The VEuPathDB ontology is an application ontology developed to encode our understanding of what data is about in the public resources developed and maintained by the Eukaryotic Pathogen, Host and Vector Genomics Resource (VEuPathDB; https://veupathdb.org). The VEuPathDB ontology was previously named the EuPathDB ontology prior to EuPathDB joining with VectorBase.The ontology was built based on the Ontology of Biomedical Investigations (OBI) with integration of other OBO ontologies such as PATO, OGMS, DO, etc. as needed for coverage. Currently the VEuPath ontology is primarily intended to be used for support of the VEuPathDB sites. Terms with VEuPathDB ontology IDs that are not specific to VEuPathDB will be submitted to OBO Foundry ontologies for subsequent import and replacement of those terms when they are available.
Relates an entity in the ontology to the name of the variable that is used to represent it in the code that generates the BFO OWL file from the lispy specification.
Really of interest to developers only
BFO OWL specification label
Relates an entity in the ontology to the term that is used to represent it in the the CLIF specification of BFO2
BFO CLIF specification label
An alternative label used in VEuPathDB project websites.
VEuPathDB alternative label
Label of terms used in Amazonia data dictionary. It is in Spanish.
obsolete Amazonia data dictionary label (es)
English label used in Amazonia project for display on the website
Spanish label used in Amazonia project for display on the website
Label of terms used in PRISM data dictionary. It is in English.
obsolete PRISM data dictionary label (en)
English label used in Prism project for display on the website
Term description provided by Amazonia group
Term description provided by PRISM group
Three options of term type: - category: used for organize the filter in the website, not ontology term - variable: term in the data dictionary of project. Should have mapped ontology term associate with it - value: controlled vocubulary used for annotation of variable in the data dictionary. Should have mapped ontology term associate with it
specify ICEMR term original from which database
An annotation property used to specify the order of terms displayed on a website.
display order
Label of terms used in Indian data dictionary. It is in English.
obsolete Indian data dictionary label (en)
English label used in Indian project for display on the website
Term description provided by Indian group
Translated English label of terms in Amazonia data dictionary.
obsolete Amazonia data dictionary label (en)
In a data file, there is a column with name 'age'. It mapped to EuPath ontology term 'age at visit'. We can add 'implements variable' annotation with value 'age' to term 'age at visit'.
Column header for each variable from the original datasets (use format from datasets, not data dictionary).
variable
The column order of variables in the original data files
The original file name for the data file the variable was found in, or a shortened version of the file name that contains all relevant information to identify the data file.
data file
The highest level parent term (Household, Participant, Observation, Specimen) the variable falls under.
category
The variable description from the data dictionary. Useful for assigning display labels. To be provided either directly from the data provider in their codebook or filled out by ClinEpi Outreach before handing over to Ontology.
codebook description
All possible responses and their mapped terms for each variable, from the data dictionary. Useful for value mapping.
codebook values
An annotation that specifies how a term is used in generation search filters on a website. It has five options: category: a term to organize the variables for exploration on the website variable: a variable in the dataset variable, derived: one term that is calculated, using the data in two or more other variables multifilter: any value below it in the hierarchy will be displayed as a multifilter value: the value of a multifilter
term type
Annotation property that records the ontology term IRI originally used in the study.
replaces
An annotation property to specify the value code used in the dataset.
Annotation property that specifies units that are associated with a variable (if any) in a human-readable format. Use abbreviations.
unit label
Annotation property that specifies the ontology term IRI of unit, generally from the unit ontology (UO).
unit IRI
Annotation property that specifies which dataset a term belongs to.
dataSet
Annotation property that indicates terms that were assessed longitudinally / repeatedly over time.
repeated
Annotation property that specifies important terms to be highlighted.
is featured
Annotation property that indicates that the term is hidden from the UI and download files.
hidden
Annotation property that identifies terms that are on the log scale or natural log scale, as opposed to on the linear scale.
scale
Annotation property that specifies terms that are related to time, to be used in visualizations looking at data over time. Also to be used in subsetting tab histograms (to indicate that the data range should not include the origin)
is temporal
Annotation property that specifies key terms with longitudinal/repeated measures in the studies.
merge key
Annotation property that specifies default minimum value for each term's range. Useful to ensure that histograms for related terms have the same x-axis range
default display range min
Annotation property that specifies the default maximum value for each term's range. Useful to ensure that histograms for related terms have the same x-axis range
default display range max
Annotation property that specifies the bin width for each term's histogram.
default bin width
Annotation property used to annotate numeric terms as strings. Numeric terms annotated as strings will ALWAYS be ordinal. Study specific.
force string type
Term ID as previously used by VectorBase
editor preferred term
The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English)
PERSON:Daniel Schober
example of usage
A phrase describing how a term should be used and/or a citation to a work which uses it. May also include other kinds of examples that facilitate immediate understanding, such as widely know prototypes or instances of a class, or cases where a relation is said to hold.
in branch
An annotation property indicating which module the terms belong to. This is currently experimental and not implemented yet.
has curation status
PERSON:Alan Ruttenberg
PERSON:Bill Bug
PERSON:Melanie Courtot
definition
The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.
2012-04-05: Barry Smith The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible. Can you fix to something like: A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property. Alan Ruttenberg Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. On the specifics of the proposed definition: We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with.
editor note
An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology.
term editor
Name of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several people
20110707, MC: label update to term editor and definition modified accordingly. See https://github.com/information-artifact-ontology/IAO/issues/115.
alternative label
A label for a class or property that can be used to refer to the class or property instead of the preferred rdfs:label. Alternative labels should be used to indicate community- or context-specific labels, abbreviations, shorthand forms and the like.
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
the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/
An IRI or similar locator for a request or discussion of an ontology term.
Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg
The 'tracker item' can associate a tracker with a specific ontology term.
ontology term requester
The name of the person, project, or organization that motivated inclusion of an ontology term by requesting its addition.
The 'term requester' can credit the person, organization or project who request the ontology term.
is denotator type
Relates an class defined in an ontology, to the type of it's denotator
In OWL 2 add AnnotationPropertyRange('is denotator type' 'denotator type')
Alan Ruttenberg
imported from
For external terms/classes, the ontology from which the term was imported
expand expression to
ObjectProperty: RO_0002104 Label: has plasma membrane part Annotations: IAO_0000424 "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.org/obo/owl/GO#GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)"
A macro expansion tag applied to an object property (or possibly a data property) which can be used by a macro-expansion engine to generate more complex expressions from simpler ones
Chris Mungall
expand assertion to
ObjectProperty: RO??? Label: spatially disjoint from Annotations: expand_assertion_to "DisjointClasses: (http://purl.obolibrary.org/obo/BFO_0000051 some ?X) (http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)"
A macro expansion tag applied to an annotation property which can be expanded into a more detailed axiom.
first order logic expression
antisymmetric property
part_of antisymmetric property xsd:true
Use boolean value xsd:true to indicate that the property is an antisymmetric property
OBO foundry unique label
An alternative name for a class or property which is unique across the OBO Foundry.
The intended usage of that property is as follow: OBO foundry unique labels are automatically generated based on regular expressions provided by each ontology, so that SO could specify unique label = 'sequence ' + [label], etc. , MA could specify 'mouse + [label]' etc. Upon importing terms, ontology developers can choose to use the 'OBO foundry unique label' for an imported term or not. The same applies to tools .
PERSON:Bjoern Peters
PERSON:Chris Mungall
GROUP:OBO Foundry <http://obofoundry.org/>
has ID digit count
Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> Annotations: 'has ID prefix': "http://purl.obolibrary.org/obo/RO_" 'has ID digit count' : 7, rdfs:label "RO id policy" 'has ID policy for': "RO"
Relates an ontology used to record id policy to the number of digits in the URI. The URI is: the 'has ID prefix" annotation property value concatenated with an integer in the id range (left padded with "0"s to make this many digits)
Person:Alan Ruttenberg
has ID range allocated
Datatype: idrange:1 Annotations: 'has ID range allocated to': "Chris Mungall" EquivalentTo: xsd:integer[> 2151 , <= 2300]
Relates a datatype that encodes a range of integers to the name of the person or organization who can use those ids constructed in that range to define new terms
has ID range allocated to
has ID policy for
Relating an ontology used to record id policy to the ontology namespace whose policy it manages
has ID prefix
Relates an ontology used to record id policy to a prefix concatenated with an integer in the id range (left padded with "0"s to make this many digits) to construct an ID for a term being created.
elucidation
person:Alan Ruttenberg
Person:Barry Smith
Primitive terms in a highest-level ontology such as BFO are terms which are so basic to our understanding of reality that there is no way of defining them in a non-circular fashion. For these, therefore, we can provide only elucidations, supplemented by examples and by axioms
has associated axiom(nl)
An axiom associated with a term expressed using natural language
has associated axiom(fol)
An axiom expressed in first order logic using CLIF syntax
is allocated id range
Relates an ontology IRI to an (inclusive) range of IRIs in an OBO name space. The range is give as, e.g. "IAO_0020000-IAO_0020999"
Add as annotation triples in the granting ontology
has ontology root term
Ontology annotation property. Relates an ontology to a term that is a designated root term of the ontology. Display tools like OLS can use terms annotated with this property as the starting point for rendering the ontology class hierarchy. There can be more than one root.
Nicolas Matentzoglu
may be identical to
A annotation relationship between two terms in an ontology that may refer to the same (natural) type but where more evidence is required before terms are merged.
David Osumi-Sutherland
VFB
Edges asserting this should be annotated with to record evidence supporting the assertion and its provenance.
scheduled for obsoletion on or after
Used when the class or object is scheduled for obsoletion/deprecation on or after a particular date.
Chris Mungall, Jie Zheng
GO ontology
has axiom id
A URI that is intended to be unique label for an axiom used for tracking change to the ontology. For an axiom expressed in different languages, each expression is given the same URI
has axiom label
term replaced by
Use on obsolete terms, relating the term to another term that can be used as a substitute
ISA alternative term
An alternative term used by the ISA tools project (http://isa-tools.org).
Requested by Alejandra Gonzalez-Beltran https://sourceforge.net/tracker/?func=detail&aid=3603413&group_id=177891&atid=886178
ISA tools project (http://isa-tools.org)
NIAID GSCID-BRC alternative term
An alternative term used by the National Institute of Allergy and Infectious Diseases (NIAID) Genomic Sequencing Centers for Infectious Diseases (GSCID) and Bioinformatics Resource Centers (BRC).
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
This is an annotation used on an object property to indicate a logical characterstic beyond what is possible in OWL.
logical characteristic of object property
'part disjoint with' 'defined by construct' """ PREFIX owl: <http://www.w3.org/2002/07/owl#> PREFIX : <http://example.org/ CONSTRUCT { [ a owl:Restriction ; owl:onProperty :part_of ; owl:someValuesFrom ?a ; owl:disjointWith [ a owl:Restriction ; owl:onProperty :part_of ; owl:someValuesFrom ?b ] ] } WHERE { ?a :part_disjoint_with ?b . }
Links an annotation property to a SPARQL CONSTRUCT query which is meant to provide semantics for a shortcut relation.
CHEBI:26523 (reactive oxygen species) has an exact synonym (ROS), which is of type OMO:0003000 (abbreviation)
A synonym type for describing abbreviations or initalisms
A synonym type for describing ambiguous synonyms
A synonym type for describing dubious synonyms
EFO:0006346 (severe cutaneous adverse reaction) has an exact synonym (scar), which is of the type OMO:0003003 (layperson synonym)
A synonym type for describing layperson or colloquial synonyms
CHEBI:23367 (molecular entity) has an exact synonym (molecular entities), which is of the type OMO:0003004 (plural form)
A synonym type for describing pluralization synonyms
CHEBI:16189 (sulfate) has an exact synonym (sulphate), which is of the type OMO:0003005 (UK spelling synonym)
A synonym type for describing UK spelling variants
An alternative label for a class or property which has a more general meaning than the preferred name/primary label.
has broad synonym
An alternative label for a class or property which has the exact same meaning than the preferred name/primary label.
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
a core relation that holds between a part and its whole
part_of
part of
a core relation that holds between a whole and its part
has_part
has part
is realized by
realized_in
realized in
realizes
x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.
precedes
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
occurs in
[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
contains process
A relation between a medication material and a disease or symptom that it may treat.
A relation between a drug product and (one of) its active ingredient.
has measurement unit label
This document is about information artifacts and their representations
A (currently) primitive relation that relates an information artifact to an entity.
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.
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
A person's name denotes the person. A variable name in a computer program denotes some piece of memory. Lexically equivalent strings can denote different things, for instance "Alan" can denote different people. In each case of use, there is a case of the denotation relation obtaining, between "Alan" and the person that is being named.
A primitive, instance-level, relation obtaining between an information content entity and some portion of reality. Denotation is what happens when someone creates an information content entity E in order to specifically refer to something. The only relation between E and the thing is that E can be used to 'pick out' the thing. This relation connects those two together. Freedictionary.com sense 3: To signify directly; refer to specifically
2009-11-10 Alan Ruttenberg. Old definition said the following to emphasize the generic nature of this relation. We no longer have 'specifically denotes', which would have been primitive, so make this relation primitive. g denotes r =def r is a portion of reality there is some c that is a concretization of g every c that is a concretization of g specifically denotes r
Conversations with Barry Smith, Werner Ceusters, Bjoern Peters, Michel Dumontier, Melanie Courtot, James Malone, Bill Hogan
denotes
m is a quality measurement of q at t. When q is a quality, there is a measurement process p that has specified output m, a measurement datum, that is about q
8/6/2009 Alan Ruttenberg: The strategy is to be rather specific with this relationship. There are other kinds of measurements that are not of qualities, such as those that measure time. We will add these as separate properties for the moment and see about generalizing later
From the second IAO workshop [Alan Ruttenberg 8/6/2009: not completely current, though bringing in comparison is probably important] This one is the one we are struggling with at the moment. The issue is what a measurement measures. On the one hand saying that it measures the quality would include it "measuring" the bearer = referring to the bearer in the measurement. However this makes comparisons of two different things not possible. On the other hand not having it inhere in the bearer, on the face of it, breaks the audit trail. Werner suggests a solution based on "Magnitudes" a proposal for which we are awaiting details. -- From the second IAO workshop, various comments, [commented on by Alan Ruttenberg 8/6/2009] unit of measure is a quality, e.g. the length of a ruler. [We decided to hedge on what units of measure are, instead talking about measurement unit labels, which are the information content entities that are about whatever measurement units are. For IAO we need that information entity in any case. See the term measurement unit label] [Some struggling with the various subflavors of is_about. We subsequently removed the relation represents, and describes until and only when we have a better theory] a represents b means either a denotes b or a describes describe: a describes b means a is about b and a allows an inference of at least one quality of b We have had a long discussion about denotes versus describes.
From the second IAO workshop: An attempt at tieing the quality to the measurement datum more carefully. a is a magnitude means a is a determinate quality particular inhering in some bearer b existing at a time t that can be represented/denoted by an information content entity e that has parts denoting a unit of measure, a number, and b. The unit of measure is an instance of the determinable quality.
