come in contact with respiratory air. These olfactory receptor nerves then synapse with the mitral cells of the olfactory lobes through the cribiform plate in the manner described above[Palaeos].
The extension of the hindgut of the primitive digestive tube of the embryo, caudal to the location of the anal opening.
Any tube, opening or passage that connects two distinct anatomical spaces.
An anatomical structure that develops (entirely or partially) from the endoderm.
An anatomical structure that develops (entirely or partially) from the mesoderm.
An anatomical structure that develops (entirely or partially) from the ectoderm.
The internal genitalia are the internal sex organs such as the uterine tube, the uterus and the vagina in female mammals, and the testis, seminal vesicle, ejaculatory duct and prostate in male mammals.
TODO: make a subdivision of reproductive system. Relabel. See https://github.com/obophenotype/uberon/issues/547
The external genitalia are the outer sex organs, such as the penis or vulva in mammals.
Organ that is part of the hematopoietic system.
A portions of the gut that is derived from endoderm.
A projection or outgrowth of tissue from a larger body or organ.
A kidney that is part of a left side of organism [Automatically generated definition].
A kidney that is part of a right side of organism [Automatically generated definition].
A structure, usually a circular muscle, that normally maintains constriction of a natural body passage or orifice and which relaxes as required by normal physiological functioning.
The deep cervical lymph nodes are a group of cervical lymph nodes found near the internal jugular vein. They can be divided into upper and lower groups, or superior and inferior groups. Alternatively, they can be divided into deep anterior cervical lymph nodes and deep lateral cervical lymph nodes. They can also be divided into three groups: superior deep jugular, middle deep jugular, and 'inferior deep jugular'.
Organ consisting of skeletal tissue. Encompasses whole bones, fused bones, cartilaginious elements, teeth, dermal denticles.
The pseudostratified ciliated epithelium that lines much of the conducting portion of the airway, including part of the nasal cavity and larynx, the trachea, and bronchi.
An epithelium that is part of a respiratory system [Automatically generated definition].
apparatus respiratorius epithelial tissue
epithelial tissue of apparatus respiratorius
An epithelium that is part of a lower respiratory tract [Automatically generated definition].
epithelial tissue of lower respiratory tract
lower respiratory tract epithelial tissue
A group of nodes lying along the external jugular vein; they drain the skin and superficial structures over the region of the sternocleidomastoid muscle and anterior cervical regions. Efferent vessels drain to the deep cervical lymph nodes. Lymph nodes can be further subdivided into anterior and lateral groupings.
Anatomical structure that connects two or more adjacent skeletal elements or hardened body parts.
A portion of the gut that is derived from ectoderm.
The region of the digestive tract extending from the beginning of the intestines to the anus[GO - gut definition].
The region of the digestive tract extending from the mouth cavity through pharynx esophagus stomach and duodenum.
A proximal-distal subdivision of the digestive tract.
A part of a wall of an organ that forms a layer.
The muscular enlargement of the alimentary canal that has usually thick muscular walls and a tough horny lining for grinding the food and when the crop is present follows it and the proventriculus.
An organ that is part of a immune system [Automatically generated definition].
A product of the somatic follicle cell epithelium and a structure that supports the egg in a hostile environment, minimizing water loss whilst allowing gas exchanges essential for embryonic respiration[GO].
Muscle structures are contractile cells, tissues or organs that are found in multicellular organisms[GO].
Any anatomical structure that is part of the reproductive system.
An organ or element that is in the abdomen. Examples: spleen, intestine, kidney, abdominal mammary gland.
An organ or element that is part of the adbominal segment of the organism. This region can be further subdivided into the abdominal cavity and the pelvic region.
An organ or element that part of the trunk region. The trunk region can be further subdividied into thoracic (including chest and thoracic cavity) and abdominal (including abdomen and pelbis) regions.
An organ or element that is in the thoracic cavity. Examples: lung, heart, longus colli.
An organ or element that is part of the pelvic region. Examples: reproductive organs (in some organisms), urinary bladder, bones of the pelvis.
An organ that part of the thoracic segment region. This region can be further subdividied chest and thoracic cavity regions.
A portion of tissue that is part of an embryo.
Organ with organ cavity, which has as parts a serous membrane and a serous cavity . Examples: pleural sac, pericardial sac, tendon sheath, bursa.[FMA].
Epithelium that derives from the endoderm. Examples: urothelium, transitional epithelium of ureter, epithelium of prostatic gland.[FMA].
The medial surface of the labyrinth of ethmoid consists of a thin lamella, which descends from the under surface of the cribriform plate, and ends below in a free, convoluted margin, the middle nasal concha. It is rough, and marked above by numerous grooves, directed nearly vertically downward from the cribriform plate; they lodge branches of the olfactory nerves, which are distributed to the mucous membrane covering the superior nasal concha.
A naris that provides one of the small external openings of the head that give passage to air for breathing.
Anatomical structure embedded in or located in the integument that is part of the integumental system. Examples: hair, follicles, skin glands, claws, nails, feathers.
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 substance formed from the secretion of one or more glands of the male genital tract in which sperm cells are suspended.
A portion of organism substance that is secreted by a male reproductive gland.
male reproductive system fluid/secretion
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.
The pharynx is the part of the digestive system immediately posterior to the mouth[GO].
A rigid covering that envelops an object.
The distalmost portion of the digestive tract, derived from the hindgut, and terminating with the anus.
Any gland that is part of the digestive system.
The inner lining of the cheeks and lips.
A multicellular organism that existence_ends_with a post-juvenile adult stage and existence_starts_with a post-juvenile adult stage.
A hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood or analogs[GO,modified].
A dark greenish mass that accumulates in the bowel during fetal life and is discharged shortly after birth.
Of or pertaining to the period of time immediately following birth, or to the newborn.
Matter ejected from the lungs, bronchi, and trachea, through the mouth.
The glandular or true stomach of a bird that is situated between the crop and gizzard.
The fourth stomach of ruminating animals, which is an elongated pear-shaped sac lying on the floor of the abdomen, on the right-hand side, and roughly between the seventh and twelfth ribs. It leads to the beginning of the small intestine. (Adapted From Black's Veterinary Dictionary, 17th ed).
Any of the first three stomachs of a ruminant, i.e., the rumen, reticulum, or omasum.
The second stomach of ruminants. It lies almost in the midline in the front of the abdomen, in contact with the liver and diaphragm and communicates freely with the RUMEN via the ruminoreticular orifice. The lining of the reticulum is raised into folds forming a honeycomb pattern over the surface. (From Concise Veterinary Dictionary, 1988).
The third stomach of ruminants, situated on the right side of the abdomen at a higher level than the fourth stomach and between this latter and the second stomach, with both of which it communicates. From its inner surface project large numbers of leaves or folia, each of which possesses roughened surfaces. In the center of each folium is a band of muscle fibers which produces a rasping movement of the leaf when it contracts. One leaf rubs against those on either side of it, and large particles of food material are ground down between the rough surfaces, preparatory to further digestion in the succeeeding parts of the alimentary canal. (Black's Veterinary Dictionary, 17th ed).
The first chamber in the alimentary canal of a ruminant stomach, composed of the rumen and reticulum.
The first compartment of the ruminant stomach. It lies on the left side of the body, occupying the whole of the left side of the abdomen and even stretching across the median plane of the body to the right side. It is capacious, divided into an upper and a lower sac, each of which has a blind sac at its posterior extremity.
The ruminants' stomach consists of four compartments: rumen, reticulum, omasum and abomasum. The first three compartments comprise the forestomach (proventriculus). They are lined with nonglandular membrane. The fourth compartment, the abomasum comprises the true stomach of the ruminants. It is lined with glandular mucous membrane. The rumen lies on the left of the abdominal cavity, the reticulum cranially and the omasum on the right. The abomasum lies ventrally, its proximal end lies ventral to the rumen, reticulum and omasum.
The epidermis is the entire outer epithelial layer of an animal, it may be a single layer that produces an extracellular material (e.g. the cuticle of arthropods) or a complex stratified squamous epithelium, as in the case of many vertebrate species[GO].
The yellow spheroidal mass of stored food that forms the inner portion of the egg of a bird or reptile and is surrounded by the white.
The hard-shelled reproductive body produced by a bird (especially by the common domestic chicken) or a reptile; also: its contents used as food.
An epithelial tube that is open at one end only.
Simple columnar epithelium in which the luminal side of the cells bears cilia. Examples: epithelium of trachea, epithelium of uterine tube.[FMA].
Epithelium bearing vibratile cilia on the free surface.
An inconstant lymph node of the anterior mediastinal group located adjacent to the ligamentum arteriosum.
A lymph node that is part of a thorax. Includes lymph nodes of the lungs and mediastinal lymph nodes.