From the second meeting on IAO: An attempt at defining assay using Barry's "reliability" wording assay: process and has_input some material entity and has_output some information content entity and which is such that instances of this process type reliably generate outputs that describes the input.
This one is the one we are struggling with at the moment. The issue is what a measurement measures. On the one hand saying that it measures the quality would include it "measuring" the bearer = referring to the bearer in the measurement. However this makes comparisons of two different things not possible. On the other hand not having it inhere in the bearer, on the face of it, breaks the audit trail. Werner suggests a solution based on "Magnitudes" a proposal for which we are awaiting details.
is quality measurement of
inverse of the relation 'denotes'
Person: Jie Zheng, Chris Stoeckert, Mike Conlon
denoted by
relating a cartesian spatial coordinate datum to a unit label that together with the values represent a point
has coordinate unit label
relates a process to a time-measurement-datum that represents the duration of the process
is duration of
inverse of the relation of is quality measurement of
2009/10/19 Alan Ruttenberg. Named 'junk' relation useful in restrictions, but not a real instance relationship
is quality measured as
The provides_service_consumer_with relation links the service to its primary process it provides for the consumer (as opposed to secondary processual parts of a service process such as payment or documentation). For example, a 'DNA sequencing service' provides_service_consumer_with 'DNA sequencing' as the essential process performed by the provider for the client.
A relation between a service and the primary processual part of the service that is performed by the provider for the consumer.
The relation between the conclusion "Gene tpbA is involved in EPS production" and the data items produced using two sets of organisms, one being a tpbA knockout, the other being tpbA wildtype tested in polysacharide production assays and analyzed using an ANOVA.
The relation between a data item and a conclusion where the conclusion is the output of a data interpreting process and the data item is used as an input to that process
has_specified_input
see is_input_of example_of_usage
The inverse property of is_specified_input_of
8/17/09: specified inputs of one process are not necessarily specified inputs of a larger process that it is part of. This is in contrast to how 'has participant' works.
PERSON: Alan Ruttenberg
some Autologous EBV(Epstein-Barr virus)-transformed B-LCL (B lymphocyte cell line) is_input_for instance of Chromum Release Assay described at https://wiki.cbil.upenn.edu/obiwiki/index.php/Chromium_Release_assay
A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of.
is_specified_input_of
has_specified_output
The inverse property of is_specified_output_of
is_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
is_specified_output_of
A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of.
A cell sorting process achieves the objective specification 'material separation objective'
This relation obtains between a planned process and a objective specification when the criteria specified in the objective specification are met at the end of the planned process.
modified according to email thread from 1/23/09 in accordince with DT and PPPB branch
the relation of the cells in the finger of the skin to the finger, in which an indeterminate number of grains are parts of the whole by virtue of being grains in a collective that is part of the whole, and in which removing one granular part does not nec- essarily damage or diminish the whole. Ontological Whether there is a fixed, or nearly fixed number of parts - e.g. fingers of the hand, chambers of the heart, or wheels of a car - such that there can be a notion of a single one being missing, or whether, by contrast, the number of parts is indeterminate - e.g., cells in the skin of the hand, red cells in blood, or rubber molecules in the tread of the tire of the wheel of the car.
Discussion in Karslruhe with, among others, Alan Rector, Stefan Schulz, Marijke Keet, Melanie Courtot, and Alan Ruttenberg. Definition take from the definition of granular parthood in the cited paper. Needs work to put into standard form
PAPER: Granularity, scale and collectivity: When size does and does not matter, Alan Rector, Jeremy Rogers, Thomas Bittner, Journal of Biomedical Informatics 39 (2006) 333-349
A relation between an organisation or person and a material entity, where the organization or person provides or supplies the material entity for others to use
5/11/2020: A prior definition contained reference to transfer of ownership. ("A relation between an organisation or person and a material entity who owned or has license to the material entity and there was a legal transfer of ownership or licensing of the material entity to the current owner"). This was left out as it was hard to read and it was unclear if/how that transfer restricts the relationship.
A relation between a material entity and an organisation or person who owned or has license to the material entity and there was a legal transfer of ownership or licensing of the material entity to the current owner.
This relation obtains between an objective specification and a planned process when the criteria specified in the objective specification are met at the end of the planned process.
Relating a legal person or organization to an organization in the case where the legal person or organization has a role as member of the organization.
2009/10/01 Alan Ruttenberg. Barry prefers generic is-member-of. Question of what the range should be. For now organization. Is organization a population? Would the same relation be used to record members of a population
JZ: Discussed on May 7, 2012 OBI dev call. Bjoern points out that we need to allow for organizations to be members of organizations. And agreed by the other OBI developers. So, human and organization were specified in 'Domains'. The textual definition was updated based on it.
2009/09/28 Alan Ruttenberg. Fucoidan-use-case
A relationship between two material entitites that each have disposition to form a complex with the other.
This is a shortcut relation, and should expand to say that the two material entities have dispositions, point to the process in which they from a complex that realizes those dispositions, and points to the complex in which the two entities are 'bound to' each other
has organization member
Relating an organization to a legal person or organization.
See tracker: https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_id=177891&atid=886178
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.
a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence.
characteristic of
Inverse of characteristic_of
has characteristic
a relation between a continuant and a process, in which the continuant is somehow involved in the process
participates in
a relation between a process and a continuant, in which the continuant is somehow involved in the process
has participant
A relationship between a generically dependent continuant and a specifically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants.
is concretized as
A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant.
concretizes
a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence
function of
A relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence.
a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence
role of
a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence
has function
a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence
has quality
a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence
has role
a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity
derives from
a relation between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity
derives into
a relation between two independent continuants, the location and the target, in which the target is entirely within the location
location of
a relation between two independent continuants, the target and the location, in which the target is entirely within the location
located in
before or simultaneous with
before
immediately preceded by
starts during
happens during
ends during
x overlaps y if and only if there exists some z such that x has part z and z part of y
overlaps
w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type.
has component
A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process.
capable of
c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p.
capable of part of
temporally related to
starts
ends
A relationship that holds between a substance and a chemical entity, if the chemical entity is part of the substance, and the chemical entity forms the biologically active component of the substance.
q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w.
characteristic of part of
A mereological relationship or a topological relationship
mereotopologically related to
A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities.
functionally related to
has member is a mereological relation between a collection and an item.
has member
relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause.
causally related to
p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q.
A relationship between a material entity and a process where the material entity has some causal role that influences the process
p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q.
A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity.
causal relation between material entity and a process
c is a substance that treats d if c is a material entity (such as a small molecule or compound) and d is a pathological process, phenotype or disease, and c is capable of some activity that negative regulates or decreases the magnitude of d.
the relationship between a fraction and the number above the line
the relationship between a fraction and the number below the line (or divisor)
has measurement value
has x coordinate value
A relation between a value specification and a number that quantifies it.
A range of 'real' might be better than 'float'. For now we follow 'has measurement value' until we can consider technical issues with SPARQL queries and reasoning.
has specified value
A relation between a value specification and a literal.
This is not an RDF/OWL object property. It is intended to link a value found in e.g. a database column of 'M' (the literal) to an instance of a value specification class, which can then be linked to indicate that this is about the biological gender of a human subject.
Tree
A taxonomy identifier that denotes a group of organisms or groups of organisms based on common ancestors.
clade name
A rate measurement datum that specifies the percentage of organisms within a population that have died over a given time interval.
mortality rate
A data item that denotes some context in which an individual realizes some employee role if he or she is a member of the labor force, or the context in which he or she is not a member of the labor force according to certain prespecified conditions.
employment status data item
Methicillin resistant Staphylococcus aureus
Any strain of Staphylococcus aureus that has tested resistant (R) to at least one of methicillin, oxacillin or cefoxitin by standard susceptibility testing methods.
methicillin-resistant Staphylococcus aureus
Julius Caesar
Verdi’s Requiem
the Second World War
your body mass index
BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81
Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf
An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])
entity
BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240
Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants
A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002])
if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001])
if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002])
if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002])
(forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002]
(forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001]
(forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002]
(forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002]
continuant
BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region
BFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players.
Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process.
Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame.
An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002])
Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001])
b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001])
(forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001]
(forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001]
occurrent
a chair
a heart
a leg
a molecule
a spatial region
an atom
an orchestra.
an organism
the bottom right portion of a human torso
the interior of your mouth
b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])
For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001])
For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002])
(forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001]
(forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002]
(iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002]
independent continuant
BFO 2 Reference: Spatial regions do not participate in processes.
Spatial region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the union of a spatial point and a spatial line that doesn't overlap the point, or two spatial lines that intersect at a single point. In both cases the resultant spatial region is neither 0-dimensional, 1-dimensional, 2-dimensional, or 3-dimensional.
A spatial region is a continuant entity that is a continuant_part_of spaceR as defined relative to some frame R. (axiom label in BFO2 Reference: [035-001])
All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001])
(forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001]
(forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001]
spatial region
Temporal region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the mereological sum of a temporal instant and a temporal interval that doesn't overlap the instant. In this case the resultant temporal region is neither 0-dimensional nor 1-dimensional
A temporal region is an occurrent entity that is part of time as defined relative to some reference frame. (axiom label in BFO2 Reference: [100-001])
All parts of temporal regions are temporal regions. (axiom label in BFO2 Reference: [101-001])
Every temporal region t is such that t occupies_temporal_region t. (axiom label in BFO2 Reference: [119-002])
(forall (r) (if (TemporalRegion r) (occupiesTemporalRegion r r))) // axiom label in BFO2 CLIF: [119-002]
(forall (x y) (if (and (TemporalRegion x) (occurrentPartOf y x)) (TemporalRegion y))) // axiom label in BFO2 CLIF: [101-001]
(forall (x) (if (TemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [100-001]
temporal region
an infinitely thin plane in space.
the surface of a sphere-shaped part of space
A two-dimensional spatial region is a spatial region that is of two dimensions. (axiom label in BFO2 Reference: [039-001])
(forall (x) (if (TwoDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [039-001]
two-dimensional spatial region
the spatiotemporal region occupied by a human life
the spatiotemporal region occupied by a process of cellular meiosis.
the spatiotemporal region occupied by the development of a cancer tumor
A spatiotemporal region is an occurrent entity that is part of spacetime. (axiom label in BFO2 Reference: [095-001])
All parts of spatiotemporal regions are spatiotemporal regions. (axiom label in BFO2 Reference: [096-001])
Each spatiotemporal region at any time t projects_onto some spatial region at t. (axiom label in BFO2 Reference: [099-001])
Each spatiotemporal region projects_onto some temporal region. (axiom label in BFO2 Reference: [098-001])
Every spatiotemporal region occupies_spatiotemporal_region itself.
Every spatiotemporal region s is such that s occupies_spatiotemporal_region s. (axiom label in BFO2 Reference: [107-002])
(forall (r) (if (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion r r))) // axiom label in BFO2 CLIF: [107-002]
(forall (x t) (if (SpatioTemporalRegion x) (exists (y) (and (SpatialRegion y) (spatiallyProjectsOntoAt x y t))))) // axiom label in BFO2 CLIF: [099-001]
(forall (x y) (if (and (SpatioTemporalRegion x) (occurrentPartOf y x)) (SpatioTemporalRegion y))) // axiom label in BFO2 CLIF: [096-001]
(forall (x) (if (SpatioTemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [095-001]
(forall (x) (if (SpatioTemporalRegion x) (exists (y) (and (TemporalRegion y) (temporallyProjectsOnto x y))))) // axiom label in BFO2 CLIF: [098-001]
spatiotemporal region
a process of cell-division, \ a beating of the heart
a process of meiosis
a process of sleeping
the course of a disease
the flight of a bird
the life of an organism
your process of aging.
p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003])
BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war)
(iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003]
process
an atom of element X has the disposition to decay to an atom of element Y
certain people have a predisposition to colon cancer
children are innately disposed to categorize objects in certain ways.
the cell wall is disposed to filter chemicals in endocytosis and exocytosis
BFO 2 Reference: Dispositions exist along a strength continuum. Weaker forms of disposition are realized in only a fraction of triggering cases. These forms occur in a significant number of cases of a similar type.
b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002])
If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002])
(forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002]
(forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002]
disposition
the disposition of this piece of metal to conduct electricity.
the disposition of your blood to coagulate
the function of your reproductive organs
the role of being a doctor
the role of this boundary to delineate where Utah and Colorado meet
To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002])
All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002])
(forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002]
(forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002]
realizable entity
A zero-dimensional spatial region is a point in space. (axiom label in BFO2 Reference: [037-001])
(forall (x) (if (ZeroDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [037-001]
zero-dimensional spatial region
the ambient temperature of this portion of air
the color of a tomato
the length of the circumference of your waist
the mass of this piece of gold.
the shape of your nose
the shape of your nostril
a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001])
If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001])
(forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001]
(forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001]
quality
Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key
of one-sided specifically dependent continuants: the mass of this tomato
of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates.
the disposition of this fish to decay
the function of this heart: to pump blood
the mutual dependence of proton donors and acceptors in chemical reactions [79
the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction
the pink color of a medium rare piece of grilled filet mignon at its center
the shape of this hole.
the smell of this portion of mozzarella
b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])
Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc.
(iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003]
specifically dependent continuant
John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married.
the priest role
the role of a boundary to demarcate two neighboring administrative territories
the role of a building in serving as a military target
the role of a stone in marking a property boundary
the role of subject in a clinical trial
the student role
BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives.
b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001])
(forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001]
role
or with divisions drawn by cognitive subjects for practical reasons, such as the division of a cake (before slicing) into (what will become) slices (and thus member parts of an object aggregate). However, this does not mean that fiat object parts are dependent for their existence on divisions or delineations effected by cognitive subjects. If, for example, it is correct to conceive geological layers of the Earth as fiat object parts of the Earth, then even though these layers were first delineated in recent times, still existed long before such delineation and what holds of these layers (for example that the oldest layers are also the lowest layers) did not begin to hold because of our acts of delineation.Treatment of material entity in BFOExamples viewed by some as problematic cases for the trichotomy of fiat object part, object, and object aggregate include: a mussel on (and attached to) a rock, a slime mold, a pizza, a cloud, a galaxy, a railway train with engine and multiple carriages, a clonal stand of quaking aspen, a bacterial community (biofilm), a broken femur. Note that, as Aristotle already clearly recognized, such problematic cases – which lie at or near the penumbra of instances defined by the categories in question – need not invalidate these categories. The existence of grey objects does not prove that there are not objects which are black and objects which are white; the existence of mules does not prove that there are not objects which are donkeys and objects which are horses. It does, however, show that the examples in question need to be addressed carefully in order to show how they can be fitted into the proposed scheme, for example by recognizing additional subdivisions [29
the FMA:regional parts of an intact human body.
the Western hemisphere of the Earth
the division of the brain into regions
the division of the planet into hemispheres
the dorsal and ventral surfaces of the body
the upper and lower lobes of the left lung
BFO 2 Reference: Most examples of fiat object parts are associated with theoretically drawn divisions
b is a fiat object part = Def. b is a material entity which is such that for all times t, if b exists at t then there is some object c such that b proper continuant_part of c at t and c is demarcated from the remainder of c by a two-dimensional continuant fiat boundary. (axiom label in BFO2 Reference: [027-004])
(forall (x) (if (FiatObjectPart x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y) (and (Object y) (properContinuantPartOfAt x y t)))))))) // axiom label in BFO2 CLIF: [027-004]
fiat object part
an edge of a cube-shaped portion of space.
A one-dimensional spatial region is a line or aggregate of lines stretching from one point in space to another. (axiom label in BFO2 Reference: [038-001])
(forall (x) (if (OneDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [038-001]
one-dimensional spatial region
a collection of cells in a blood biobank.
a swarm of bees is an aggregate of members who are linked together through natural bonds
a symphony orchestra
an organization is an aggregate whose member parts have roles of specific types (for example in a jazz band, a chess club, a football team)
defined by fiat: the aggregate of members of an organization
defined through physical attachment: the aggregate of atoms in a lump of granite
defined through physical containment: the aggregate of molecules of carbon dioxide in a sealed container
defined via attributive delimitations such as: the patients in this hospital
the aggregate of bearings in a constant velocity axle joint
the aggregate of blood cells in your body
the nitrogen atoms in the atmosphere
the restaurants in Palo Alto
your collection of Meissen ceramic plates.
An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects
BFO 2 Reference: object aggregates may gain and lose parts while remaining numerically identical (one and the same individual) over time. This holds both for aggregates whose membership is determined naturally (the aggregate of cells in your body) and aggregates determined by fiat (a baseball team, a congressional committee).
ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158.
b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004])
(forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004]
object aggregate
a cube-shaped region of space
a sphere-shaped region of space,
A three-dimensional spatial region is a spatial region that is of three dimensions. (axiom label in BFO2 Reference: [040-001])
(forall (x) (if (ThreeDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [040-001]
three-dimensional spatial region
Manhattan Canyon)
a hole in the interior of a portion of cheese
a rabbit hole
an air traffic control region defined in the airspace above an airport
the Grand Canyon
the Piazza San Marco
the cockpit of an aircraft
the hold of a ship
the interior of a kangaroo pouch
the interior of the trunk of your car
the interior of your bedroom
the interior of your office
the interior of your refrigerator
the lumen of your gut
your left nostril (a fiat part – the opening – of your left nasal cavity)
b is a site means: b is a three-dimensional immaterial entity that is (partially or wholly) bounded by a material entity or it is a three-dimensional immaterial part thereof. (axiom label in BFO2 Reference: [034-002])
(forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002]
site
atom
cell
cells and organisms
engineered artifacts
grain of sand
molecule
organelle
organism
planet
solid portions of matter
star
BFO 2 Reference: BFO rests on the presupposition that at multiple micro-, meso- and macroscopic scales reality exhibits certain stable, spatially separated or separable material units, combined or combinable into aggregates of various sorts (for example organisms into what are called ‘populations’). Such units play a central role in almost all domains of natural science from particle physics to cosmology. Many scientific laws govern the units in question, employing general terms (such as ‘molecule’ or ‘planet’) referring to the types and subtypes of units, and also to the types and subtypes of the processes through which such units develop and interact. The division of reality into such natural units is at the heart of biological science, as also is the fact that these units may form higher-level units (as cells form multicellular organisms) and that they may also form aggregates of units, for example as cells form portions of tissue and organs form families, herds, breeds, species, and so on. At the same time, the division of certain portions of reality into engineered units (manufactured artifacts) is the basis of modern industrial technology, which rests on the distributed mass production of engineered parts through division of labor and on their assembly into larger, compound units such as cars and laptops. The division of portions of reality into units is one starting point for the phenomenon of counting.
BFO 2 Reference: Each object is such that there are entities of which we can assert unproblematically that they lie in its interior, and other entities of which we can assert unproblematically that they lie in its exterior. This may not be so for entities lying at or near the boundary between the interior and exterior. This means that two objects – for example the two cells depicted in Figure 3 – may be such that there are material entities crossing their boundaries which belong determinately to neither cell. Something similar obtains in certain cases of conjoined twins (see below).
BFO 2 Reference: To say that b is causally unified means: b is a material entity which is such that its material parts are tied together in such a way that, in environments typical for entities of the type in question,if c, a continuant part of b that is in the interior of b at t, is larger than a certain threshold size (which will be determined differently from case to case, depending on factors such as porosity of external cover) and is moved in space to be at t at a location on the exterior of the spatial region that had been occupied by b at t, then either b’s other parts will be moved in coordinated fashion or b will be damaged (be affected, for example, by breakage or tearing) in the interval between t and t.causal changes in one part of b can have consequences for other parts of b without the mediation of any entity that lies on the exterior of b. Material entities with no proper material parts would satisfy these conditions trivially. Candidate examples of types of causal unity for material entities of more complex sorts are as follows (this is not intended to be an exhaustive list):CU1: Causal unity via physical coveringHere the parts in the interior of the unified entity are combined together causally through a common membrane or other physical covering\. The latter points outwards toward and may serve a protective function in relation to what lies on the exterior of the entity [13, 47
BFO 2 Reference: an object is a maximal causally unified material entity
BFO 2 Reference: ‘objects’ are sometimes referred to as ‘grains’ [74
b is an object means: b is a material entity which manifests causal unity of one or other of the types CUn listed above & is of a type (a material universal) instances of which are maximal relative to this criterion of causal unity. (axiom label in BFO2 Reference: [024-001])
object
The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity.
the pdf file on your laptop, the pdf file that is a copy thereof on my laptop
the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule.
b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001])
(iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001]
generically dependent continuant
the function of a hammer to drive in nails
the function of a heart pacemaker to regulate the beating of a heart through electricity
the function of amylase in saliva to break down starch into sugar
BFO 2 Reference: In the past, we have distinguished two varieties of function, artifactual function and biological function. These are not asserted subtypes of BFO:function however, since the same function – for example: to pump, to transport – can exist both in artifacts and in biological entities. The asserted subtypes of function that would be needed in order to yield a separate monoheirarchy are not artifactual function, biological function, etc., but rather transporting function, pumping function, etc.
A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001])
(forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001]
function
the boundary between the 2nd and 3rd year of your life.
p is a process boundary =Def. p is a temporal part of a process & p has no proper temporal parts. (axiom label in BFO2 Reference: [084-001])
Every process boundary occupies_temporal_region a zero-dimensional temporal region. (axiom label in BFO2 Reference: [085-002])
(forall (x) (if (ProcessBoundary x) (exists (y) (and (ZeroDimensionalTemporalRegion y) (occupiesTemporalRegion x y))))) // axiom label in BFO2 CLIF: [085-002]
(iff (ProcessBoundary a) (exists (p) (and (Process p) (temporalPartOf a p) (not (exists (b) (properTemporalPartOf b a)))))) // axiom label in BFO2 CLIF: [084-001]
process boundary
the temporal region during which a process occurs.
BFO 2 Reference: A temporal interval is a special kind of one-dimensional temporal region, namely one that is self-connected (is without gaps or breaks).
A one-dimensional temporal region is a temporal region that is extended. (axiom label in BFO2 Reference: [103-001])
(forall (x) (if (OneDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [103-001]
one-dimensional temporal region
a flame
a forest fire
a human being
a hurricane
a photon
a puff of smoke
a sea wave
a tornado
an aggregate of human beings.
an energy wave
an epidemic
the undetached arm of a human being
BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60
BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity.
BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here.
A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002])
Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002])
every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002])
(forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002]
(forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002]
(forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002]
material entity
b is a continuant fiat boundary = Def. b is an immaterial entity that is of zero, one or two dimensions and does not include a spatial region as part. (axiom label in BFO2 Reference: [029-001])
BFO 2 Reference: In BFO 1.1 the assumption was made that the external surface of a material entity such as a cell could be treated as if it were a boundary in the mathematical sense. The new document propounds the view that when we talk about external surfaces of material objects in this way then we are talking about something fiat. To be dealt with in a future version: fiat boundaries at different levels of granularity.More generally, the focus in discussion of boundaries in BFO 2.0 is now on fiat boundaries, which means: boundaries for which there is no assumption that they coincide with physical discontinuities. The ontology of boundaries becomes more closely allied with the ontology of regions.
BFO 2 Reference: a continuant fiat boundary is a boundary of some material entity (for example: the plane separating the Northern and Southern hemispheres; the North Pole), or it is a boundary of some immaterial entity (for example of some portion of airspace). Three basic kinds of continuant fiat boundary can be distinguished (together with various combination kinds [29
Continuant fiat boundary doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the mereological sum of two-dimensional continuant fiat boundary and a one dimensional continuant fiat boundary that doesn't overlap it. The situation is analogous to temporal and spatial regions.
Every continuant fiat boundary is located at some spatial region at every time at which it exists
(iff (ContinuantFiatBoundary a) (and (ImmaterialEntity a) (exists (b) (and (or (ZeroDimensionalSpatialRegion b) (OneDimensionalSpatialRegion b) (TwoDimensionalSpatialRegion b)) (forall (t) (locatedInAt a b t)))) (not (exists (c t) (and (SpatialRegion c) (continuantPartOfAt c a t)))))) // axiom label in BFO2 CLIF: [029-001]
continuant fiat boundary
BFO 2 Reference: Immaterial entities are divided into two subgroups:boundaries and sites, which bound, or are demarcated in relation, to material entities, and which can thus change location, shape and size and as their material hosts move or change shape or size (for example: your nasal passage; the hold of a ship; the boundary of Wales (which moves with the rotation of the Earth) [38, 7, 10
immaterial entity
The Equator
all geopolitical boundaries
all lines of latitude and longitude
the line separating the outer surface of the mucosa of the lower lip from the outer surface of the skin of the chin.
the median sulcus of your tongue
a one-dimensional continuant fiat boundary is a continuous fiat line whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [032-001])
(iff (OneDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (OneDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [032-001]
one-dimensional continuant fiat boundary
On a somewhat higher level of complexity are what we shall call rate process profiles, which are the targets of selective abstraction focused not on determinate quality magnitudes plotted over time, but rather on certain ratios between these magnitudes and elapsed times. A speed process profile, for example, is represented by a graph plotting against time the ratio of distance covered per unit of time. Since rates may change, and since such changes, too, may have rates of change, we have to deal here with a hierarchy of process profile universals at successive levels
One important sub-family of rate process profiles is illustrated by the beat or frequency profiles of cyclical processes, illustrated by the 60 beats per minute beating process of John’s heart, or the 120 beats per minute drumming process involved in one of John’s performances in a rock band, and so on. Each such process includes what we shall call a beat process profile instance as part, a subtype of rate process profile in which the salient ratio is not distance covered but rather number of beat cycles per unit of time. Each beat process profile instance instantiates the determinable universal beat process profile. But it also instantiates multiple more specialized universals at lower levels of generality, selected from rate process profilebeat process profileregular beat process profile3 bpm beat process profile4 bpm beat process profileirregular beat process profileincreasing beat process profileand so on.In the case of a regular beat process profile, a rate can be assigned in the simplest possible fashion by dividing the number of cycles by the length of the temporal region occupied by the beating process profile as a whole. Irregular process profiles of this sort, for example as identified in the clinic, or in the readings on an aircraft instrument panel, are often of diagnostic significance.
The simplest type of process profiles are what we shall call ‘quality process profiles’, which are the process profiles which serve as the foci of the sort of selective abstraction that is involved when measurements are made of changes in single qualities, as illustrated, for example, by process profiles of mass, temperature, aortic pressure, and so on.
b is a process_profile =Def. there is some process c such that b process_profile_of c (axiom label in BFO2 Reference: [093-002])
b process_profile_of c holds when b proper_occurrent_part_of c& there is some proper_occurrent_part d of c which has no parts in common with b & is mutually dependent on b& is such that b, c and d occupy the same temporal region (axiom label in BFO2 Reference: [094-005])
(forall (x y) (if (processProfileOf x y) (and (properContinuantPartOf x y) (exists (z t) (and (properOccurrentPartOf z y) (TemporalRegion t) (occupiesSpatioTemporalRegion x t) (occupiesSpatioTemporalRegion y t) (occupiesSpatioTemporalRegion z t) (not (exists (w) (and (occurrentPartOf w x) (occurrentPartOf w z))))))))) // axiom label in BFO2 CLIF: [094-005]
(iff (ProcessProfile a) (exists (b) (and (Process b) (processProfileOf a b)))) // axiom label in BFO2 CLIF: [093-002]
process profile
a marriage bond, an instance of requited love, an obligation between one person and another.
b is a relational quality = Def. for some independent continuants c, d and for some time t: b quality_of c at t & b quality_of d at t. (axiom label in BFO2 Reference: [057-001])
(iff (RelationalQuality a) (exists (b c t) (and (IndependentContinuant b) (IndependentContinuant c) (qualityOfAt a b t) (qualityOfAt a c t)))) // axiom label in BFO2 CLIF: [057-001]
relational quality
a two-dimensional continuant fiat boundary (surface) is a self-connected fiat surface whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [033-001])
(iff (TwoDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (TwoDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [033-001]
two-dimensional continuant fiat boundary
the geographic North Pole
the point of origin of some spatial coordinate system.
the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet
zero dimension continuant fiat boundaries are not spatial points. Considering the example 'the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet' : There are many frames in which that point is zooming through many points in space. Whereas, no matter what the frame, the quadripoint is always in the same relation to the boundaries of Colorado, Utah, New Mexico, and Arizona.
a zero-dimensional continuant fiat boundary is a fiat point whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [031-001])
(iff (ZeroDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (ZeroDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [031-001]
zero-dimensional continuant fiat boundary
a temporal region that is occupied by a process boundary
right now
the moment at which a child is born
the moment at which a finger is detached in an industrial accident
the moment of death.
temporal instant.
A zero-dimensional temporal region is a temporal region that is without extent. (axiom label in BFO2 Reference: [102-001])
(forall (x) (if (ZeroDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [102-001]
zero-dimensional temporal region
A history is a process that is the sum of the totality of processes taking place in the spatiotemporal region occupied by a material entity or site, including processes on the surface of the entity or within the cavities to which it serves as host. (axiom label in BFO2 Reference: [138-001])
history
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.
1-ethyl-7-methyl-4-oxo-1,4-dihydro-1,8-naphthyridine-3-carboxylic acid
A triazole-based antifungal agent used for the treatment of esophageal candidiasis, invasive pulmonary aspergillosis, and serious fungal infections caused by Scedosporium apiospermum and Fusarium spp. It is an inhibitor of cytochrome P450 2C9 (CYP2C9) and CYP3A4.
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.
1-cyclopropyl-6-fluoro-4-oxo-7-(piperazin-1-yl)-1,4-dihydroquinoline-3-carboxylic acid
A member of the class of fluorenes that is 9-(p-chlorobenzylidene)-9H-fluorene which is substitutec by chlorine at positions 2 and 7, and by a 2-(dibutylamino)-1-hydroxyethyl group at position 4. An antimalarial drug used in combination with artemether for the treatment of multi-drug resistant strains of falciparum malaria.
A straight-chain, sixteen-carbon, saturated long-chain fatty acid.