Any bodily fluid that has passed through a membrane such as the capillary wall, as a result of unbalanced hydrostatic and osmotic forces.
A bone that is part of a craniocervical region.
The irregular bones are bones which, from their peculiar form, cannot be grouped as long bone, short bone, flat bone or sesamoid bone. Irregular bones serve various purposes in the body, such as protection of nervous tissue, affording multiple anchor points for skeletal muscle attachment (as with the sacrum), and maintaining pharynx and trachea support, and tongue attachment (such as the hyoid bone). They consist of cancellous tissue enclosed within a thin layer of compact bone. The irregular bones are: the vertebrC&, sacrum, coccyx, temporal, sphenoid, ethmoid, zygomatic, maxilla, mandible, palatine, inferior nasal concha, and hyoid.
The mouth of a starfish is located on the underside of the body, and opens through a short esophagus into firstly a cardiac stomach, and then, a second, pyloric stomach. Each arm also contains two pyloric caeca, long hollow tubes branching outwards from the pyloric stomach. Each pyloric caecum is lined by a series of digestive glands, which secrete digestive enzymes and absorb nutrients from the food. A short intestine runs from the upper surface of the pyloric stomach to open at an anus in the center of the upper body.
The pyloric ceca (or digestive glands) and the cardiac stomach produce digestive enzymes in starfishes. Digested material is absorbed through the pyloric ceca for transport to the rest of the body. Each pyloric cecum extends the length of each arm.
In starfishes the cardiac stomach is connected to a pyloric stomach which is located above it. Food can be brought into the stomach through the mouth or, in many species, the cardiac stomach can be extended out through the mouth to digest food outside the body. Suspension-feeding starfish use their tube feet to pass food to the mouth.
A calcareous exoskeleton which encloses, supports and protects the soft parts of an animal in the phylum Mollusca, which includes snails, clams, tusk shells, and several other classes. Not all shelled molluscs live in the sea, many live on the land and in freshwater.
poultry fluff
A feather lacking a vane and having a rudimentary rachis and a tuft of non-interlocked barbs with elongated barbules extending from the calamus.
Damion Dooley's note: Poultry fluff is both an 'anatomical structure' and a body product when it is shed.
A limb segment that is part of a forelimb.
A distinct rodent non-glandular region of the stomach which is demarcated from the glandular stomach by the limiting ridge (margo plicatus).
An out-pocket of thickened ventral foregut epithelium adjacent to the developing heart. Constitutes the first morphological sign of the embryonic liver. The anterior portion of the hepatic diverticulum gives rise to the liver and intrahepatic biliary tree, while the posterior portion forms the gall bladder and extrahepatic bile ducts.
The short narrow part of the stomach extending from the pyloric antrum to the pyloric sphincter.
Albumen is the clear liquid contained within an egg and consists of water and proteins, among which are ovomucin and ovomucoid. It protects the egg yolk and provides additional nutrition for the growth of the embryo.
Stomach found in horses; includes cardiac, proper gastric and pyloric glandular zones.
One of several small inconstant lymph nodes, proximal, intermediate and distal deep to the fascia lata and medial to the femoral vein; they receive lymph from the deep structures of the lower limb, from the glans penis and from superficial inguinal nodes; efferents pass to the external iliac nodes.
A group of 12-20 lymph nodes that lie in the subcutaneous tissue below the inguinal ligament and along the terminal part of the great saphenous vein; they drain the skin and subcutaneous tissue of the lower abdominal wall, perineum, buttocks, external genitalia, and lower limbs.
nodus lymphaticus inguinalis superficialis
Any of the membranous air-filled extensions of the lungs of birds, which increase the efficiency of gaseous exchange in the lungs.
Three distinct sets of organs perform respiration-the anterior air sacs (interclavicular, cervicals, and anterior thoracics), the lungs, and the posterior air sacs (posterior thoracics and abdominals). The posterior and anterior air sacs, typically nine, expand during inhalation. Air enters the bird via the trachea. Half of the inhaled air enters the posterior air sacs, the other half passes through the lungs and into the anterior air sacs. Air from the anterior air sacs empties directly into the trachea and out the bird's mouth or nares. The posterior air sacs empty their air into the lungs. Air passing through the lungs as the bird exhales is expelled via the trachea. Some taxonomic groups (Passeriformes) possess 7 air sacs, as the clavicular air sacs may interconnect or be fused with the cranial thoracic air sacs[WP]
An organism containing a developing embryo, fetus, or unborn offspring within the body.
The axilla is the area directly under the joint where the forelimb connects to the shoulder.
An epithelium that is part of a foregut-midgut junction.
A serous sac that has the pleura and the pleural cavity as parts.
Branch or outpocketing of the digestive tract.
Non-contractile pouch that is connected to the anterior stomach through a slit-like opening. This pouch is also well-connected to the haemal system through numerous haemal ducts within its connective tissue layer.
The digestive tract of many metazoan invertebrates is characterized by the presence of caeca or diverticula that serve secretory and/or absorptive functions. With the development of various feeding habits, distinctive digestive organs may be present in certain taxa. This also holds true for sea urchins (Echinodermata: Echinoidea), in which a highly specialized gastric caecum can be found in members of a derived subgroup, the Irregularia (cake urchins, sea biscuits, sand dollars, heart urchins, and related forms)... Homologous with the more or less pronounced dilation of the anterior stomach that is observed in most "regular" sea urchin taxa[PMID:20955602]
A division of the stomach. The stomach can be divided based on mucosal histology (glandular epithelium and gastric glands) and the relative position and type of gastric gland.
The collection of all skeletal elements in a mesopodium. Examples: the tarsal skeleton, the carpal skeleton.
Subdivision of skeleton that consists of the endochondral elements distal to the anterior limb/fin zeugopodial skeletal elements which constitute the proximal region of the anterior autopod skeleton[PHENOSCAPE:ad].
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.
A variant of the ascending colon in ruminants and pigs.
An anatomical structure that develops from the neural crest.
An anatomical structure that has some part that develops from the neural crest.
structure with developmental contribution from neural crest
A skeletal element that has the potential to participate in endochondral ossification, and may participate in intramembranous ossification.
Epithelium composed of cells that develops from the ectoderm[FMA,modified].
A simple columnar epithelium that looks stratified but is not, because its cells are arranged with their nuclei at different levels.
Epithelium composed of a single layer of cells, appearing as layered because the column-shaped cells vary in height so the nuclei are at different levels. The basal portions of all the cells are in contact with the basement membrane. It lines the respiratory system and the male reproductive tract. The cilia in the respiratory tract are motile, while the stereocilia in the male reproductive tract are immobile.
epithelium pseudostratificatum columnare ciliatum (trachea et bronchi)
pseudostratified ciliated columnar epithelium
An appendage segment that is part of a limb/fin.
Skeletal subdivision that is a segment of the limb skeleton.
A major subdivision of an organism that divides an organism along an axis perpedicular to the main body anterior-posterior axis. In vertebrates, this is typically a fin or limb segment. In insects, this includes segments of appendages such as antennae, as well as segments of the insect leg.
subdivision of organism along appendicular axis
Anatomical cluster consisting of the skeletal elements (i.e. bone elements, cartilage elements, cartilage condensations) that are part of an individual subdivision of the organism. Excludes joints.
Any synovial joint that is part of a (free) limb.
A bone that is part of a neurocranium [Automatically generated definition].
A sphincter muscle that is part of the gastrointestinal system.
A retractable double-layered fold of skin and mucous membrane that covers the glans penis or clitoris. Glands may also be present.
An epithelium that develops_from a ectoderm and is part of a oral epithelium.
Portion of midgut after it bends around the superior mesenteric artery.
A region of the stomach that is lined with glandular epithelium.
A region of the stomach is lined with non-glandular epithelium. Examples of a stomach non-glandular region are found in rodents.
Blood that remains in the placenta and in the attached umbilical cord after childbirth[WP].
Cord blood is collected because it contains stem cells, which can be used to treat hematopoietic and genetic disorders.[WP]
The intercostal lymph nodes (intercostal glands ) occupy the posterior parts of the intercostal spaces, in relation to the intercostal vessels. They receive the deep lymphatics from the postero-lateral aspect of the chest; some of these vessels are interrupted by small lateral intercostal glands.
An epithelium that consists of columnar epithelial cells. Columnar epithelia are epithelial cells whose heights are at least four times their width. Columnar epithelia are divided into simple (or unilayered), and the rarer stratified (or multi-layered).[WP, modified].
An epithelial sac that is part of a Rathke's pouch.
A cervical lymph nodes are found in proximity to an internal or external jugular vein.
The anterior cervical lymph nodes are a group of nodes found on the anterior part of the neck.
The superficial lateral cervical lymph nodes are found in proximity to the external jugular vein.