An optically active form of dopa having L-configuration. Used to treat the stiffness, tremors, spasms, and poor muscle control of Parkinson's disease
(2S)-2-amino-3-(3,4-dihydroxyphenyl)propanoic acid
A long-chain fatty acid that is a C20, polyunsaturated fatty acid having four (Z)-double bonds at positions 5, 8, 11 and 14.
(5Z,8Z,11Z,14Z)-icosa-5,8,11,14-tetraenoic acid
A cinchona alkaloid that is cinchonidine in which the hydrogen at the 6-position of the quinoline ring is substituted by methoxy.
A chlorophenylethane that is 1,1,1-trichloro-2,2-diphenylethane substituted by additional chloro substituents at positions 4 of the phenyl substituents. It is a commonly used organochlorine insecticide.
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.
An octadec-9-enoic acid in which the double bond at C-9 has Z (cis) stereochemistry.
A carbonyl group with two C-bound amine groups. The commercially available fertilizer has an analysis of 46-0-0 (N-P2O5-K2O).
An inorganic peroxide consisting of two hydroxy groups joined by a covalent oxygen-oxygen single bond.
A one-carbon compound with formula CO2 in which the carbon is attached to each oxygen atom by a double bond. A colourless, odourless gas under normal conditions, it is produced during respiration by all animals, fungi and microorganisms that depend directly or indirectly on living or decaying plants for food.
Any member of the class of organooxygen compounds that is a polyhydroxy-aldehyde or -ketone or a lactol resulting from their intramolecular condensation (monosaccharides); substances derived from these by reduction of the carbonyl group (alditols), by oxidation of one or more hydroxy groups to afford the corresponding aldehydes, ketones, or carboxylic acids, or by replacement of one or more hydroxy group(s) by a hydrogen atom; and polymeric products arising by intermolecular acetal formation between two or more such molecules (disaccharides, polysaccharides and oligosaccharides). Carbohydrates contain only carbon, hydrogen and oxygen atoms; prior to any oxidation or reduction, most have the empirical formula Cm(H2O)n. Compounds obtained from carbohydrates by substitution, etc., are known as carbohydrate derivatives and may contain other elements. Cyclitols are generally not regarded as carbohydrates.
Amide derived from two or more amino carboxylic acid molecules (the same or different) by formation of a covalent bond from the carbonyl carbon of one to the nitrogen atom of another with formal loss of water. The term is usually applied to structures formed from alpha-amino acids, but it includes those derived from any amino carboxylic acid. X = OH, OR, NH2, NHR, etc.
An organic thiophosphate that is O,O-dimethyl O-phenyl phosphorothioate substituted by a chloro group at position 3 and a nitro group at position 4. It is a potent cholinesterase inhibitor and used as an insecticide for the control of a wide range of insects.
O-(3-chloro-4-nitrophenyl) O,O-dimethyl phosphorothioate
A lactam obtained by formal cyclocondensation of creatine. It is a metabolite of creatine.
A member of the class of biladienes that is a linear tetrapyrrole with the dipyrrole units being of both exovinyl and endovinyl type. A product of heme degradation, it is produced in the reticuloendothelial system by the reduction of biliverdin and transported to the liver as a complex with serum albumin.
3,18-diethenyl-2,7,13,17-tetramethyl-1,19-dioxo-1,10,19,22,23,24-hexahydro-21H-biline-8,12-dipropanoic acid
High molecular weight, linear polymers, composed of nucleotides containing deoxyribose and linked by phosphodiester bonds; DNA contain the genetic information of organisms.
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.
An octadecadienoic acid in which the two double bonds are at positions 9 and 12 and have Z (cis) stereochemistry.
The carbon oxoanion resulting from the removal of a proton from carbonic acid.
An organochlorine compound that is dichloro-substituted acetamide containing a nitrobenzene ring, an amide bond and two alcohol functions.
Any of a group of aminoglycoside antibiotics produced by fermentation of some Micromonospora spp.
4,6-diamino-3-[3-deoxy-4-C-methyl-3-(methylamino)pentopyranosyloxy]-2-hydroxycyclohexyl 2-amino-2,3,4,6,7-pentadeoxy-6-(methylamino)heptopyranoside
An elemental molecule consisting of two hydrogens joined by a single bond.
An artemisinin derivative that is artemisinin in which the lactone has been converted to the corresponding lactol methyl ether. It is used in combination with lumefantrine as an antimalarial for the treatment of multi-drug resistant strains of falciparum malaria.
A cephalosporin compound having acetoxymethyl and [2-(2-amino-1,3-thiazol-4-yl)-2-(methoxyimino)acetyl]amino side groups.
3-(acetoxymethyl)-7beta-{[(2Z)-2-(2-amino-1,3-thiazol-4-yl)-2-(methoxyimino)acetyl]amino}-3,4-didehydrocepham-4-carboxylic acid
Any aromatic carboxylic acid that consists of benzene in which at least a single hydrogen has been substituted by a carboxy group.
An insecticide compound naturally occurring in plants.
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.
Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity.
Any substance which when absorbed into a living organism may modify one or more of its functions. The term is generally accepted for a substance taken for a therapeutic purpose, but is also commonly used for abused substances.
An icosanoid comprising icosanoic acid having one C=C bond at any position.
A substance used to destroy fungal pests.
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.
Strictly, a substance intended to kill members of the class Insecta. In common usage, any substance used for preventing, destroying, repelling or controlling insects.
A molecular entity having a net electric charge.
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.
A macrocyclic lactone with a ring of twelve or more members derived from a polyketide.
A member of the class of phenylethanolamines that is 4-(2-amino-1-hydroxyethyl)-2-(hydroxymethyl)phenol having a tert-butyl group attached to the nirogen atom. It acts as a beta-adrenergic agonist used in the treatment of asthma and chronic obstructive pulmonary disease (COPD).
A class of neuro-active insecticides that act at the nicotinic acetylcholine receptor.
Strictly, a substance intended to kill pests. In common usage, any substance used for controlling, preventing, or destroying animal, microbiological or plant pests.
Salts and esters of phosphoric and oligophosphoric acids and their chalcogen analogues. In inorganic chemistry, the term is also used to describe anionic coordination entities with phosphorus as central atom.
A class of aromatic heterocyclic compounds each of which contains a benzene ring ortho fused to carbons 2 and 3 of a pyridine ring.
A quinoline having a chloro group at the 7-position and an aryl amino group at the 4-position.
A penicillin in which the substituent at position 6 of the penam ring is a 2-amino-2-(4-hydroxyphenyl)acetamido group.
6beta-[(2R)-2-amino-2-(4-hydroxyphenyl)acetamido]-2,2-dimethylpenam-3alpha-carboxylic acid
A macrolide antibiotic used to treat potentially life-threatening fungal infections.
An oxopurine that is the final oxidation product of purine metabolism.
Any member of a group of fat-soluble hydroxy seco-steroids that exhibit biological activity against vitamin D deficiency. Vitamin D can be obtained from sun exposure, food and supplements and is biologically inactive and converted into the biologically active calcitriol via double hydroxylation in the body.
A linolenic acid with cis-double bonds at positions 9, 12 and 15. Shown to have an antithrombotic effect.
(9Z,12Z,15Z)-octadeca-9,12,15-trienoic acid
A 9-octadecenoic acid and the trans-isomer of oleic acid.
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.
(3S,6R,7R,11R,23S,26S,30aS,36R,38aR)-44-[2-O-(3-amino-2,3,6-trideoxy-3-C-methyl-alpha-L-lyxo-hexopyranosyl)-beta-D-glucopyranosyloxy]-3-(carbamoylmethyl)-10,19-dichloro-2,3,4,5,6,7,23,25,26,36,37,38,38a-tetradecahydro-7,22,28,30,32-pentahydroxy-6-(N-methyl-D-leucyl)-2,5,24,38,39-pentaoxo-1H,22H-23,36-(epiminomethano)-8,11:18,21-dietheno-13,16:31,35-di(metheno)[1,6,9]oxadiazacyclohexadecino[4,5-m][10,2,16]benzoxadiazacyclotetracosine-26-carboxylic acid
A member of the class of acrylamides that results from the formal condensation of acrylic acid with ammonia.
A C18, omega-6 acid fatty acid comprising a linolenic acid having cis- double bonds at positions 6, 9 and 12.
(6Z,9Z,12Z)-octadeca-6,9,12-trienoic acid
A hexadec-9-enoic acid in which the double bond at position C-9 has cis configuration.
A C20 striaght-chain saturated fatty acid which forms a minor constituent of peanut (L. arachis) and corn oils. Used as an organic thin film in the production of liquid crystals for a wide variety of technical applications.
A C18 straight-chain saturated fatty acid component of many animal and vegetable lipids. As well as in the diet, it is used in hardening soaps, softening plastics and in making cosmetics, candles and plastics.
A amino cyclitol glycoside that is kanamycin B lacking the 3-hydroxy substituent from the 2,6-diaminoglucose ring.
(1S,2S,3R,4S,6R)-4,6-diamino-3-(2,6-diamino-2,3,6-trideoxy-alpha-D-ribo-hexopyranosyloxy)-2-hydroxycyclohexyl 3-amino-3-deoxy-alpha-D-glucopyranoside
A C24 straight-chain saturated fatty acid.
A straight-chain, fourteen-carbon, long-chain saturated fatty acid mostly found in milk fat.
A straight-chain, C22, long-chain saturated fatty acid.
A penicillin in which the substituent at position 6 of the penam ring is a 2-amino-2-phenylacetamido group.
6beta-[(2R)-2-amino-2-phenylacetamido]-2,2-dimethylpenam-3alpha-carboxylic acid
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.
7beta-{[(2Z)-2-(2-amino-1,3-thiazol-4-yl)-2-(methoxyimino)acetyl]amino}-3-{[(2-methyl-5,6-dioxo-1,2,5,6-tetrahydro-1,2,4-triazin-3-yl)sulfanyl]methyl}-3,4-didehydrocepham-4-carboxylic acid
A macrolide antibiotic useful for the treatment of bacterial infections.
(2R,3S,4R,5R,8R,10R,11R,12S,13S,14R)-2-ethyl-3,4,10-trihydroxy-3,5,6,8,10,12,14-heptamethyl-15-oxo-11-{[3,4,6-trideoxy-3-(dimethylamino)-beta-D-xylo-hexopyranosyl]oxy}-1-oxa-6-azacyclopentadecan-13-yl 2,6-dideoxy-3-C-methyl-3-O-methyl-alpha-L-ribo-hexopyranoside
A hexitol produced by a variety of organisms including bacteria, fungi, lichens and plants.
Particle of zero charge, zero rest mass, spin quantum number 1, energy hnu and momentum hnu/c (h is the Planck constant, nu the frequency of radiation and c the speed of light), carrier of electromagnetic force.
A straight-chain, twelve-carbon medium-chain saturated fatty acid with strong bactericidal properties; the main fatty acid in coconut oil and palm kernel oil.
A C10, straight-chain saturated fatty acid.
A carboxylic ester obtained by formal condensation of cis-3-(2-chloro-3,3,3-trifluoroprop-1-enyl)-2,2-dimethylcyclopropanecarboxylic acid and [(2-methyl-1,1'-biphenyl)-3-yl]methanol.
(2-methyl-[1,1'-biphenyl]-3-yl)methyl rel-(1R,3R)-3-[(1Z)-2-chloro-3,3,3-trifluoroprop-1-en-1-yl]-2,2-dimethylcyclopropanecarboxylate
A chemical entity constituting the smallest component of an element having the chemical properties of the element.
A substance that kills or slows the growth of microorganisms, including bacteria, viruses, fungi and protozoans.
A substance (or active part thereof) that kills or slows the growth of bacteria.
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 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.
When two or more amino acids combine to form a peptide, the elements of water are removed, and what remains of each amino acid is called an amino-acid residue.
A macromolecule is a molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass.
A carbamate ester obtained by the formal condensation of 1-naphthol with methylcarbamic acid.
An alkenyl alcohol with a structure based on a C8 unbranched chain with the hydroxy group at C-2 and unsaturation at C-1-C-2. It is a major volatile compound present in many mushrooms and fungi.
2,2-dimethyl-1,3-benzodioxol-4-yl methylcarbamate
An organic thiophosphate that is O,O-diethyl hydrogen phosphorothioate in which the hydrogen of the hydroxy group has been replaced by a 3,5,6-trichloropyridin-2-yl group.
O,O-diethyl O-(3,5,6-trichloropyridin-2-yl) phosphorothioate
An organic thiophosphate that is O,O-dimethyl hydrogen phosphorothioate in which the hydrogen of the hydroxy group has been replaced by a 3,5,6-trichloropyridin-2-yl group.
O,O-dimethyl O-(3,5,6-trichloropyridin-2-yl) phosphorothioate
An alkenyl phosphate that is the 2,2-dichloroethenyl ester of dimethyl phosphate.
An organochlorine compound resulting from the epoxidation of the double bond of aldrin. It is the active metabolite of the proinsecticde aldrin.
A benzoylurea insecticide that is urea in which a hydrogen attached to one of the nitrogens is replaced by a 4-chlorophenyl group, and a hydrogen attached to the other nitrogen is replaced bgy a 2,6-difluorobenzoyl group.
A monocarboxylic acid amide that is N-methylacetamide in which one of the hydrogens of the methyl group attached to the carbonyl moiety is replaced by a (dimethoxyphosphorothioyl)sulfanediyl group.
O,O-dimethyl S-[2-(methylamino)-2-oxoethyl] phosphorodithioate
An organic thiophosphate that is O,O-dimethyl O-phenyl phosphorothioate substituted by a methyl group at position 3 and a nitro group at position 4.
O,O-dimethyl O-(3-methyl-4-nitrophenyl)phosphorothioate
An organic thiophosphate that is O,O-dimethyl hydrogen phosphorothioate in which the hydrogen atom of the hydroxy group is replaced by a 3-methyl-4-(methylsulfanyl)phenyl group. It exhibits acaricidal and insecticidal activities.
O,O-dimethyl O-[3-methyl-4-(methylsulfanyl)phenyl] phosphorothioate
propan-2-yl (2E,4E)-11-methoxy-3,7,11-trimethyldodeca-2,4-dienoate
An organic cation that consists of 4,4'-bipyridine bearing two N-methyl substituents loctated at the 1- and 1'-positions.
A cyclopropanecarboxylate ester in which the esterifying alcohol is 3-phenoxybenzyl alcohol and the cyclopropane ring is substituted with a 2,2-dichlorovinyl group and with gem-dimethyl groups.
3-phenoxybenzyl 3-(2,2-dichloroethenyl)-2,2-dimethylcyclopropanecarboxylate
3-phenoxybenzyl 2,2-dimethyl-3-(2-methylprop-1-en-1-yl)cyclopropanecarboxylate
An organic thiophosphate that is ethyl mandelate in which the hydroxy group has been replaced by a (dimethoxyphosphorothioyl)sulfanediyl group.
ethyl [(dimethoxyphosphorothioyl)sulfanyl](phenyl)acetate
A carbamate ester that is phenyl methylcarbamate substituted at position 2 by a propan-2-yloxy group.