The superficial anterior cervical lymph nodes are found in proximity to the anterior jugular vein.
superficial anterior cervical lymph node
The deep lateral cervical lymph nodes are found near the upper part of the internal jugular vein in the neck, lateral or posterior to the carotid sheath.
The deep anterior cervical lymph nodes are found near the middle cricothyroid ligament and the trachea.
A ventral evagination extending anteriorly in the mid-portion of the intestine in Amphioxi.
The subdivision of the digestive tract that consists of the colon and the rectum.
The upper one third of esophagus in which the muscle layer is composed of muscle cells of the striated type.
The lower one third of the esophagus in which the muscle layer is composed of muscle cells predominantly of the smooth type.
The middle one third of the esophagus in which the muscle layer is composed of muscle cells of the striated and smooth types.
The very first part of the duodenum which is slightly dilated.
Anatomical projection that is part of the integumentl system.
Any of the organs or elements that are part of the digestive system. Examples: tongue, esophagus, spleen, crop, lunge feeding organ, tooth elements.
Any structure that is placed on one side of the left-right axis of a bilaterian.
A hollow, muscular organ, which, by contracting rhythmically, contributes to the circulation of lymph, blood or analogs. Examples: a chambered vertebrate heart; the tubular peristaltic heart of ascidians; the dorsal vessel of an insect; the lymoh heart of a reptile.
The feeding organ, a neuro-muscular pump in the head of the animal, used to ingest food, bacteria suspended in liquid, filter them out, grind them up and transport posteriorly into the instestine.
A lymph node that is part of a hypodermis.
The splenic lymph nodes (or pancreaticolienal) accompany the lienal (splenic) artery, and are situated in relation to the posterior surface and upper border of the pancreas; one or two members of this group are found in the gastrolienal ligament. Their afferents are derived from the stomach, spleen, and pancreas, their efferents join the celiac group of preaortic glands.
A lymph node located near the bifurcation of the trachea.
An epithelium that is part of a foregut.
A lymph node found near the parotid gland.
Any of the lymph nodes adjacent to the stomach and duodenum.
A lymph node along the left gastric artery or greater omentum.
Lymph nodes of the pancreatic tail and spleen, receiving afferents from both organs plus the greater curvature of the stomach; they drain to the celiac lymph nodes.
lymph node of anterior border of epiploic foramen
lymph node of anterior border of omental foramen
node of anterior border of epiploic foramen
node of anterior border of omental foramen
The retropharyngeal lymph nodes, from one to three in number, lie in the buccopharyngeal fascia, behind the upper part of the pharynx and in front of the arch of the atlas, being separated, however, from the latter by the Longus capitis. Their afferents drain the nasal cavities, the nasal part of the pharynx, and the auditory tubes. Their efferents pass to the superior deep cervical glands. They are in the retropharyngeal space.
Any of the lymph nodes that are part of a face.
The mandibular lymph node is a lymph node found near the jaw.
Editor nodes: consider merging with submandibular, at least for mouse, see http://www.ncbi.nlm.nih.gov/pubmed/16624319
Any lymph node within the abdominal pelvic region.
The external iliac lymph nodes, from eight to ten in number, lie along the external iliac vessels. They are arranged in three groups, one on the lateral, another on the medial, and a third on the anterior aspect of the vessels; the third group is, however, sometimes absent. Their principal afferents are derived from the inguinal lymph nodes, the deep lymphatics of the abdominal wall below the umbilicus and of the adductor region of the thigh, and the lymphatics from the glans penis vel clitoridis, the membranous urethra, the prostate, the fundus of the urinary bladder, the cervix uteri, and upper part of the vagina.
The internal iliac lymph nodes (or hypogastric) surround the internal iliac artery and its branches (the hypogastric vessels), and receive the lymphatics corresponding to the distribution of the branches of it, i. e. , they receive lymphatics from all the pelvic viscera, from the deeper parts of the perineum, including the membranous and cavernous portions of the urethra, and from the buttock and back of the thigh. It does not receive lymph from the ovary, testis, or superior half of the rectum; the gonads drain to the paraaortic lymph nodes, while the superior half of the rectum drains to the pararectal lymph nodes.
One of the deep inguinal lymph nodes located in or adjacent to the femoral canal; sometimes mistaken for a femoral hernia when enlarged.
nodus lymphoideus inguinales profundi proximalis
A lymph node that is located close to the surface.
A lymph node that is located deeper within the organism, further from the surface.
A parotid lymph node that is located superficially.
A lymph node that is medial to the gluteus superficialis m., caudal to gluteus medius m. and sciatic nerve lymph node.
One of the lymph nodes that form a chain around the ileocolic artery.
The paraaortic lymph nodes (also known as para-aortic, periaortic, and peri-aortic) are a group of lymph nodes that lie in front of the lumbar vertebral bodies near the aorta. These lymph nodes receive drainage from the lower gastrointestinal tract and the pelvic organs.
The mastoid lymph nodes (retroauricular lymph nodes, posterior auricular glands), usually two in number, are situated on the mastoid insertion of the Sternocleidomastoideus, beneath the Auricularis posterior. Their afferent vessels drain the posterior part of the temporoparietal region, the upper part of the cranial surface of the auricula or pinna, and the back of the external acoustic meatus; their efferents pass to the superior deep cervical glands.
The deep parotid lymph nodes are lymph nodes found below the parotid gland. The afferents of the subparotid glands drain the nasal part of the pharynx and the posterior parts of the nasal cavities. Their efferents pass to the superior deep cervical glands.
The preauricular deep parotid lymph nodes (anterior auricular glands or preauricular glands), from one to three in number, lie immediately in front of the tragus. Their afferents drain the lateral surface of the auricula and the skin of the adjacent part of the temporal region; their efferents pass to the superior deep cervical glands.
The infra-auricular deep parotid lymph nodes are a group of lymph nodes found underneath the ear.
The submental lymph nodes (or suprahyoid) are situated between the anterior bellies of the Digastrici. Their afferents drain the central portions of the lower lip and floor of the mouth and the apex of the tongue. Their efferents pass partly to the submandibular lymph nodes and partly to a gland of the deep cervical group situated on the internal jugular vein at the level of the cricoid cartilage.
A lymph node that is part of a hindlimb.
A lymph node that is part of a forelimb.
A lymph node that is part of a bronchus.
A life cycle stage that starts at completion of development and growth of the sexually mature adult animal, and ends before senescence.
A membranous sac in animals that serves as the receptacle of a liquid or contains gas.
A portion of organism substance that is secreted by a reproductive gland.
A part of an organism or organ that is continuous with its surroundings and distinguished from its surroundings based on morphology.
Any substance in the body or expelled from the body that is in a gaseous state.
The stage of being no more dependent of the nest and/or from caregivers for subsistence while having not reach sexual maturity.
Nursing stage that follows the neonate stage in mammals and ends at weaning.
An multicellular anatomical structure that has subparts of multiple organs as a part.
Material anatomical entity consisting of multiple anatomical structures that are not connected to each other.
A collection of anatomical structures that are alike in terms of their morphology or developmental origin.
A region or zone on the surface of an organism that encompasses skin and any adnexa, down through muscles and bounded by underlying skeletal support structures.
Any gaseous product of an excretory process.
Any excreted gas that is produced by the digestive tract.
In mammals, mostly produced as a byproduct of bacterial fermentation in the gastrointestinal (GI) tract, especially the colon, and excreted through the rectum
The intraglandular deep parotid lymph nodes are a group of lymph nodes found inside the parotid gland.
A lymph node located in the area below the clavicle.
nodus lymphaticus infraclavicularis axillae
A lymph node located in the back of the head adjacent to the trapezius muscle.
Any of the lymph nodes of the breast located under the ribcage, near the sternum.
A lymph node which is located above the clavicle.
nodus lymphaticus supraclavicularis axillae
A lymph node located in the retroperitoneal space.
A lymph node located in the superior mediastinum that collects lymph from the thymus, the pericardium, and the right side of the heart.
A skeletal element of the ethmoid region with complex morphology that are lined with mucuous membranes involved in either olfaction or air conditioning.
The lymph nodes around the subsegmental bronchi.
A bodily fluid that is located in the coelom.
Fluid that lines the vaginal walls that consists of multiple secretions that collect in the vagina from different glands.
Gastric lymph node located around the cardia of stomach.
An axillary lymph node that is placed along the lower margin of the posterior wall of the axilla in the course of the subscapular artery.
An axiallary lymph node along the lower border of the Pectoralis minor, in relation with the lateral thoracic artery. Their afferents drain the skin and muscles of the anterior and lateral thoracic walls, and the central and lateral parts of the mamma; their efferents pass partly to the central and partly to the subclavicular groups of axillary glands.
An axillary lymph node that is imbedded in the adipose tissue near the base of the axilla.