2-(propan-2-yloxy)phenyl methylcarbamate
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.
7beta-[(2Z)-2-(2-amino-1,3-thiazol-4-yl)-2-(methoxyimino)acetamido]-3-(methoxymethyl)-3,4-didehydrocepham-4-carboxylic acid
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 aliphatic monocarboxylic acid derived from or contained in esterified form in an animal or vegetable fat, oil or wax. Natural fatty acids commonly have a chain of 4 to 28 carbons (usually unbranched and even-numbered), which may be saturated or unsaturated. By extension, the term is sometimes used to embrace all acyclic aliphatic carboxylic acids.
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.
7beta-[(2R)-2-(cyclohexa-1,4-dienyl)-2-phenylacetamido]-3-methyl-3,4-didehydrocepham-4-carboxylic acid
A lactam in which the amide bond is contained within a four-membered ring, which includes the amide nitrogen and the carbonyl carbon.
An antimicrobial agent that destroys fungi by suppressing their ability to grow or reproduce.
An azole in which the five-membered heterocyclic aromatic skeleton contains three N atoms and two C atoms.
A phosphorus oxoanion that is the conjugate base of phosphoric acid.
Any C22 polyunsaturated fatty acid containing six double bonds.
Any straight-chain, C20 polyunsaturated fatty acid having five C=C double bonds.
A drug used to treat or prevent bacterial infections.
An aminoquinoline that is quinoline which is substituted at position 4 by a [5-(diethylamino)pentan-2-yl]amino group at at position 7 by chlorine. It is used for the treatment of malaria, hepatic amoebiasis, lupus erythematosus, light-sensitive skin eruptions, and rheumatoid arthritis.
A two-component mixture comprising trimethoprim and sulfamethoxazole.
4-amino-N-(5-methyl-1,2-oxazol-3-yl)benzenesulfonamide - 5-(3,4,5-trimethoxybenzyl)pyrimidine-2,4-diamine (1:1)
A multi-component mixture comprising mostly of colistin A (R = Me) and B (R = H), with small amounts of colistin C and other polymyxins, produced by certain strains of Bacillus polymyxa var. colistinus. An antibiotic, it is used as its sulfate salt (for oral or topical use) or as the sodium salt of the N-methylsulfonic acid derivative (the injectable form) in the treatment of severe Gram-negative infections, partiularly those due to Pseudomonas aeruginosa.
A drug used in the treatment of malaria. Antimalarials are usually classified on the basis of their action against Plasmodia at different stages in their life cycle in the human.
Derivatives of carbamic acid with insecticidal properties of general formula ROC(=O)NR(1)R(2), where ROH is an alcohol, oxime, or phenol and R(1) is hydrogen or methyl. Like organophosphate insecticides, they are cholinesterase inhibitors, but carbamate insecticides differ in action from the organophosphates in that the inhibitory effect on cholinesterase is generally brief.
2,2-dimethyl-2,3-dihydro-1-benzofuran-7-yl [(dibutylamino)sulfanyl](methyl)carbamate
O-[4-(dimethylsulfamoyl)phenyl] O,O-dimethyl phosphorothioate
ethyl 3-methyl-4-(methylsulfanyl)phenyl N-(propan-2-yl)phosphoramidate
An organic thiophosphate that is O,O-dimethyl O-pyrimidin-4-yl phosphorothioate substituted by a methyl group at position 6 and a diethylamino group at position 2.
O-[2-(diethylamino)-6-methylpyrimidin-4-yl] O,O-dimethyl phosphorothioate
O-(4-bromo-2-chlorophenyl) O-ethyl S-propyl phosphorothioate
An organic sulfide that is diphenyl sulfide in which the hydrogen at the para position of each of the phenyl groups has been replaced by a (dimethoxyphosphorothioyl)oxy group.
O,O,O',O'-tetramethyl O,O'-(sulfanediyldibenzene-4,1-diyl) bis(phosphorothioate)
The active insecticidal constituents of Chrysanthemum cinerariifolium flowers.
An N-nitro compound consisting of 2-nitroguanidine having a (2-chloro-1,3-thiazol-5-yl)methyl group at position 1 and a methyl group at position 3.
A two-component mixture comprising spinosyn A and spinosyn D in a ratio of approximately 5:1. Obtained from the fermentation of the naturally occurring soil dwelling bacterium Saccharopolyspora spinosa, it is used for the topical treatment of head lice.
An aromatic ether that consists of propylene glycol having a 2-pyridyl group at the O-1 position and a 4-phenoxyphenyl group at the O-3 position.
A diastereoisomeric mixture comprising the enantiomeric pair (1R)-cis-(alphaS)- and (1S)-cis-(alphaR)-cyfluthrin in ratio 1:2 with the enantiomeric pair (1R)-trans-(alphaS)- and (1S)-trans-(alphaR)-cyfluthrin.
Reaction product comprising equal quantities of CHEBI:39323 and CHEBI:39327.
A racemate comprising equimolar amounts of (1R)-cis-(alphaS)- and (1S)-cis-(alphaR)-cypermethrin.
A diastereoisomeric mixture comprising the enantiomeric pair (1R)-cis-(alphaS)- and (1S)-cis-(alphaR)-cypermethrin in ratio approximately 2:3 with the enantiomeric pair (1S)-trans-(alphaR)- and (1R)-trans-(alphaS)-cypermethrin.
A member of the class of pyrroles that is 4-bromo-1H-pyrrole-3-carbonitrile which is substituted at positions 1, 2 and 5 by ethoxymethyl, p-chlorophenyl and trifluoromethyl groups, respectively. A proinsecticide used for termite control and crop protection against several insects and mite pests.
An aromatic ether that is the 3-phenoxybenzyl ether of 2-(4-ethoxyphenyl)-2-methylpropan-1-ol.
(1,3-dioxo-1,3,4,5,6,7-hexahydro-2H-isoindol-2-yl)methyl 2,2-dimethyl-3-(2-methylprop-1-en-1-yl)cyclopropanecarboxylate
A carboxylic ester obtained by formal condensation between 3-(2,2-dichloroethenyl)-2,2-dimethylcyclopropanecarboxylic acid and (4-fluoro-3-phenoxyphenyl)(hydroxy)acetonitrile.
cyano(4-fluoro-3-phenoxyphenyl)methyl 3-(2,2-dichloroethenyl)-2,2-dimethylcyclopropanecarboxylate
A carboxylic ester obtained by formal condensation between 3-(2-chloro-3,3,3-trifluoroprop-1-en-1-yl)-2,2-dimethylcyclopropanecarboxylic acid and cyano(3-phenoxyphenyl)methanol.
cyano(3-phenoxyphenyl)methyl 3-[(1Z)-2-chloro-3,3,3-trifluoroprop-1-en-1-yl]-2,2-dimethylcyclopropanecarboxylate
A carboxylic ester resulting from the formal condensation between 3-(2,2-dichlorovinyl)-2,2-dimethylcyclopropanecarboxylic acid and the alcoholic hydroxy group of hydroxy(3-phenoxyphenyl)acetonitrile.
cyano(3-phenoxyphenyl)methyl 3-(2,2-dichloroethenyl)-2,2-dimethylcyclopropanecarboxylate
An optically active form of lactic acid having (S)-configuration.
A cyclopropanecarboxylate ester obtained by formal condensation between 3-(2,2-dibromovinyl)-2,2-dimethylcyclopropanecarboxylic acid and cyano(3-phenoxyphenyl)methanol. It is the active insecticide of the proinsecticide tralomethrin.
(S)-cyano(3-phenoxyphenyl)methyl (1R,3R)-3-(2,2-dibromoethenyl)-2,2-dimethylcyclopropanecarboxylate
A tetracosenoic acid having a cis-double bond at position 15.
A member of the class of triazoles that is propan-2-ol substituted at position 1 and 3 by 1H-1,2,4-triazol-1-yl groups and at position 2 by a 2,4-difluorophenyl group. It is an antifungal drug used for the treatment of mucosal candidiasis and for systemic infections including systemic candidiasis, coccidioidomycosis, and cryptococcosis.
A liquid that can dissolve other substances (solutes) without any change in their chemical composition.
A semisynthetic cyclic hexapeptide echinocandin antibiotic which exerts its effect by inhibiting the synthesis of 1,3-beta-D-glucan, an integral component of the fungal cell wall.
A monocarboxylic acid amide that is lysergamide in which one of the hydrogens attached to the amide nitrogen is substituted by a 1-hydroxypropan-2-yl group (S-configuration). An ergot alkaloid that has a particularly powerful action on the uterus, its maleate (and formerly tartrate) salt is used in the active management of the third stage of labour, and to prevent or treat postpartum of postabortal haemorrhage caused by uterine atony: by maintaining uterine contraction and tone, blood vessels in the uterine wall are compressed and blood flow reduced.
Any of several wide-spectrum macrolide antibiotics obtained from actinomycete Saccharopolyspora erythraea (formerly known as Streptomyces erythraeus).
A semisynthetic penicillin antibiotic carrying a 3-(2-chlorophenyl)-5-methylisoxazole-4-carboxamido group at position 6.
2,2-dimethyl-6beta-({[5-methyl-3-(2-chlorophenyl)isoxazol-4-yl]carbonyl}amino)penam-3alpha-carboxylic acid
A retinoid consisting of 3,7-dimethylnona-2,4,6,8-tetraen-1-ol substituted at position 9 by a 2,6,6-trimethylcyclohex-1-en-1-yl group (geometry of the four exocyclic double bonds is not specified).
A racemate comprising equimolar amounts of (R)- and (S)-fipronil.
A penicillanic acid ester that is the [(2,2-dimethylpropanoyl)oxy]methyl ester and prodrug of mecillinam.
[(2,2-dimethylpropanoyl)oxy]methyl 6beta-[(azepan-1-ylmethylidene)amino]-2,2-dimethylpenam-3alpha-carboxylate
An icosatrienoic acid having three cis double bonds at positions 8, 11 and 14.
(8Z,11Z,14Z)-icosa-8,11,14-trienoic acid
The all-cis-isomer of a C22 polyunsaturated fatty acid having five double bonds in the 7-, 10-, 13-, 16- and 19-positions.
(7Z,10Z,13Z,16Z,19Z)-docosapentaenoic acid
A semisynthetic echinocandin anti-fungal drug. It is active against Aspergillus and Candida species and is used for the treatment of invasive candidiasis.
An aminoquinoline that is chloroquine in which one of the N-ethyl groups is hydroxylated at position 2. An antimalarial with properties similar to chloroquine that acts against erythrocytic forms of malarial parasites, it is mainly used as the sulfate salt for the treatment of lupus erythematosus, rheumatoid arthritis, and light-sensitive skin eruptions.
An imidazolidine that is N-nitroimidazolidin-2-imine bearing a (6-chloro-3-pyridinyl)methyl substituent at position 1.
A straight-chain, monounsaturated, 16-carbon fatty acid with a trans-double bond at position C-9; the trans-isomer of palmitoleic acid and predominant trans-16:1 isomer in cheeses from goat and ewe milk. Major dietary sources are partly hydrogenated vegetable oils.
A chemical substance is a portion of matter of constant composition, composed of molecular entities of the same type or of different types.
A cyclic hexapeptide echinocandin antibiotic which exerts its effect by inhibiting the synthesis of 1,3-beta-D-glucan, an integral component of the fungal cell wall. It is used as the sodium salt for the treatment of invasive candidiasis, and of aspergillosis in patients who are intolerant of other therapy.
5-[(1S,2S)-2-{(2R,6S,9S,11R,12R,14aS,15S,16S,20S,23S,25aS)-20-[(1R)-3-amino-1-hydroxy-3-oxopropyl]-2,11,12,15-tetrahydroxy-6-[(1R)-1-hydroxyethyl]-16-methyl-5,8,14,19,22,25-hexaoxo-9-[(4-{5-[4-(pentyloxy)phenyl]isoxazol-3-yl}benzoyl)amino]tetracosahydro-1H-dipyrrolo[2,1-c:2',1'-l][1,4,7,10,13,16]hexaazacyclohenicosin-23-yl}-1,2-dihydroxyethyl]-2-hydroxyphenyl hydrogen sulfate
An N-arylpiperazine that is cis-ketoconazole in which the imidazol-1-yl group is replaced by a 1,2,4-triazol-1-yl group and in which the actyl group attached to the piperazine moiety is replaced by a p-[(+-)1-sec-butyl-5-oxo-1,5-dihydro-4H-1,2,4-triazol-4-yl]phenyl group. A potent P-glycoprotein and CYP3A4 inhibitor, it is used as an antifungal drug for the treatment of various fungal infections, including aspergillosis, blastomycosis, candidiasis, chromoblastomycosis, coccidioidomycosis, cryptococcosis, histoplasmosis, and sporotrichosis.
A racemate is an equimolar mixture of a pair of enantiomers.
Any straight-chain, C22 fatty acid having four C=C double bonds.
A synthetic galactosylfructose disaccharide used in the treatment of constipation and hepatic encephalopathy.
A racemate composed of (+)-(11R,2'S)- and (-)-(11S,2'R)-enantiomers of mefloquine. An antimalarial agent which acts as a blood schizonticide; its mechanism of action is unknown.
An N-arylpiperazine that consists of piperazine carrying two 4-substituted phenyl groups at positions 1 and 4. A triazole antifungal drug.
The all-cis-isomer of a C22 polyunsaturated fatty acid having five double bonds in the 4-, 7-, 10-, 13- and 16-positions. It is a member of n-6 PUFA and a product of linoleic acid metabolism.
A racemate comprising equimolar amounts of (R) and (S)-malaoxon. It is the active insecticide of the proinsecticide malathion.
rac-diethyl 2-[(dimethoxyphosphoryl)thio]succinate
A racemate comprising equimolar amounts of (R) and (S)-malathion. It is a broad spectrum organophosphate proinsecticide used to control a wide range of pests including Coleoptera, Diptera, fruit flies, mosquitos and spider mites.
rac-diethyl 2-[(dimethoxyphosphorothioyl)thio]succinate
A chemosterilant intended to sterilize insects.
Any monocyclic heteroarene consisting of a five-membered ring containing nitrogen. Azoles can also contain one or more other non-carbon atoms, such as nitrogen, sulfur or oxygen.
A phosphonic ester that is dimethyl phosphonate in which the hydrogen atom attched to the phosphorous is substituted by a 2,2,2-trichloro-1-hydroxyethyl group.
dimethyl (2,2,2-trichloro-1-hydroxyethyl)phosphonate
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 20-carbon, polyunsaturated fatty acid having two double bonds at unspecified positions.
An octadecadienoic acid containing two E (trans) double bonds at positions 9 and 12.
An N-substituted diamine that is pentane-1,4-diamine substituted by a 6-methoxyquinolin-8-yl group at the N(4) position. It is a drug used in the treatment of malaria and Pneumocystis pneumonia.
Any antifungal agent used to prevent or treat fungal infections in humans or animals.
A member of the class of furans used to treat peptic ulcer disease (PUD) and gastroesophageal reflux disease.