An axillary lymph node that is situated partly posterior to the upper portion of the Pectoralis minor and partly above the upper border of this muscle.
intermediate lymph node of small intestine
Pancreaticosplenioc lymph node located along the inferior margin of pancreas.
Gastric lymph node located along the lesser curvature of stomach.
lateral superior deep cervical lymph node
anterior superior deep cervical lymph node
lateral inferior deep cervical lymph node
anterior inferior deep cervical lymph node
lymph node of inferior pulmonary ligament
Left gastric lymph node located along the left gastric artery.
Left gastric lymph node located along the cardiac half of the lesser curvature of stomach in the lesser omentum.
Hepatic lymph node located along the common hepatic artery.
Hepatic lymph node located along the portal vein.
Superior pancreatic lymph node located along the proximal segment of splenic artery.
proximal superior pancreaticosplenic lymph node
Superior pancreatic lymph node located along the distal segment of splenic artery.
distal superior pancreaticosplenic lymph node
Superior pancreaticoduodenal lymph node located on the anterior anterior of superior region of head of pancreas.
anterosuperior pancreaticoduodenal lymph node
anterior superior pancreaticoduodenal lymph node
Superior pancreaticoduodenal lymph node located on the posterior aspect of superior portion of head of pancreas.
posterosuperior pancreaticoduodenal lymph node
posterior superior pancreaticoduodenal lymph node
Inferior pancreaticoduodenal lymph node located on the anterior aspect of inferior region of head of pancreas.
anteroinferior pancreaticoduodenal lymph node
anterior inferior pancreaticoduodenal lymph node
Inferior pancreaticoduodenal lymph node located on the posterior aspect of inferior region of head of pancreas.
posteroinferior pancreaticoduodenal lymph node
posterior inferior pancreaticoduodenal lymph node
Intestinal lymph node located anterior to aorta.
Gastric lymph node located along the greater curvature of stomach.
lymph node of greater curvature of stomach
Lymph node located in either head and neck region.
nodus lymphoideus inguinales profundi intermedius
nodus lymphoideus inguinales profundi distalis
nodus mediastinale posteriore lymphaticus
nodus tracheobronchiale superiore lymphaticus
nodus tracheobronchialis inferioris lymphaticus
superior deep lateral cervical lymph node
inferior deep lateral cervical lymph node
Pylorioc lymph node located near the bifurcation of gastroduodenal artery and superior to the pylorus.
Pylorioc lymph node located in the angle between the superior and descending parts of duodenum.
A tracheobronchial lymph node situated in the hilum of a lung.
Structures of the dermis, epidermis, glands and pigment cells recognizable on the external surfaces of the integument.
Not clear how this differs from parent class. See https://github.com/obophenotype/uberon/issues/1305
A finger-like out-pocketing of the intestine where it meets the end of the stomach (pylorus). Also spelled cecum (ceca). Serves to aid digestion.
Section of the insect foregut anterior to the esophagus.
A subdivision of the digestive tract in humans that includes the rectum, the anal canal and the anus.
A lymph node with a lymph center located within the caudal abdomen and pelvis, on the ventral side of the lumbar region. Includes the medial iliac, internal iliac (previously termed hypogastric) and sacral lymph nodes.
A lymph node located inferior to the ilium.
Mesenteric lymph node embedded in the ileocecal fold at both sides of the concavity of the cecum. It drains the terminal ileum.
Superior mediastinal lymph node located in the thoracic cavity between the lungs. It is bordered by the carina of the trachea, the lower lobe bronchus on the left and the intermediate bronchus on the right.
Supraclavicular lymph node located on the left side of a entire appendicular skeleton. The left supraclavicular lymph node drains the kidney, cervix, testis, and pancreas into the thoracic duct.
Supraclavicular lymph node located on the right side of a entire appendicular skeleton. The right supraclavicular lymph node drains the breast, lung and upper esophagus into the right lymphatic duct.
Lymph node that is the most proximal of the left supraclavicular lymph nodes. It receives afferent lymphatic drainage from the left head, neck, chest, abdomen, pelvis, and bilateral lower extremities, and drains into the jugulo-subclavian venous junction via the thoracic duct.
Lymph node located in the perigastric region.
"A unit of measurement is a standardized quantity of a physical quality." [Wikipedia:Wikipedia]
Damion Dooley's note: Need to build this out further with reference to http://unitsofmeasure.org/trac and other unit ontologies: [1] R. Hodgson and P. J. Keller, "QUDT-quantities, units, dimensions and data types in OWL and XML." Online (September 2011) http://www. qudt.org [2] M. van Assem, H. Rijgersberg, and J. Top, "Ontology of units of measure and related concepts." Semantic Web 4, no. 1 (2013): 3-13. [3] G. V. Gkoutos, P. N. Schofield, and R. Hoehndorf, "The Units Ontology: a tool for integrating units of measurement in science." Database2012 (2012): bas033.
"A unit which is a standard measure of the distance between two points." [Wikipedia:Wikipedia]
"A unit which is a standard measure of the dimension in which events occur in sequence." [Wikipedia:Wikipedia]
"A unit which is a standard measure of the average kinetic energy of the particles in a sample of matter." [Wikipedia:Wikipedia]
"A unit which is a standardised quantity of an element or compound with uniform composition." [Wikipedia:Wikipedia]
"A unit which is one of a particular measure to which all measures of that type can be related." [NIST:NIST]
"A unit which represents a standard measurement of how much of a given substance there is mixed with another substance." [UOC:GVG]
"A density unit which is a standard measure of the mass of a substance in a given volume." [UOC:GVG]
"A unit which is a standard measure of the volume of a homogeneous substance containing 6.02 x 1023 atoms or molecules." [Wikipedia:Wikipedia]
"A unit which is a standard measure of the volume of a given mass of substance (the reciprocal of density)." [Wikipedia:Wikipedia]
"A unit which is a standard measure of the rate of movement. Speed is measured in the same physical units of measurement as velocity, but does not contain the element of direction that velocity has. Speed is thus the magnitude component of velocity." [Wikipedia:Wikipedia]
"A concentration unit which is a standard measure of the number of moles of a given substance per kilogram of solvent." [UOC:GVG]
"A unit which is a standard measure of the amount of space occupied by any substance, whether solid, liquid, or gas." [NIST:NIST]
"A unit which is a standard measure of the figure or space formed by the junction of two lines or planes." [Wikipedia:Wikipedia]
"A unit which is a standard measure of the angle formed by two straight lines in the same plane." [Wikipedia:Wikipedia]
"A unit which is a standard measure of the influence exerted by some mass." [Wikipedia:Wikipedia]
"A unit which is a standard measure of physical quantity consisting of only a numerical number without any units." [Wikipedia:Wikipedia]
"A dimensionless ratio unit which denotes numbers as fractions of 100." [Wikipedia:Wikipedia]
"A dimensionless unit which denotes a simple count of things." [MGED:MGED]
"A dimensionless unit which denotes an amount or magnitude of one quantity relative to another." [Wikipedia:Wikipedia]
"A dimensionless ratio unit which relates the part (the numerator) to the whole (the denominator)." [Wikipedia:Wikipedia]
"A dimensionless concentration unit which denotes the given volume of the solute in the total volume of the resulting solution." [NIST:NIST]
"A concentration unit which a measure of viable bacterial numbers in a given volume." [Wikipedia:Wikipedia]
"A unit which is a standard measure of the work done per unit charge as a charge is moved between two points in an electric field." [Wikipedia:Wikipedia]
"A unit which represents a standard measurement of the transmission of an entity through a medium." [UOC:GVG]
"A unit which represents a standard measurement of the movement of electrically charged particles through a transmission medium (electrical conductor)." [UOC:GVG]
"A unit used to indicate the clarity of water or other solutions or suspensions, as measured by the ability of the solution or suspension to scatter light of a defined wavelength range." [UO:PC]
"1000 formazin turbidity units (FNU) on the empirical formazin turbidity scale represents reflectance of insol. reaction products of 0.0725 g hydrazine sulfate with 0.7250 g hexamethylenetetramine diluted to 1 L." [AOAC:192]
"A unit equal to one thousand base pairs." [UOC:GVG]
"A United States customary units teaspoon is a unit of measurement of volume widely used in cooking recipes and pharmaceutic prescriptions in America. It equals a 4.93 mL volume." [Wikipedia:https://en.wikipedia.org/wiki/United_States_customary_units#Cooking_measures]
"A metric tablespoon is a unit of measurement of volume widely used in cooking recipes and pharmaceutic prescriptions. It equals a 15mL volume." [Wikipedia:https://en.wikipedia.org/wiki/Tablespoon]
"An Australian metric tablespoon is a unit of measurement of volume used in Australia for cooking recipes and pharmaceutic prescriptions. It equals a 20mL volume." [Wikipedia:https://en.wikipedia.org/wiki/Tablespoon]
"A United States customary units tablespoon is a unit of measurement of volume widely used in cooking recipes and pharmaceutic prescriptions in America. It equals a 14.79 mL volume." [Wikipedia:https://en.wikipedia.org/wiki/United_States_customary_units#Cooking_measures]
"A metric cup is a unit of measurement of volume widely used in cooking recipes and pharmaceutic prescriptions. It equals a 250mL volume." [Wikipedia:https://en.wikipedia.org/wiki/Cooking_weights_and_measures]
"A United States customary units cup is a unit of measurement of volume widely used in cooking recipes and pharmaceutic prescriptions in America. It equals a 236.59 mL volume." [Wikipedia:https://en.wikipedia.org/wiki/United_States_customary_units#Cooking_measures]
"A United States FDA cup is a unit of measurement of volume used by the US Federal Department of Agriculture as a nutritional serving measure. It equals a 240 mL volume." [Wikipedia:https://en.wikipedia.org/wiki/United_States_customary_units#Cooking_measures]
pg/mL
A gram per milliliter unit which is equal to one picogram per one milliliter.