(5-benzylfuran-3-yl)methyl 2,2-dimethyl-3-(2-methylprop-1-en-1-yl)cyclopropanecarboxylate
An organic heterotricyclic compound that is 4,9-dihydro-10H-benzo[4,5]cyclohepta[1,2-b]thiophen-10-one which is substituted at position 4 by a 1-methylpiperidin-4-ylidene group. A blocker of histamine H1 receptors with a stabilising action on mast cells, it is used (usually as its hydrogen fumarate salt) for the treatment of asthma, where it may take several weeks to exert its full effect.
The representation of a negative conclusion of a diagnostic process for the COVID-19 coronavirus disease.
negative COVID-19 diagnosis conclusion
A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane.
A cell that is found in a natural setting, which includes multicellular organism cells 'in vivo' (i.e. part of an organism), and unicellular organisms 'in environment' (i.e. part of a natural environment).
A cell in vitro that is or has been maintained or propagated as part of a cell culture.
A leukocyte with abundant granules in the cytoplasm.
A red blood cell. In mammals, mature erythrocytes are biconcave disks containing hemoglobin whose function is to transport oxygen.
A mononuclear phagocyte present in variety of tissues, typically differentiated from monocytes, capable of phagocytosing a variety of extracellular particulate material, including immune complexes, microorganisms, and dead cells.
Myeloid mononuclear recirculating leukocyte that can act as a precursor of tissue macrophages, osteoclasts and some populations of tissue dendritic cells.
An achromatic cell of the myeloid or lymphoid lineages capable of ameboid movement, found in blood or other tissue.
Any of the immature or mature forms of a granular leukocyte that in its mature form has an irregularly shaped, pale-staining nucleus that is partially constricted into two lobes, and with cytoplasm that contains coarse, bluish-black granules of variable size. Basophils contain vasoactive amines such as histamine and serotonin, which are released on appropriate stimulation. A basophil is CD123-positive, CD193-positive, CD203c-positive, and FceRIa-positive.
Any of the immature or mature forms of a granular leukocyte that in its mature form has a nucleus with three to five lobes connected by slender threads of chromatin, and cytoplasm containing fine inconspicuous granules and stainable by neutral dyes.
A cell that is maintained or propagated in a controlled artificial environment for use in an investigation.
The minimum arterial pressure within the cardiac cycle, usually at the point at which the heart is in a state of relaxation and expansion. This is the time when the ventricles fill with blood.
Measurement of the structure or forms of the entire body or parts of the body of an organism.
The amount of hemoglobin in a specific volume of blood, expressed as grams per deciliter of whole blood in humans.
The number of white blood cells in a specified volume of blood.
A measurement relating body weight to height in an organism; typically calculated as the weight of an individual divided by the height of that individual squared. For quadrupeds, the square of body height is often replaced by the square of body length.
Fraction of forced vital capacity that is exhaled in a specific number of seconds.
The number of breaths taken by an organism per unit of time.
The force per unit area attributable to the oxygen, the chemical element with atomic number 8 which is the essential agent in the respiration of plants and animals, dissolved in a specified volume of blood, defined as the force per unit area exerted by oxygen in a mixture of gases in equilibrium with such a sample of blood at the same temperature.
A disease that involving errors in metabolic processes of building or degradation of molecules.
A bacterial infectious disease has_material_basis_in Bacteria.
A viral infectious disease that results_in infection located_in joint, has_material_basis_in Chikungunya virus, which is transmitted_by Aedes mosquito bite. The infection has_symptom fever, has_symptom arthralgia, and has_symptom maculopapular rash.
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.
A fungal infectious disease that results_in infection of the keratinized layers located_in skin, located_in hair or located_in nail, which extends deeper into the epidermis, has_material_basis_in Fungi and results_in_formation_of skin lesions.
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).
A respiratory system disease which involves the lower respiratory tract.
An opportunistic mycosis that has_material_basis_in Penicillium marneffei, results_in systemic infection and has_symptom fever, has_symptom anemia, has_symptom weight loss, has_symptom lymphadenopathy, has_symptom hepatosplenomegaly, has_symptom respiratory signs, and has_symptom skin lesions.
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.
A skin disease that is characterized by a rash that results from a variety of causes including bacteria, viruses, toxins, drugs and autoimmune disorders.
A tuberculosis that occurs at body sites other than the lung.
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 musculoskeletal system.
autoimmune disease of musculoskeletal system
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 skin and connective tissue.
autoimmune disease of skin and connective tissue
A cheilitis characterized by inflammation of one or both of the corners of the mouth.
An intestinal disease characterized by a protrusion of abdominal cavity contests through the inguinal canal.
A middle ear disease characterized by an inflammation of the mucosal lining of the mastoid antrum and the mastoid air cell system inside the mastoid process.
A tooth disease characterized by a localized collection of pus associated with a tooth.
A connective tissue disease that affects the structure or development of bone or causes an impairment of normal bone function.
A disease that has_material_basis_in a genetic abnormality, error with embryonic development, infection or compromised intrauterine environment.
A physical disorder characterized by incomplete closure of the neural tube.
An autoimmune disease of skin and connective tissue that is characterized by subepidermal blistering especially in the lower abdomen, groin, and flexor surfaces of the extremities, creating tense blisters that do not break easily.
pemphigoid
An inner ear disease that is characterized by hearing loss resulting from damage to the cochlea, auditory nerve and/or brainstem.
A bone inflammation disease that has_material_basis_in infection located_in bone or located_in bone marrow.
A viral infectious disease that results in inflammation located in salivary gland, has_material_basis_in Mumps rubulavirus, which is transmitted by droplet spread of saliva or mucus from the mouth, nose, or throat of an infected person, or transmitted by contaminated fomites. The infection has symptom fever, has symptom headache, has symptom muscle aches, has symptom tiredness, has symptom loss of appetite, has symptom swollen and tender salivary glands under the ears or jaw on one or both sides of the face.
A parotid disease characterized by the inflammation of one or both parotid glands.
A disease by infectious agent that results_in infection, has_material_basis_in Bacteria.
An upper respiratory tract disease which is characterized by inflammation of the tonsils resulting from bacterial (Group A streptococcus) and viral (Epstein-Barr virus, adenovirus) infections. Symptoms include a severe sore throat, painful or difficult swallowing, coughing, headache, myalgia, fever and chills.
An upper respiratory tract disease which involves inflammation of the mucous membranes of the nose, throat, eyes, and eustachian tubes with watery then purulent discharge. This is an acute contagious disease caused by rhinoviruses, human parainfluenza viruses, human respiratory syncytial virus, influenza viruses, adenoviruses, enteroviruses, or metapneumovirus.
A kidney disease characterized by the failure of the kidneys to adequately filter waste products from the blood.
A otitis which involves inflammation of the middle ear.
A mouth disease located_in the salivary gland.
A viral infectious disease that results in infection located in mouth, has_material_basis_in Human coxsackievirus A16, Human enterovirus 71, group B coxsackievirus, or echoviruses, which are transmitted by ingestion of food contaminated with feces, transmitted by contact with pharyngeal secretions, or transmitted by droplet spread of oronasal secretions. The infection has symptom fever, has symptom sore throat, and has symptom lesions in the back area of the mouth, particularly the soft palate or tonsillar pillars.
A blood protein disease that is characterized by low number of red blood cells, repeated infections, and periodic episodes of pain, resulting from atypical hemoglobin molecules called hemoglobin S, which can distort red blood cells into a sickle, or crescent, shape.
A lung disease that is characterized by a newborn breathing in a mixture of meconium and amniotic fluid into the lungs around the time of delivery.
A lung disease characterized by inadequate gas exchange by the respiratory system.
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.
An opportunistic mycosis that is located in lungs, but can also occur in eyes, ears, skin, thyroid, pituitary, palate, parathyroid, esophagus, pleura, heart, liver, spleen, small intestine, adrenals, kidneys, bone marrow, and lymph nodes, has_material_basis_in Pneumocystis jirovecii that effects interstitial and alveolar tissues and has symptom nonproductive cough, has symptom shortness of breath, and has symptom fever.
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.
A lower respiratory tract disease that affects the airways leading into the lungs, which is caused due to inflammation of the bronchi and bronchioles, infection, or blockage.
A nutritional deficiency disease that is characterized by inadequate dietary protein and calories, which can have profound systemic effects including decreased metabolism, altered tissue distribution, compromised immunity, and impaired growth, and has_material_basis_in dietary deprivation.
A viral infectious disease that results in infection, has_material_basis_in Dengue virus [NCBITaxon:12637] with four serotypes (Dengue virus 1, 2, 3 and 4), which are transmitted by Aedes mosquito bite. The infection has symptom fever, has symptom severe headache, has symptom severe pain behind the eyes, has symptom joint pain, has symptom muscle and bone pain, has symptom rash, and has symptom mild bleeding.
A protein-energy malnutrition that is characterized by severe caloric deprivation, has_symptom emaciation, decreased height and weight gain, and decreased metabolism with hypothermia, bradycardia, and constipation, and has_material_basis_in severe caloric deprivation.
A parasitic protozoa infectious disease characterized as a vector-borne infectious disease caused by the presence of protozoan parasites of the genus Plasmodium in the red blood cells, transmitted from an infected to an uninfected individual by the bite of anopheline mosquitoes, and characterized by periodic attacks of chills and fever that coincide with mass destruction of blood cells and the release of toxic substances by the parasite at the end of each reproductive cycle.
An intestinal infectious disease that involves inflammation of the intestines, especially colon, due to chemical irritants, bacteria, protozoa, or parasitic worms, which results in severe diarrhea with passage of mucus and blood.
A viral infectious disease that results_in infection located_in upper respiratory tract or located_in lower respiratory tract, has_material_basis_in Human respiratory syncytial virus, which is transmitted_by droplet spread of nasal secretions from an infected person while coughing or sneezing, or transmitted_by contaminated fomites. The infection has_symptom runny nose, has_symptom fever, has_symptom cough, has_symptom wheezing, and has_symptom respiratory distress.
respiratory syncytial virus infectious disease
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.
A nail disease characterized by often-tender bacterial or fungal hand infection or foot infection due to either bacteria or fungus (Candida albicans) where the nail and skin meet at the side or the base of a finger or toe nail. The infection can start suddenly (acute paronychia) or gradually (chronic paronychia). Puss is usually present, along with gradual thickening and browning discoloration of the nail plate.
A cystitis characterized by a sudden onset or severe symptoms.
A gastrointestinal system disease described as the condition of having frequent loose or liquid bowel movements. Acute diarrhea is a common cause of death in developing countries and the second most common cause of infant deaths worldwide. The loss of fluids through diarrhea can cause severe dehydration which is one cause of death in diarrhea sufferers. Along with water, sufferers also lose dangerous amounts of important salts, electrolytes, and other nutrients. There are at least four types of diarrhea: secretory diarrhea, osmotic diarrhea, motility-related diarrhea, and inflammatory diarrhea.
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.
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.
A protein-energy malnutrition that is characterized by severe lack of protein and edema or anasarca, has_symptom swelling, gastrointestinal upset, dehydration, thin dry skin, and cough, and has_material_basis_in severe deficit of protein, resulting in lack of albumin causing decreased oncotic pressure in the vasculature and increased activation of the renin-angiotensin axis and antidiuretic hormone.
A parasitic helminthiasis infectious disease that involves infection of the intestine, urinary tract, skin, liver and spleen caused by multiple species of the trematode fluke of the genus Schistosoma. The symptoms include fever, chills, nausea, abdominal pain, diarrhea, malaise, myalgia, liver and spleen enlargement, rash and hematuria.
A disease by infectious agent that is carried out by a parasite which by definition is a pathogen that simultaneously injures and derives sustenance from its host.
A malaria that involves neurologic damage resulting from blockage of the blood vessels, caused due to the infection of the red blood cells by Plasmodium species.
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.
An opportunistic mycosis that involves fungal infection of the mouth, throat, skin, scalp, vagina, fingers, nails, bronchi, lungs, heart and brain by Candida species, of which Candida albicans is the most common. Systemic Candida infections are usually confined to severely immunocompromised persons.
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.
A skin disease characterized by skin rash notable for pale red, raised and itchy bumps, located_in the upper dermis.
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.
A disease of anatomical entity that located_in the respiratory system which extends from the nasal sinuses to the diaphragm.
A disease of anatomical entity that is located_in the integumentary system comprising the skin and its appendages.
A lymph node disease that is characterized by an acute or chronic inflammation of one or more lymph nodes.
A pleural disease that is characterized as an abnormal collection of air in the pleural space between the lung and the chest wall.
A disease of anatomical entity that occurs in the muscular and/or skeletal system.
A disease of anatomical entity that is located_in kidney, ureter, bladder and urethra.
A brain disease that is characterized by the occurrance of at least two unprovoked seizures resulting from a persistent epileptogenic abnormality of the brain that is able to spontaneously generate paroxysmal activity and typically manifested by sudden brief episodes of altered or diminished consciousness, involuntary movements, or convulsions.
A hepatitis that involves viral infection causing inflammation of the liver.
A brain disease that is caused by damage to the motor control centers of the developing brain during pregnancy, during childbirth or after birth, which affects muscle movement and balance.
A candidiasis that refers to a heterogeneous group of disorders characterized by recurrent or persistent superficial fungal infections located_in skin, located_in mucous membrane, or located_in nail due to T-cell defects, has-agent Candida species and has_symptom scaling of skin lesions, has_symptom thickening of nails, has_symptom swollen periungal tissue, and has_symptom scarring of the scalp.
A teeth hard tissue disease that is characterized by damage to a tooth that can happen when decay-causing bacteria in your mouth make acids that attack the tooth’s surface, or enamel.
An upper respiratory tract disease involving inflammation of the throat or pharynx resulting from bacterial, viral, fungal infections or irritants like pollutants or chemical substances and smoking. The infection is often referred to as sore throat. The symptoms include pain during swallowing, enlarged tonsils coated with a white discharge, runny nose, cough and slight fever.
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.
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.
A hematopoietic system disease that is characterized by a decrease in the normal number of red blood cells.
A systemic mycosis that results_in fungal infection located_in human body of immunocompromised individuals, has_material_basis_in Fungi. The organisms invade via the respiratory tract, alimentary tract, or intravascular devices.
A skin disease characterized by itchy, erythematous, vesicular, weeping and crusting patches of skin.
A sensory system disease that is characterized by auditory dysfunction located_in the auditory system.
A parasitic infectious disease that is caused by parasitic protozoa which are microorganisms classified as unicellular eukaryotes.
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.
A bronchial disease that is characterized by chronic inflammation and narrowing of the airways, which is caused by a combination of environmental and genetic factors. The disease has_symptom recurring periods of wheezing (a whistling sound while breathing), has_symptom chest tightness, has_symptom shortness of breath, has_symptom mucus production and has_symptom coughing.
A disease of anatomical entity that is located_in the immune system.
A lung disease that is an inflammation of the bronchioles, the smallest air passages of the lungs. It is caused by viruses and bacteria. The disease has_symptom cough, has_symptom wheezing, has_symptom shortness of breath, has_symptom fever, has_symptom nasal flaring in infants and has_symptom bluish skin due to lack of oxygen.