picogram per milliliter
mcg/mcL
ug/uL
µg/µL
"A mass unit density which is equal to mass of an object in nanograms divided by the volume in microliters." [UOB:LTS]
microgram per microliter
colony forming unit per milliliter based unit
The human age is classified into four categories as Child (0-12 years), Adolescence (13-18 years), Adult (19-59 years) and Senior Adult (60 years and above) which is discussed in the paper. Reference: https://ieeexplore.ieee.org/abstract/document/6416855.
Any measurable or observable characteristic of a vertebrate organism.
The length of time between when a fertilized egg implants in the wall of the uterus and the birth of offspring.
ongoing pregnancy
The state of a female and/or her offspring, and the processes which occur, during the period from conception to birth or termination of the pregnancy.
ancestral group
A description of the biological sample analysed.
specimen description
A personal health datum which specifies host role at time of specimen collection.
host role at time of specimen collection
MLVA typing
MLVA stands for Multilocus Variable Number of Tandem Repeats Analysis. This method can be performed by three distinct methodologies: by running the amplified locus in a gel , using a capilary electrophoresis apparatus or sequencing the resulting amplified fragment. The first two infer the number of repeats on each locus indirectly by the fragment size.
Multilocus Variable Number of Tandem Repeats Analysis typing
A description is language entity in which elements of a language (formal or natural) are used to characterize an entity.
description
A polygon edge is a line segment joining two polygon vertices.
A polygon edge must exist in the same 2 dimensional space (plane or quadratic surface) as the polygon's other edges. Each polygon edge vertex must join to exactly 1 other polygon edge. A polygon's edges exist in exactly 1 circuit.
polygon edge
A polygon serves as a boundary for an area of interest that exists within a larger area.
Damion Dooley's comment: On spheroids a polygon can be minimally defined by latitude and longitude coordinates, however technically this is ambiguous whether the larger or smaller area is being referred to. Unambiguously, such a polygon could be defined by an epicenter, and a latitude width and longitude height.
polygonal face
In elementary geometry, a polygon is a plane figure that is bounded by a finite chain of straight line segments closing in a loop to form a closed chain or circuit.
polygon
A point is a geometric entity that is located in a zero-dimensional spatial region and whose position is defined by its coordinates in some coordinate system.
point
A line is curve that extends in a single dimension (e.g. straight line; exhibits no curvature), and is composed of at least two fully connected points.
line
A line segment is a line and a part of a curve that is (inclusively) bounded by two terminal points.
line segment
collection of points
A curve is a geometric entity that may be located in n-dimensional spatial region whose extension may be n-dimensional, is composed of at least two fully connected points and does not intersect itself.
curve
An attribute is a characteristic of some entity.
attribute
A record identifier is an identifier for a database entry.
PulseNet: Key
record identifier
A Uniform Resource Locator or Universal Resource Locator (URL) is a specific character string that constitutes a reference to an Internet resource.
URL
A standard operating procedure is a specification approved for use in specific environments.
standard operating procedure
A medical health record is a record of a single patient's medical history.
medical health record
medical health record (history / timeline)
an IP number is an number to connect to a device on the internet.
IP number
life status is the quality of whether something is alive or dead.
life status
An assay for detecting bacteria by subjecting them to strain-specific bacteriophages.
Bacterial bacteriophage typing
A microplate having 96 wells.
96 well plate
obsolete: ancestral group
A temporal measurement of the time period elapsed since an identifiable point in the life cycle of an organism. If a developmental stage is specified, the identifiable point would be the beginning of that stage. Otherwise the identifiable point must be specified such as planting (e.g. 3 days post planting).
A disease is a disposition that describes states of disease associated with a particular sample and/or organism.
A temporal measurement of the period after successful treatment in which there is no appearance of the symptoms or effects of the disease.
Is a temporal measure from a defined start point e.g. diagnosis, or treatment of the period to appearance of a distant metastasis. A distant metastasis refers to cancer that has spread from the original (primary) tumor to distant organs or distant lymph nodes. Also known as distant cancer.
time to development of distant metastases
A temporal measurement of the time between two specified points.
Is the survival of a subject (or group of subjects) measured from the date of diagnosis until locoregional or systemic recurrence, second malignancy, or death from any cause or disease progression or relapse, institution of new unplanned anticancer treatment, or death from any cause.
Disorder of reproductive system (disorder)
Non-neoplastic Reproductive system disease
A measurement of the survival rate for a group of individuals suffering from a disease.
A role played by a a biological sample in the context of an experiment where the intent is that biological or technical variation is measured.
Time of survival is an information entity which is about the length of time a material entity has survived after some adverse event, such as infection from a disease.
A temporal entity is an entity that has temporal parts and that happens, unfolds or develops through time. An occurrent is something which exists over time, rather than existing completely at many times
Time point at which a sample or observation is made or taken from a biomaterial as measured from some reference point.
A measurement is an information entity that is a recording of the output of a measurement such as produced by an instrument.
A social group characterized by a distinctive social and cultural tradition maintained from generation to generation, a common history and origin and a sense of identification with the group; members of the group have distinctive features in their way of life, shared experiences and often a common genetic heritage; these features may be reflected in their experience of health and disease. (NCI); Ethnicity - an arbitrary classification of the social group a person belongs to, and either identifies with or is identified with by others, as a result of a complex of cultural, biological, geographical and other factors such as linguistic, dietary and religion traditions; ancestry, background, allegiance, or association; and physical characteristics traditionally associated with race. Increasingly the concept is used synonymously with race but this use trend has a pragmatic basis rather than scientific. (NCI); The concept of ethnic origin is an attempt to classify people, not according to their current ethnicity, but according to where their ancestors came from. Ethnic origin has become a popular classification in statistics, where the concept of race has been largely discarded. (from Wikipedia) (NCI); a group of people with a common cultural heritage that sets them apart from others in a variety of social relationships. (CSP)
A technical replicate is a replicate role where the same BioSample is use e.g. the same pool of RNA used to assess technical (as opposed to biological) variation within an experiment.
A biological replicate is a replicate role that consists of independent biological replicates made from different individual biosamples.
The status during which female mammals carry their developing young (EMBRYOS or FETUSES) in utero before birth, beginning from FERTILIZATION to BIRTH.
Anthropometry is a measurement of the size, weight, and proportions of the human or other primate body.
Inhaling and exhaling the smoke of tobacco or something similar to tobacco.
Measurements of the height, weight, length, area, etc., of the human and animal body or its parts.
An indicator of body density as determined by the relationship of BODY WEIGHT to BODY HEIGHT. BMI=weight (kg)/height squared (m2). BMI correlates with body fat (ADIPOSE TISSUE). Their relationship varies with age and gender. For adults, BMI falls into these categories: below 18.5 (underweight); 18.5-24.9 (normal); 25.0-29.9 (overweight); 30.0 and above (obese). (National Center for Health Statistics, Centers for Disease Control and Prevention)
Quantification of the number of deaths in a population.
The first time point measured at the start of some process.
Is the quantification of some measureable quality of a population e.g. birth rate.
The age of onset of (human) menarche, the beginning of the first menstrual cycle in an individual
The age of onset of (human) menopause, the beginning of the first menstrual cycle in an individual
The age at which some process, or disease started in a human individual.
The age, measured from some defined time point e.g. birth at which a subject (e.g. a human patient) is diagnosed with some disease e.g. breast cancer.
The percentage of subjects in a study who have survived without cancer spread for a defined period of time. Usually reported as time since diagnosis or treatment. Can be reported for an individual or a study population.
Progression free survival is a measurement from a defined time point e.g. diagnosis and indicates that the disease did not progress i.e. tumours did not increase in size and new incidences did not occur. PFS is usually used in analyzing results of treatment for advanced disease.
A temporal measurement related to disease progression
The point in time at which an individual was born.
A clinical temporal measurement indicating that the subject is alive at the end of the clinical investigation.
The recurrence of a disease after treatment
The point at which a clinical diagnosis is made.
The age of the conceptus, beginning from the time of FERTILIZATION. In clinical obstetrics, the gestational age is often estimated as the time from the last day of the last MENSTRUATION which is about 2 weeks before OVULATION and fertilization.
The age at which an alcohol diagnosis was made in a human patient
The age at which a breast cancer diagnosis was made in a human patient
The date or time of the last check of a patient by a medical professional.
The age of onset of (human) voice drop, the deepening of the voice of adolescents as they reach puberty
The age of an individual at the time an assessment takes place
quantification of some aspect of disease progression such as speed or symptom variability. Disease progression can be quantified in a number of ways, for example as a correlated measure of progression scores from different symptom areas
A disease involving the female reproductive system.
disease or disorder of female reproductive system
female reproductive system disease or disorder
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. [def-source: NCI]
EFO:0009642 'follow-up' refers to the medical procedure process of running follow-ups; EFO:0030038 'follow up status' refers to an observed quality.
The age of a person's father at which father's death occurred.
The age of a person's mother at which mother's death occurred.
Death in during childhood, defined here as between the ages of 2 and 10 years.
The determination of the amount of eicosanoids present in a sample, typically blood
The determination of the amount of prostaglandins present in a sample, typically blood
Age at initiation of a medical treatment, such as a drug, therapy or medical device.
age at initiation of treatment
Age at initiation of hormone replacement therapy, the therapeutic use of hormones to alleviate the effects of hormone deficiency.
age at initiation of hormone replacement therapy
Age at initiation of the use of corrective lenses, such as glasses or contact lenses, to treat an abnormality of the eye.
age at initiation of corrective lens use
Age at initiation of the use of an oral contraceptive pill.
age at initiation of oral contraceptive pill use
Age at the time of a specific medical procedure or intervention intended to alter the course of a disease.
age at medical procedure
Age of initation of the habit of smoking, the inhaling and exhaling of tobacco smoke.
age at initiation of smoking
Age of initiation of the consumption of the drug cannabis.
age at initiation of cannabis consumption
age at initiation of cannabis use
the ending of pregnancy by removing a fetus or embryo before it can survive outside the uterus.
Welcome to the GenEpiO ontology! The "information content entity" class has many GenEpiO terms. "data item > measurement data item" has many datum terms; see "data representational model" for collections of terms set up for compatibility with 3rd party sources. Note that this file contains examples of cities, provinces, states, territories, and soverign nations from around the world; customization of this geographical content would be expected for particular regional use.
acquaintance
address
Base class for definitions.
A named element in the model.
Usage example and description.
An attributed label.
A permissible value, accompanied by intended text and an optional mapping to a concept URI.
A collection of subset, type, slot and class definitions.
The definition of a property or a slot.
INSDC:country:democratic republic of the congo
ISO3166-2 codes for 2009 revision of admin. units seem not to have been assigned.
INSDC:country:french southern and antarctic lands
Territoire des Terres australes et antarctiques francaises
Geographically the western regions of Kazakhstan may be in Europe.
INSDC:country:former yugoslav republic of macedonia
INSDC:country:heard island and mcdonald islands
North East Pacific Ocean coastal waters of Central America and Columbia
Northwest Atlantic Ocean coastal waters of Canada
begin_date: 1943-11-29. end_date: 1991-06-25. Previous to 1943: Kingdom of Yugoslavia, begins_in: 1918-12-01; end_date: 1941-04_17.
Northeast Atlantic Ocean coastal waters of Africa
Northwest Atlantic Ocean coastal waters of Barbados
Northwest Atlantic Ocean coastal waters of Bermuda
Western Indian Ocean coastal waters of Southern Africa and Madagascar
Northwest Atlantic Ocean coastal waters of Greenland
INSDC:country:saint vincent and the grenadines
Damion Dooley's note: Here we are exploring the use of individuals/instances to describe local picklists for GenEpiO driven software.
A data field which describes the name and version number of the protocol used for diagnostic marker amplification.
gene name 1
gene name 1 field
gene name 1 slot
gene name one
Example Guidance: Select a gene from the pick list. If the gene of interest is not in the list, provide the full name of the gene or the gene symbol (short form of gene name). Standardized gene names and symbols can be found in the Gene Ontology using this look-up service: https://bit.ly/2Sq1LbI
diagnostic pcr protocol 1
diagnostic pcr protocol 1 field
diagnostic pcr protocol 1 slot
diagnostic pcr protocol one
Example Guidance: The name and version number of the protocol used for carrying out a diagnostic PCR test. This information can be compared to sequence data for evaluation of performance and quality control.
A data field which describes the Ct value result from a diagnostic SARS-CoV-2 RT-PCR test.
diagnostic pcr Ct value 1
diagnostic pcr Ct value 1 field
diagnostic pcr Ct value 1 slot
diagnostic pcr Ct value one
Example Guidance: Provide the cycle threshold (Ct) value of the sample from the diagnostic RT-PCR test.
gene name 2
gene name 2 field
gene name 2 slot
gene name two
diagnostic pcr protocol 2
diagnostic pcr protocol 2 field
diagnostic pcr protocol 2 slot
diagnostic pcr protocol two
Example Guidance: The name and version number of the protocol used for carrying out a second diagnostic PCR test. This information can be compared to sequence data for evaluation of performance and quality control.
diagnostic pcr Ct value 2
diagnostic pcr Ct value 2 field
diagnostic pcr Ct value 2 slot
diagnostic pcr Ct value two
Example Guidance: Provide the cycle threshold (Ct) value of the sample from the second diagnostic RT-PCR test.
A data field which describes the name of the gene used in the diagnostic RT-PCR test.
gene name 3
gene name 3 field
gene name 3 slot
gene name three
Example Guidance: Provide the full name of another gene used in an RT-PCR test. The gene symbol (short form of gene name) can also be provided. Standardized gene names and symbols can be found in the Gene Ontology using this look-up service: https://bit.ly/2Sq1LbI
diagnostic pcr protocol 3
diagnostic pcr protocol 3 field
diagnostic pcr protocol 3 slot
diagnostic pcr protocol three
diagnostic pcr Ct value 3
diagnostic pcr Ct value 3 field
diagnostic pcr Ct value 3 slot
diagnostic pcr Ct value three
Example Guidance: Provide the CT value of the sample from the second diagnostic RT-PCR test.
United Nations
MSH
NCI_Thesaurus
_test_individual
LabID assigned by NLEP
A country where an isolate was collected.
SourceCountry
A PulseNet field which describes the country where an isolate was collected.
Currently not used for PulseNet Canada
(Province for PNC) where isolate was collected.
Site of the source type where isolate was collected, e.g. blood, CSF, etc.
The source type of the isolate, e.g. human, environmental, etc.
Other countries where the patient traveled
Further description of the source type, e.g. bovine, chicken
Submitted isolate # (if diff. From Key #), NLEP will enter Prov. Submitted # if sample was sent to NLEP for PFGE
(Province for PNC) additional number used to identify the isolate
Age of patient when isolate was collected
Sex of patient when isolate was collected
Date of collection
Date the isolate is uploaded to the national database after initial upload
Antigenic Formula
Subspecies, I - VI (roman numerals)
O polysaccharide (LPS) Group
Serotype of isolate
Code issued by CDC; see: 'Naming of outbreaks…' on WebBoard. (format YYMMLabIDLITScode-#)
Number issued by CDC if isolate is run at CDC (Key will be # issued by NLEP if isolate run at NLEP)
Enzyme name present if part of that national list.
Phage type
Provides LabID, gel and lane information
Status of the isolate; this is only confirmed once CDC runs it.
checked if the isolate is part of NARMS.
Checked if the isolate is part of FoodNet.
XbaI gel where the isolate is located, lane of gel
XbaI pattern assigned by CDC (format XXXXXX.####)
The date the XbaI gel is run
Once the XbaI pattern is named, the status is confirmed by CDC
BlnI gel where the isolate is located, lane of gel
BlnI pattern assigned by CDC (format XXXXXX.####).
The date the BlnI gel is run
Once the BlnI pattern is named, the status is confirmed by CDC
SpeI gel where the isolate is located, lane of gel.
SpeI pattern assigned by CDC (format XXXXXX.####).
The date the SpeI gel is run.
Once the SpeI pattern is named, the status is confirmed by CDC.
Date WHICH (PH?) lab received isolate.
ISO_23418.organization_contact.service
Date the isolate uploaded to the national database.
A Canadian public research university in the province of Manitoba.