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.
A nervous system disease that affects either the spinal cord (myelopathy) or brain (encephalopathy) of the central nervous system.
A bone disease that results_in inflammation of the located_in bone.
A mouth disease that is relating to or affecting the structures surrounding and supporting the teeth.
A skin disease where there is a diffuse infection of connective tissue with severe inflammation of dermal and subcutaneous layers of the skin. Cellulitis can be caused by normal skin flora or by exogenous bacteria, and often occurs where the skin has previously been broken: cracks in the skin, cuts, blisters, burns, insect bites, surgical wounds, or sites of intravenous catheter insertion.
An integumentary system disease that is located_in skin.
A soft tissue infectious disease that involves accumulation of pus in the pleural cavity as a result of infection within the lung (pneumonia) or a lung abscess spreading into the space. The symptoms include cough, fever, chest pain, sweating and shortness of breath.
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.
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.
A gastrointestinal system disease that is located_in the mouth.
An integumentary system disease that is located_in nail.
A dermatitis that is characterized by a pyogenic infection causing the formation of pus.
A dermatophytosis that results_in contagious fungal infection located_in scalp, located_in hair of head, located_in eyebrow or located_in eyelash, has_material_basis_in Ascomycota fungi that belong to a group called dermatophytes and has_symptom itching of the scalp, has_symptom pus filled lesions on the scalp, and has_symptom patches of hair loss, sometimes with a 'black dot' pattern.
A rhinitis that is an allergic inflammation and irritation of the nasal airways involving sneezing, runny nose, nasal congestion, itching and tearing of the eyes caused by exposure to an allergen such as pollen, dust, mold, animal dander and droppings of cockroaches or house dust mites.
A upper respiratory infectious disease which involves irritation and inflammation of the mucous membrane of the nose due to viruses, bacteria or irritants. The inflammation results in generation of excessive amounts of mucus leading to runny nose, as well as nasal congestion and post-nasal drip.
A pancreas disease that is characterized by inflammation of the pancreas.
A nutrition disease that is characterized by deficiency of a nutritional element, such as a vitamin, mineral, carbohydrate, protein, fat, or general energy content.
A viral infectious disease that results in destruction of immune system, leading to life-threatening opportunistic infections and cancers, has_material_basis_in Human immunodeficiency virus 1 or has_material_basis_in Human immunodeficiency virus 2, which are transmitted by sexual contact, transmitted by transfer of blood, semen, vaginal fluid, pre-ejaculate, or breast milk, transmitted by congenital method, and transmitted by contaminated needles. The virus infects helper T cells (CD4+ T cells) which are directly or indirectly destroyed, macrophages, and dendritic cells. The infection has symptom diarrhea, has symptom fatigue, has symptom fever, has symptom vaginal yeast infection, has symptom headache, has symptom mouth sores, has symptom muscle aches, has symptom sore throat, and has symptom swollen lymph glands.
human immunodeficiency virus infectious disease
A gastrointestinal system disease that is located_in the intestine.
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.
An eye and adnexa disease that is located_in the eye.
A bronchial disease that is an inflammation of the bronchial tubes. It is caused by bacteria and viruses. The disease has_symptom cough with mucus, has_symptom shortness of breath, has_symptom low fever and has_symptom chest tightness.
A conjunctival disease characterized by an inflammation of the conjunctiva, the outermost layer of the eye and the inner surface of the eyelids.
An arthritis that is an autoimmune disease which develops due to an infection located elsewhere in the body.
A disease that has_material_basis_in genetic variations in the human genome.
A Human immunodeficiency virus infectious disease that results_in reduction in the numbers of CD4-bearing helper T cells below 200 per microliter of blood or 14% of all lymphocytes thereby rendering the subject highly vulnerable to life-threatening infections and cancers, has_material_basis_in Human immunodeficiency virus 1 or has_material_basis_in Human immunodeficiency virus 2, which are transmitted_by sexual contact, transmitted_by transfer of blood, semen, vaginal fluid, pre-ejaculate, or breast milk, transmitted_by congenital method, and transmitted_by contaminated needles. Opportunistic infections are common in people with AIDS.
A musculoskeletal system disease that affects tissues such as skin, tendons, and cartilage.
A disease of metabolism that is characterized by enzyme deficiency or accumulation of enzymes or toxins which interfere with normal function due to inherited enzyme abnormality.
A disease that manifests in a defined anatomical structure.
A disease of anatomical entity that has_material_basis_in hematopoietic cells.
An immune system disease that is located_in the lymphatic system.
A disease of anatomical entity that is located_in the gastrointestinal tract.
An arthritis that involves infection by a pathogen located_in joint.
A mite infestation that is a contagious ectoparasite skin infection caused by human itch mite Sarcoptes scabiei type hominis, which burrows into the upper layer of the skin but never below the stratum corneum causing severe itching and a rash found on the hands, folds of the wrist, elbow or knee, penis, breast, and shoulder blades.
A bone marrow disease characterized by an increased number of red blood cells in the bloodstream resulting in thicker blood and reduced blood flow.
A bone inflammation disease that involves a response to irritation or injury, characterized by joint pain, swelling, stiffness located_in joint.
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.
A pyoderma consisting of three forms of skin lesions having either a thick, adherent, recurrent, dirty yellow crust with an erythematous margin (common or superficial impetigo) or lessions which are superficial, thin-walled, and bullous as found in bullous impetigo. The lesions in bullous (staphylococcal) impetigo, which are always caused by S aureus, are superficial, thin-walled, and bullous.
A pemphigoid that is characterized by large blisters.
A viral infectious disease that results_in infection located_in nerve fiber, has_material_basis_in Human herpesvirus 3, which reactivates after appearing as chickenpox in childhood. The virus is transmitted_by direct contact with the rash, which can develop into chickenpox in newly-infected individuals. The infection has_symptom rash which is followed by blisters, has_symptom headache, has_symptom fever, has_symptom malaise, has_symptom itching, has_symptom burning pain, and has_symptom paresthesia.
A viral infectious disease that results_in_formation_of lesions, located_in mouth, located_in face, located_in genitalia, or located_in hands, has_material_basis_in Human herpesvirus 1 or has_material_basis_in Human herpesvirus 2, which are transmitted_by direct contact with an active lesion or body fluid of an infected person.
A viral infectious disease that results_in infection located_in skin, has_material_basis_in Measles virus, which is transmitted_by contact with oronasal secretions, or semen of an infected person. The infection has_symptom fever, has_symptom cough, has_symptom coryza, has_symptom conjunctivitis, and has_symptom maculopapular, erythematous rash.
A disease of anatomical entity that is located_in the central nervous system or located_in the peripheral nervous system.
A viral infectious disease that results_in infection located_in skin, has_material_basis_in Human herpesvirus 3, which is transmitted_by direct contact with secretions from the rash, or transmitted_by droplet spread of respiratory secretions. The infection has_symptom anorexia, has_symptom myalgia, has_symptom nausea, has_symptom fever, has_symptom headache, has_symptom sore throat, and has_symptom blisters.
A parasitic infectious disease that occurs when part of the body is infested with parasitic worms such as cestodes, nematodes and trematodes.
parasitic helminthiasis infectious disease
A parasitic protozoa infectious disease that involves infection caused by protozoan parasite of the genus Leishmania, which is transmitted by the bite of sand fly (subfamily Phlebotominae).
A leishmaniasis that involves skin infection caused by Leishmania species, resulting in one or more cutaneous lesions.
A leishmaniasis that is the most severe form of the disease caused by protozoan parasites of the Leishmania genus, resulting in the infection of the internal organs such as liver, spleen and bone marrow. The symptoms include fever, weight loss, and an enlarged spleen and liver.
A parasitic protozoa infectious disease that involves infection caused by the amoeba Entamoeba histolytica. Amebic invasion of the intestinal lining causes dysentery, colitis or diarrhea. The infection can also spread through the blood to the liver and, rarely, to the lungs, brain or other organs.
A disease by infectious agent that results in infection, has_material_basis_in Viruses.
A central nervous system disease that is located_in the brain.
An external ear disease that involves inflammation of the outer ear and ear canal. It can be caused by active bacterial or fungal infections.
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.
A stomatitis characterized by the repeated formation of benign and non-contagious mouth ulcers.
A bacterial conjuctivitis that is characterized by pain and tenderness in the eyeball and conjuctival discharge.
A respiratory system disease which involves the upper respiratory tract.
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.
A glucose metabolism disease that is characterized by abnormally low levels of blood glucose.
the role of a material entity to prevent, diagnose, treat, or study disease and/or its effects
clinical drug role
a material entity (1) containing at least one scattered molecular aggregate as part that is the bearer of an active ingredient role and (2) that is itself the bearer of a clinical drug role
drug product
a portion of cream that is the bearer of a clinical drug role
drug cream
a portion of lotion that is the bearer of a drug role
drug lotion
a portion of solution that is the bearer of a clinical drug role
drug solution
a portion of suspension that is the bearer of a clinical drug role
drug suspension
a solid object typically of discoid, spheroid, or elliptic-cylindrical shape or approximations thereof, that bears a clinical drug role.
drug tablet
an object that is the bearer of a drug role and is comprised of a solid shell of elliptical-cylindrical shape and another object contained in the shell that has a scattered molecular aggregate as a proper part
drug capsule
amoxicillin syrup
amoxicillin suspension
Folic acid tablet
Clotrimazole skin cream
Nystatin suspension
Gentamicin solution
Gentamicin injectable solution
Dexamethasone injection
Chloramphenicol solution for otic and ophthalmic administration
Ceftriaxone injectable solution
Metronidazole solution
prednisolone tablet
salbutamol syrup
salbutamol suspension
Gentamicin Sulfate (USP) / Hydrocortisone Topical Ointment
Guaifenesin / Pseudoephedrine / Triprolidine Oral Solution
Sulfamethoxazole / Trimethoprim Oral Solution
A data item that is used to indicate consent permissions for datasets and/or materials, and relates to the purposes for which datasets and/or material might be removed, stored or used.
data use permission
A primary administrative division of a country, such as a state in the United States.
A subdivision of a first-order administrative division.
A subdivision of a second-order administrative division.
A subdivision of a third-order administrative division.
A political association with effective dominion over a geographic area.
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 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.
An artificial body of water, often contained by a dam, constructed for the purpose of water storage.
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.
A body of water, usually of smaller size than a lake.
A wetland ecosystem which includes communities of grasses, rushes, reeds, typhas, sedges, and other herbaceous plants (possibly with low-growing woody plants).
A spring through which groundwater, heated by geothermal energy, flows.
A pond or lake used for the artificial culture of fish.
Place or area with clustered or scattered buildings and a permanent human population.
An accumulation of water of varying size.
https://en.wikipedia.org/wiki/ 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.
An area of land which is used for the cultivation of crops or grazing of livestock, including any agricultural constructions therein.
A landform that extends above the surrounding terrain in a limited area.
Area of dry or relatively dry land surrounded by water or low wetland.
An area with a high density of trees. A small forest may be called a wood.
A landform elevated above the surrounding area.
An elevated and comparatively level expanse of land.
A wetland ecosystem in which land mass is permanently inundated by shallow bodies of water, generally with a substantial number of hummocks, or dry-land protrusions.
A paddy field for the cultivation of rice.
A speleothem projecting vertically upwards from a cave floor and formed by precipitation from drips.
A biome is an ecosystem to which resident ecological communities have evolved adaptations.
A reservoir constructed for the purpose of providing drinking water.
A two-dimensional continuant fiat boundary which is located between a landmass and a water body.
1) this term is usually used for larger water bodies like lakes and oceans, 2) that the actual spatial extent of a shoreline, and the sharpness of its boundaries, is often arbitrarily or operationally defined, and 3) this term is for the physical shoreline, not the one- or two-dimensional representation of shorelines.
The portion of the ground surface which lies below water.
A rock is a naturally occurring solid aggregate of one or more minerals or mineraloids.
From https://en.wikipedia.org/wiki/ [A mineral] is different from a rock, which can be an aggregate of minerals or non-minerals and does not have a specific chemical composition. The exact definition of a mineral is under debate, especially with respect to the requirement a valid species be abiogenic, and to a lesser extent with regards to it having an ordered atomic structure.
An environmental material which is primarily composed of minerals, varying proportions of sand, silt, and clay, organic material such as humus, interstitial gases, liquids, and a broad range of resident micro- and macroorganisms.
'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 significant accumulation of water which is part of a marine biome.
Ideas like "significant" are fuzzy and need to be modelled more accurately. The definition is a candidate for review.
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.
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.
An environmental material primarily composed of dihydrogen oxide in its liquid form.
Sediment is an environmental substance comprised of any particulate matter that can be transported by fluid flow and which eventually is deposited as a layer of solid particles on the bedor bottom of a body of water or other liquid.
It is recommended to use a combination of sediment terms to describe a more specific sediment type.
Particulate environmental material with diameters less than 500 micrometers.
Dust occurs in and may be deposited from the atmosphere.
Water which contains a significant concentration of dissolved salts.
The threshold salt concentration for classifying water as saline varies, but typically begins at about 1,000 to 3,000 parts salt per million parts water or 0.1–0.3% salt by weight.
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 complex aggregation of microorganisms marked by the excretion of a protective and adhesive matrix; usually adhering to a substratum.
Water that is found on the surface of an astronomical object.
The residual semi-solid material left from domestic or industrial processes, or wastewater treatment processes.
Manure which has been derived from the aerobically decomposed remnants of organic materials.
A portion of soil which is found in a forested area.
A material which is not the desired output of a process and which is typically the input of a process which removes it from its producer (e.g. a disposal process).
Hay is grass, legumes or other herbaceous plants that have been cut, dried, and stored for use as animal fodder, particularly for grazing livestock such as cattle, horses, goats, and sheep.
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.
A portion of soil which is part of a cropland or a rangeland biome.
A portion of soil which is found in a grassland.
Soil in which trees from an orchard grow.
Soil which is found in a pasture and in which vegetation, such as the grass used for the grazing of ungulates, grows.
The narrow region of soil that is directly influenced by root secretions and associated soil microorganisms.
A portion of environmental material is a fiat object part which forms the medium or part of the medium of an environmental system.
Everything under this parent must be a mass noun. 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". This class is currently being aligned to the Basic Formal Ontology. Following this alignment, its definition and the definitions of its subclasses will be revised.
A layer of some material entity which is adjacent to one or more of its external boundaries and directly interacts with its immediate surroundings.
This class is distinct from a geometric surface, which is two-dimensional. The idea of "uppermost" may be problematic. Further, the definition of layer (the superclass of surface in rev 133) references surface. This may be another issue. Perhaps this can be made into an inferred class using 'bounding layer of' some material entity, note that 'bounding layer' implies containment, which may not be valid here.
Airborne solid particles (also called dust or particulate matter (PM)) or liquid droplets.
Should connect to PATO as "quality of an aerosol"
Anthropogenic material in or on which organisms may live.
This is quite odd and it probably should be obsoleted. Any material that is a participant in an agricultural process can be seen as an agricultural material.
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.
Environmental material derived from living organisms and composed primarily of one or more biomacromolecules.