The Public Health Agency of Canada is an agency of the Government of Canada that is responsible for public health, emergency preparedness and response, and infectious and chronic disease control and prevention.
PHAC
The Canadian Food Inspection Agency is a regulatory agency that is dedicated to the safeguarding of food, plants, and animals in Canada
CFIA
Agriculture and Agri-Food Canada is the department of the Government of Canada responsible for the federal regulation of agriculture, including policies governing the production, processing, and marketing of all farm, food, and agri-based products.
AAFC
Health Canada is the department of the Government of Canada responsible for national health policy.
Environment and Climate Change Canada, is the department of the Government of Canada, that is responsible for coordinating environmental policies and programs, as well as preserving and enhancing the natural environment and renewable resources. It is also colloquially known by its former name, Environment Canada.
ECCC
Environment Canada
Environment and Climate Change Canada (ECCC)
Fisheries and Oceans Canada, is a department of the Government of Canada that is responsible for developing and implementing policies and programs in support of Canada's economic, ecological and scientific interests in oceans and inland waters.
DFO
gene name 4
gene name 4 field
gene name 4 slot
gene name four
Example Guidance: Select the name of the gene used for the diagnostic PCR from the standardized pick list.
diagnostic pcr Ct value 4
diagnostic pcr Ct value 4 field
gene name 5
gene name 5 slot
gene name five
gene name5 field
gene name 5 field
diagnostic pcr Ct value 5
diagnostic pcr Ct value 5 field
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.
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.
Pacific Biosciences
An organization that supplies tools for studying the synthesis and regulation of DNA, RNA and protein. It developed a powerful technology platform called single molecule real-time (SMRT) technology which enables real-time analysis of biomolecules with single molecule resolution.
Damion Dooley's note: this BFO class is incompatible with "immaterial entity" "n-dimensional concept".
Note that this can refer to a material entity like an organ or muscle, or an immaterial entity (a site or fiat boundary) like skin, stomach cavity or lung surface.
asian tiger shrimp
black tiger shrimp
[Oceans and Seas]
INSDC:country:falkland islands (islas malvinas)
populated place, Republic of South Africa
Census Regions and Divisions are groupings of States that subdivide the United States.
United States Census Bureau
Region (contiguous United States of America)
A census region in the United States of America
populated place, contiguous United States of America
The 2nd level administrative regions of Egypt are very confusuing and different sources conflicting. Those in gaz.obo are from GeoHive (http://www.xist.org/default1.aspx) and are not fully in agreement with those from the WHO (the file EGY_SALB_table.xls downloaded from http://www.who.int/whosis/database/gis/salb/salb_coding.aspx#DATA).
INSDC:country:south georgia and the south sandwich islands
South Georgia and South Sandwich Islands
Villages and Cities from SALB; divided into communities from http://www.armstat.am/en/?nid=52.
When an authorative list of Divisions of the new (2007) Districts is available this needs revision.
The provinces are under reorganization, this list is part new part old. See: http://www.statoids.com/ucd.html
populated place, Democratic Republic of Congo
populated place, Central African Republic
Pitcairn, Henderson, Ducie and Oeno Islands
INSDC:country:ashmore and cartier islands
Territory of Ashmore and Cartier Islands
Territory of the Cocos (Keeling) Islands
Heard Island and McDonald Islands Territory
directly governed city (North Korea)
populated place, Palestinian Territories
INSDC:country:the former yugoslav republic of macedonia
This is a catch-all category for Gazetteer items that have "located in" relations but not an imported GAZETTEER class parent in GenEpiO.
home
phone type - home
The butchery leg cut of a chicken
obsolete: chicken leg
Having a gender (identity) which is different from the sex one was assigned at birth: being assigned male at birth but having a female gender or vice versa; or, pertaining to such people.
Not identifying with culturally conventional gender roles and categories of male or female; having changed gender identity from male to female or female to male, or identifying with elements of both, or having some other gender identity; or, pertaining to such people.
Transgender people have a gender identity or gender expression that differs from their assigned sex. In some select cases, transgender people are sometimes called transsexual if they desire medical assistance to transition from one sex to another. "Transgender" is also an umbrella term: in addition to including people whose gender identity is the opposite of their assigned sex (trans men and trans women), it may include people who are not exclusively masculine or feminine (people who are genderqueer or non-binary, including bigender, pangender, genderfluid, or agender). Other definitions of transgender also include people who belong to a third gender, or else conceptualize transgender people as a third gender.
transgender and nonbinary
"Transgender" and its derivatives ("transgender male", "transgender female", "transgender woman", "transgender man", etc.) are generally not considered genders and/or gender identities. Listing "male" separate from "transgender male" or listing "transgender" separate from "male"/"female" is transphobic in the sense that it denies a transgender person's gender, forcing them to choose in an unclear situation, and implies that they are somehow deviant from "normal" maleness/femaleness. A few transgender persons still utilize these terms in identifying, however, but an "other (please specify)" option is much more functional in this regard (as well as a "select all that apply" for gender/gender identity).
"Transgender" is an adjective and should not be formed into a collective noun. This terminology is often used by anti-transgender activists aiming to dehumanize transgender people.
The adjective "transgender" should never have an extraneous "-ed" attached to it. This is confusing and grammatically unnecessary.
transcinsiyet
transgender
transgenre
transgjinor
transgénero
transgênero
transkjønnet
transkønnet
տրանսգենդեր
ट्रांसजेंडर
ট্রান্সজেন্ডার
Gender variance, or, sometimes, gender nonconformity, is behavior or gender expression exhibited by an individual that does not match cultural/social masculine and feminine gender norms and/or expectations.
gender variance among youth
"Gender non-conforming" and "gender diverse" are often preferred to "gender variant" because "gender variant" (and, by extension, "gender variance") implies a standard normative for gender (i.e. a way gender is "supposed to be"). However, many resources emply the term as a helpful "catch-all" for various transgender and cultural gender roles and identities.
gender variance
kønsvarians
The correspondence (or lack thereof) between one's assigned gender at birth and one's actual gender and/or gender presentation. The two primary, and most well known gender modalities are cisgender and transgender. However those are not the only possible relations for one to have. Gender modality is an open-ended category which welcomes the elaboration of further terms.
gender modality
"A length unit which is equal to the length of the path traveled by light in vacuum during a time interval of 1/299 792 458 of a second." [BIPM:BIPM, NIST:NIST]
"A time unit which is equal to the duration of 9 192 631 770 periods of the radiation corresponding to the transition between the two hyperfine levels of the ground state of the caesium 133 atom." [BIPM:BIPM, NIST:NIST]
"A thermodynamic temperature unit which is equal to the fraction 1/273.16 of the thermodynamic temperature of the triple point of water." [BIPM:BIPM, NIST:NIST]
"A length unit which is equal to one hundredth of a meter or 10^[-2] m." [NIST:NIST]
"A length unit which is equal to one thousandth of a meter or 10^[-3] m." [NIST:NIST]
"A length unit which is equal to one millionth of a meter or 10^[-6] m." [NIST:NIST]
"A length unit which is equal to one thousandth of one millionth of a meter or 10^[-9] m." [NIST:NIST]
"A length unit which is equal to 10 [-10] m." [NIST:NIST]
"A length unit which is equal to 10^[-12] m." [NIST:NIST]
"A temperature unit which is equal to one kelvin degree. However, they have their zeros at different points. The centigrade scale has its zero at 273.15 K." [NIST:NIST]
"A time unit which is equal to one thousandth of a second or 10^[-3] s." [NIST:NIST]
"A time unit which is equal to one millionth of a second or 10^[-6] s." [NIST:NIST]
"A time unit which is equal to 10^[-12] s." [NIST:NIST]
"A time unit which is equal to 60 seconds." [Wikipedia:Wikipedia]
"A time unit which is equal to 3600 seconds or 60 minutes." [Wikipedia:Wikipedia]
"A time unit which is equal to 24 hours." [Wikipedia:Wikipedia]
"A time unit which is equal to 7 days." [Wikipedia:Wikipedia]
"A time unit which is approximately equal to the length of time of one of cycle of the moon's phases which in science is taken to be equal to 30 days." [Wikipedia:Wikipedia]
"A time unit which is equal to 12 months which in science is taken to be equal to 365.25 days." [Wikipedia:Wikipedia]
"A substance unit equal to a millionth of a mol or 10^[-6] mol." [NIST:NIST]
"A concentration unit which denotes the number of moles of solute as a proportion of the total number of moles in a solution." [Wikipedia:Wikipedia]
"A mass unit density which is equal to mass of an object in kilograms divided by the volume in cubic meters." [UOC:GVG]
"A mass unit density which is equal to mass of an object in grams divided by the volume in cubic centimeters." [UOC:GVG]
"A molar volume unit which is equal to 1 cubic meter occupied by one mole of a substance in the form of a solid, liquid, or gas." [NIST:NIST]
"A molar volume unit which is equal to 1 cubic centimeter occupied by one mole of a substance in the form of a solid, liquid, or gas." [NIST:NIST]
"A specific volume unit which is equal to one cubic meter volume occupied by one kilogram of a particular substance." [NIST:NIST]
"A speed/velocity unit which is equal to the speed of an object traveling 1 meter distance in one second." [NIST:NIST]
"A volume unit which is equal to the volume of a cube with edges one meter in length. One cubic meter equals to 1000 liters." [NIST:NIST]
"A volume unit which is equal to one millionth of a cubic meter or 10^[-9] m^[3], or to 1 ml." [NIST:NIST]
"A volume unit which is equal to one thousandth of a liter or 10^[-3] L, or to 1 cubic centimeter." [NIST:NIST]
"A volume unit which is equal to one thousandth of a cubic meter or 10^[-3] m^[3], or to 1 decimeter." [NIST:NIST]
"A volume unit which is equal to one thousand of a cubic meter or 10^[-3] m^[3], or to 1 L." [NIST:NIST]
"A volume unit which is equal to one millionth of a liter or 10^[-6] L." [NIST:NIST]
"A volume unit which is equal to one thousandth of one millionth of a liter or 10^[-9] L." [NIST:NIST]
"A volume unit which is equal to 10^[-12] L." [NIST:NIST]
"A volume unit which is equal to 10^[-15] L." [NIST:NIST]
"A plane angle unit which is equal to the angle subtended at the center of a circle by an arc equal in length to the radius of the circle, approximately 57 degrees 17 minutes and 44.6 seconds." [NIST:NIST]
"A time unit which is equal to one thousandth of one millionth of a second or 10^[-9] s." [NIST:NIST]
"A time unit which is equal to 100 years." [Wikipedia:Wikipedia]
"A time unit which represents the period over which the activity or concentration of a specified chemical or element falls to half its original activity or concentration." [MGED:MGED]
"A dimensionless concentration unit which denotes the mass of a substance in a mixture as a percentage of the mass of the entire mixture." [Wikipedia:Wikipedia]
"A dimensionless concentration unit which denotes the mass of the substance in a mixture as a percentage of the volume of the entire mixture." [UOC:GVG]
"A dimensionless concentration unit which denotes the volume of the solute in mL per 100 mL of the resulting solution." [UOC:GVG]
"A mass unit density which is equal to mass of an object in grams divided by the volume in milliliter." [UOC:GVG]
"A mass unit density which is equal to mass of an object in kilograms divided by the volume in liters." [UOC:GVG]
"A mass unit density which is equal to mass of an object in grams divided by the volume in liters." [UOC:GVG]
"A mass unit density which is equal to mass of an object in milligrams divided by the volume in milliliters." [UOC:GVG]
"A plane angle unit which is equal to 1/360 of a full rotation or 1.7453310^[-2] rad." [Wikipedia:Wikipedia]
"A dimensionless percent unit which denotes the homogeneity of a biomaterial." [MGED:MGED]
"A dimensionless percent unit which denotes the density of an attached or monolayer culture (e.g., cell culture)." [MGED:MGED]
"A temperature unit which is equal to 5/9ths of a kelvin. Negative 40 degrees Fahrenheit is equal to negative 40 degrees Celsius." [Wikipedia:Wikipedia]
"A dimensionless concentration notation which denotes the acidity of a solution in terms of activity of hydrogen ions (H+)." [Wikipedia:Wikipedia]
"A specific volume unit which is equal to one liter volume occupied by one kilogram of a particular substance." [NIST:NIST]
"A specific volume unit which is equal to a thousandth of a liter per kilogram or 10^[-3] l/kg." [NIST:NIST]
"A specific volume unit which is equal to one millionth of a liter per kilogram or 10^[-6] l/kg." [NIST:NIST]
"A mass density unit which is equal to mass of an object in grams divided by the volume in deciliters." [UOC:GVG]
"A volume unit which is equal to one tenth of a liter or 10^[-1] L." [NIST:NIST]
"A dimensionless count unit which a measure of viable bacterial numbers." [Wikipedia:Wikipedia]
"A colony forming unit which a measure of viable bacterial numbers in one milliliter." [Wikipedia:Wikipedia]
A count unit which contains one nucleotide.
"A count unit which contains one nucleotide." [UO:GVG]
"An electric potential difference unit which is equal to one thousandth of a volt or 10^[-3] V." [UOC:GVG]
"An electrical conduction unit which is equal to A/V." [NIST:NIST]
"A mass unit density which is equal to mass of an object in milligrams divided by the volume in liters." [UOC:GVG]
mcg/mL
µg/mL
"A mass unit density which is equal to mass of an object in micrograms divided by the volume in millliters." [UOC:GVG]
"A mass unit density which is equal to mass of an object in nanograms divided by the volume in milliliters." [UOC:GVG]
"A mass unit density which is equal to mass of an object in micrograms divided by the volume in liters." [UOC:GVG]
"A unit used to express distances on a genetic map. In genetic mapping, distances between markers are determined by measuring the rate of meoitic recombination between them, which increases proportionately with the distance separating them. A cM is defined as the length of an interval in which there is a 1% probability of recombination. On the average, 1 cM is roughly equivalent to 1 megabase (Mb) of DNA, although this can vary widely due to hot and cold spots of recombination." [NCBI:http\://www.ncbi.nlm.nih.gov/SCIENCE96/Glossary.html]
"A unit of genetic map distance defined corresponding to an interval in which there is a 1% probability of X-irradiation induced breakage. To be completely specified, the unit must be qualified by the radiation in dosage in rads (e.g. cR8000), because this determines the actual breakage probability." [NCBI:http\://www.ncbi.nlm.nih.gov/SCIENCE96/Glossary.html]
"A unit equal to one million base pairs" [UOC:GVG]
"A unit equal to one billion base pairs." [UOC:GVG]
"An electrical conduction unit which is equal to one thousandth of a siemen or 10^[-3] siemens." [NIST:NIST]
"A specific concentration unit which is equal to 1 micromole in a given volume of one thousandth of a cubic meter." [NIST:NIST]
"A specific concentration unit which is equal to 1 micromole of a given substance per kilogram of solvent." [UOB:LKSR]
"A length unit which is equal to 0.0254 metres." [Wikipedia:Wikpiedia]
"A length unit which is equal to 0.0254 millimetres." [Wikipedia:Wikpiedia]
"A length unit which is equal to 0.3048 metres, or 12 inches." [Wikipedia:Wikpiedia]
"A length unit which is equal to 0.9144 metres, or 3 feet." [Wikipedia:Wikpiedia]
"A length unit which is equal to 20.1168 metres, 66 feet, or 22 yards." [Wikipedia:Wikpiedia]
"A length unit which is equal to 20,116.8 metres, 660 feet, or 10 chains." [Wikipedia:Wikpiedia]
"A length unit which is equal to 1,609.344 metres, or 8 furlongs." [Wikipedia:Wikpiedia]
"A length unit which is equal to 3 miles, or 4,828.032 metres" [Wikipedia:Wikpiedia]
"A maritime length unit is one used primarily at sea." [Wikipedia:Wikpiedia]
"A maritime length unit which is equal to 6.08 feet, or 1.853184 metres" [Wikipedia:Wikpiedia]
"A maritime length unit which is equal to 608 feet, 100 fathoms, or 185.3184 metres" [Wikipedia:Wikpiedia]
"A maritime length unit which is equal to 6,080 feet, 10 cables, or 1,853.184 metres" [Wikipedia:Wikpiedia]
"An imperial volume unit which is equivalent to 28.413,0625 millilitres." [Wikipedia:Wikipedia]
"An imperial volume unit which is equivalent to 142.065,3125 millilitres." [Wikipedia:Wikipedia]
"An imperial volume unit which is equivalent to 568.261,25 millilitres." [Wikipedia:Wikipedia]
"An imperial volume unit which is equivalent to 1,136.5225 millilitres, or two pints." [Wikipedia:Wikipedia]
"An imperial volume unit which is equivalent to 4,546.09 millilitres, or 8 pints." [Wikipedia:Wikipedia]
"A metric teaspoon is a unit of measurement of volume widely used in cooking recipes and pharmaceutic prescriptions. It equals a 5mL volume." [Wikipedia:https://en.wikipedia.org/wiki/Teaspoon]
"A unit of mass concentration defined as the number of micrograms of a substance per 250 ml Wheaton bottle." [UOB:LTS]
"A length unit which is equal to one thousand meters." [UOB:LKSR]
"A mass unit density which is equal to mass of an object in milligrams divided by the volume in deciliters." [UOB:LKSR]
"A mass unit density which is equal to mass of an object in micrograms divided by the volume in deciliters." [UOB:LKSR]