A system which has the disposition to environ one or more material entities.
A layer is a quantity of some material which is spatially continuous, has comparable thickness, and usually covers some surface.
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 building part is a construction which is part of a building.
Not recommended for annotation. This class is likely to be made into an inferred class as its subclasses are distributed among more meaningful superclasses (i.e. ceiling is_a surface layer). See for example, "building floor". The boundaries between building parts may be bona fide or fiat.
A building part which is separated from other building parts by one or more interior walls and, optionally, outdoor areas by one or more exterior walls.
Concrete is a composite material composed of an aggregate bonded together with a fluid cement which hardens over time.
Missing the class for "aggregate" - tricky to define what it is, exactly. Again, seems more like some sort of material/disposition hybrid.
Masonry cement is a substance used in construction that has the disposition to set and harden and thus may be used to bind materials together.
"Cement" refers more to a disposition than a specific material.
An exterior wall is a building wall which separates the interior of a building from the buildings surrounding environment.
A roof is the covering on the uppermost part of a building which provides protection from animals and weather, notably rain, but also heat, wind and sunlight. A roof is also the framing or structure which supports the covering
This class is meant to represent roofs which are parts of buildings, rather than a roofs of cave and other natural formations.
Thatch is material composed of dry vegetation such as straw, water reed, sedge (Cladium mariscus), rushes, or heather.
Some sort of logical definition towards: composed_primarily_of some ((straw or 'water reed' or rushes or sedge or heather) and has_quality dry) should be considered, where "rushes", "sedge", etc are represented as materials rather than some sort of taxon.
A brick is a masonry unit which is composed of kneaded clay-bearing soil, expanded clay aggregate, sand and lime, or concrete material, fire-hardened or air-dried.
Generally used to refer to the masonry unit rather than a material.
A thatched building roof is a building roof that is built by thatching (or out of thatch).
A tile is a manufactured piece of hard-wearing material such as ceramic, stone, metal, or even glass, generally used for covering roofs, floors, walls, showers, or other objects such as tabletops. Alternatively, tile can sometimes refer to similar units made from lightweight materials such as perlite, wood, and mineral wool, typically used for wall and ceiling applications.
A fixture which is used primarily for the collection and, in some cases, disposal of human urine and feces.
"disposal" may not be the most precise way to describe fill-in latrines. Note that no assertion is made on whether these fixtures are in- or outdoors.
A pit latrine is a latrine which is constructed by digging a hole in the ground.
This class refers to human latrines. Note that some pit latrines can use pour-flush mechanisms. "Infectious diarrhea resulted in about 0.7 million deaths in children under five years old in 2011 and 250 million lost school days.[4][5] Pit latrines are the lowest cost method of separating feces from people.[3]" - https://en.wikipedia.org/wiki/Pit_latrine
A toilet fixture which uses water to flush liquid and solid excreta into a sewage containment or processing facility through a drainpipe.
A ventilated improved pit latrine is a pit latrine which includes a vent pipe fitted to the pit with a flyscreen covering the pipe's outlet. Air currents moving across the outlet of the vent pipe create a vaccum which draws odors out of the latrine's superstructure.
A covered pit latrine is a building which comprises a pit latrine sheltered by an outhouse.
A covered pit latrine with slab is a building which comprises a pit latrine with a slab floor sheltered by an outhouse.
A composting toilet fixture is a dry toilet fixture in which managed, aerobic decomposition converts human excreta into organic matter suitable for the fertilisation or amendment of soils.
composting toilet
Charcoal is a light, black residue, consisting of carbon and any remaining ash, obtained by removing water and other volatile constituents from animal and vegetation substances. Charcoal is usually produced by slow pyrolysis, the heating of wood or other substances in the absence of oxygen.
charcoal
A flat-wick lamp is a simple type of paraffin lamp, which burns paraffin drawn up through a wick by capillary action.
flat-wick lamp
A paraffin lantern is a lantern which houses a parrafin lamp in a structure of soldered or crimped-together sheet metal stampings and glass or other translucent material.
paraffin lantern
An electric lamp is a lamp which produces light from electricity.
electric lamp
A battery-powered electric lamp is an electric lamp which draws its power from a device composed of two or more electrochemical cells that convert stored chemical energy into electrical energy.
battery-powered electric lamp
A candle is a lamp composed of a wax within which an ignitable wick is embedded.
candle
A device capable of receiving and/or transmitting information encoded in electromagnetic radiation through wave modulation.
radio device
A cassette deck is a device capable of playing and recording audio compact cassettes.
cassette player
A television set is a device that combines a tuner, display, and loudspeakers for the purpose of converting digital or analog information signals into moving images and sound.
television set
A telephone is a telecommunications device which converts sound into electronic signals suitable for transmission via cables or other transmission media, and reconverts such signals into sound waves.
telephone
A mobile phone is a telephone which transmits sound information to a mobile phone network via radio transmissions.
mobile phone
A landline telephone is a telephone which is connected to a telephone network with wires through which electronic signals are carried.
landline telephone
A refrigerator is a device which consists of a thermally insulated compartment and a mechanical, chemical, or electronic heat pump that transfers heat from the inside of the fridge to its external environment such that the inside of the fridge is cooled to a temperature below the ambient temperature of the room
refrigerator
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 chair is a piece of furniture with a raised surface commonly used to seat a single person.
This class, along with benches, stools, and the like, can be grouped under "seating furniture" or similar. However, this is probably better as an inferred class using some sort of BFO:function in the subclass annotation.
chair
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 sofa is a bench which is partially or entirely upholstered, and often fitted with springs and tailored cushions.
sofa
A cabinet is a roughly cuboidal piece of furniture which is used to store miscellaneous items in compartments accessible through doors or drawers.
cabinet
A cupboard is a cabinet which is used indoors to store household objects such as food, crockery, textiles and liquor, and to protect them from dust and dirt
cupboard
A clock is an instrument which may indicate, keep, and/or co-ordinate time.
clock
A pressure lamp is a portable paraffin or oil lamp in which fuel is forced up into the mantle or burner by air pressure in the reservoir, which can be increased by pumping with a plunger.
pressure lamp
A spring through which fresh water flows.
freshwater spring
river water
Rainwater is liquid water which has precipitated in the form of droplets through the condensation of atmospheric water vapour.
rainwater
A motor vehicle is a vehicle which is propelled by an engine or motor and that does not operate on rails.
motor vehicle
A water truck is a truck which transports water.
water truck
A vehicle is a mobile machine which transports people or cargo.
vehicle
A bicycle is a human-powered, pedal-driven, single-track vehicle, having two wheels attached to a frame, one behind the other.
bicycle
A motorcycle is a two- or three-wheeled motor vehicle.
motorcycle
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
planetary landmass
An environmental system which can sustain and allow the growth of an ecological population.
A habitat's specificity to an ecological population differentiates it from other environment classes.
habitat
A self-contained constructed feature used by one or more households as a home, such as a house, apartment, mobile home, houseboat or other 'substantial' structure. A dwelling typically includes nearby outbuildings, sheds etc. within the curtilage of the property, excluding any 'open fields beyond'. It has significance in relation to search and seizure, conveyancing of real property, burglary, trespass, and land use planning.
human dwelling
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 part of an astronomical body.
astronomical body part
A part of a building roof which overhangs the face of a wall and, normally, projects beyond the side of a building.
The primary function of the eaves is to keep rain water off the walls and to prevent the ingress of water at the junction where the roof meets the wall. The secondary function is to control solar penetration; the eaves overhang can be designed to adjust the building's solar heat gain to suit the local climate, the latitude and orientation of the building, refer to passive solar building design. The eaves overhang may also shelter openings to ventilate the roof space.
eaves
An environmental system determined by an animal.
animal-associated environment
A material which is composed primarily of one or more pure metals and which shows their properties.
While this class allows for some degree of contamination by non-metal substances, the material represented should show at least some of the typical features of a pure metal: hardness (except for liquid metals), opacity, lustre, malleability, fusibility, ductile and good electrical and thermal conductivity.
metallic material
Environmental variability which inheres in an astronomical body part or in outer space.
This class refers to all weather, including atmospheric and space weather. Please use a subclass for more specificity.
weather
An environmental system which includes both living and non-living components.
ecosystem
Manure which is composed primarily of the feces of poultry.
poultry manure
A terrestrial ecosystem which is inundated or saturated by surface or ground water at a frequency and duration sufficient to support, and that under normal circumstances does support, a prevalence of vegetation typically adapted for life in saturated soil conditions.
wetland ecosystem
A process during which materials deemed to be waste are transported away from a site.
waste disposal process
A surface layer which is composed primarily of solid environmental material.
solid surface layer
A surface layer where the solid or liquid material of an astronomical body comes into contact with an atmosphere or outer space.
a useful class: this can be used to define sub-terrestrial and sub-marine entities
surface of an astronomical body
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
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.
An environmental material consisting of organic matter from plants and/or animals that is used in agriculture as fertilizer.
Most manure consists of animal feces; other sources include compost and green manure.
manure
A material entity used to build a dwelling or part of a dwelling.
building material
A material entity for accommodation, such as a building, part of a building, caravan, houseboat or other mobile home. A tent is not normally considered to be substantial.
A building material used in the construction of a roof.
roof material
A building material used in the construction of a floor
floor material
A building material used in the construction of a wall.
wall material
A processed material shaped a small rectangular block typically made of clay mixed with sand and fired in a kiln or baked by the sun, used in building wall construction.
was ICEMR PRISM household, no longer used
A data item of a household's cumulative living standard represented in a numerical datum. The wealth index is calculated using easy-to-collect data on a household's ownership of selected assets, such as televisions and bicycles; materials used for housing construction; and types of water access and sanitation facilities.
numerical household wealth index
A processed material that is the bottom edge of a roof. The primary function of the eaves is to keep rain water off the walls and to prevent the ingress of water at the junction where the roof meets the wall. The secondary function is to control solar penetration; the eaves overhang can be designed to adjust the building's solar heat gain to suit the local climate, the latitude and orientation of the building, refer to passive solar building design. The eaves overhang may also shelter openings to ventilate the roof space.
A brick with holes which is embedded in a wall to allow ventilation through it.
air brick
A scalar measurements datum of resident in a dwelling.
number of residents in a dwelling
An information content entity to indicate whether a household has electricity in a dwelling.
obsolete household having electricity information
A material entity that consists of fuel mainly used for cooking.
cooking fuel material
A material entity that consists of an energy source for lighting.
number of rooms in a dwelling that are used for sleeping.
number of rooms for sleeping in a dwelling
A scalar measurement datum of land such as land owned by a household.
land area measurement datum
A scalar measurement datum of meals per day in a household
number of meals per day
A scalar measurement datum of days eating meat in a week in a household
number of days per week eating meat
A categorical measurement datum that specifies how frequently the food needs of a household were not met.
frequency of not satisfying food needs
A length measurement datum of the distance from a dwelling to the nearest health facility.
A genotype information which is about the presence of certain genetic variants of glucose-6-phosphate dehydrogenase.
glucose 6 phosphate dehydrogenase genotype
A genotype information which is about the presence and degree of alpha-thalassemia, a form of thalassemia involving the number of functional HBA1 and HBA2 genes.
alpha thalassemia genotype
A genotype information which is about the presence of sickle-cell hemoglobin (HbS), an abnormal form of hemoglobin which is the oxygen-carrying protein within the red blood cells.
sickle hemoglobin genotype
A diagnosis that is an assertion that a patient has a parasitic infectious disease.
diagnosis of parasitic infectious disease
A phenotypic abnormality of the presence of bacteria in the blood.
not in use; will replace w/Bacteremia from HP if equivalent term needed
obsolete presence of bacteria in the blood
A diagnosis of malaria without evidence of complicated malaria.
Person: Jie Zheng, Chris Stoeckert, Grant Dorsey
obsolete diagnosis of uncomplicated malaria
A phenotypic abnormality of the presence of a virus in the blood. It is a medical condition where viruses enter the bloodstream and hence have access to the rest of the body.
not in use; will replace w/Viremia from HP if equivalent term needed
A diagnosis of malaria with the presence of any danger signs including inability to sit up or stand, vomiting everything, unable to breastfeed or drink and lethargy or meeting criteria for severe malaria.
diagnosis of complicated malaria
was ICEMR PRISM observation, no longer used
obsolete diagnosis of complicated malaria with high parasite density
A diagnosis of complicated malaria with signs and symptoms, such as inability to sit up or stand, vomiting everything, unable to breastfeed or drink, lethargy, which are not listed as WHO criteria used to diagnose severe malaria.
obsolete diagnoses of complicated malaria with danger signs
A diagnosis of complicated malaria based on WHO criteria that include the presence of parasite infections, most commonly P.falciparum, and any one or more of symptoms/signs of serious organ failures or abnormalities, including cerebral malaria, severe anemia, generalized convulsions, hypoglycemia, respiratory distress, fluid and electrolyte disturbances, acute renal failure, ARDS, circulatory collapse, abnormal bleeding, and Jaundice.
diagnosis of severe malaria
a malaria characterized by serious organ failures or abnormalities including cerebral malaria, severe anemia, generalized convulsions, hypoglycemia, respiratory distress, fluid and electrolyte disturbances, acute renal failure, ARDS, circulatory collapse, abnormal bleeding, and jaundice.
Centers for Disease Control and Prevention
Symptom or sign information that is used for the diagnosis of severe malaria based on World Health Organization (WHO) criteria.
severe malaria symptom or sign information
A scalar measurement datum about the level of hemoglobin in the blood.
Plasmodium asexual stages, by microscopy
A categorical measurement datum that indicates the presence of asexual parasites in blood cells by microscopy using a value of positive or negative.
blood smear reading as positive or negative
A planned process in which a patient is seen by a medical practitioner.
A clinical visit that is primarily for a regular examination.
a human being who bears a participant under investigation role
human participant under investigation
A material entity whichis part of a dwelling for providing fresh air to the dwelling.
A fourth-order administrative region of Uganda.
subcounty of Uganda
A role borne by some material entity which can be delivered/administrated into some organisms and the role is realized during clinical treatment process aiming to treat symptoms, signs or diagnosed disease.
blood used in transfusion for replacement blood lost during surgery or due to a serious injury.
A material entity that is bearer of a medication role.
A medication material intended to prevent or treat malaria.
malaria medication
A medication material intended to prevent or treat a disease other than malaria.
non-malaria medication
A drug product that has the chemical ingredient quinine and has antipyretic (fever-reducing), antimalarial, analgesic (painkilling), and anti-inflammatory properties.
A drug product that is the of combination artemether/lumefantrine (trade names Coartem and Riamet, Falcynate-LF). It is generally used for the treatment of acute uncomplicated Plasmodium falciparum malaria.
obsolete artemether-lumefantrine drug product
A dependent continuant which is either disease or phenotypic abnormality.
An information content entity is about household.
household information
A diagnosis of uncomplicated malaria that occurs with the first trimester of pregnancy.
obsolete diagnosis of uncomplicated malaria in the 1st trimester of pregnancy
A diagnosis based on presence of asexual parasites by microscopy in the absence of subjective fever or documented elevated temperature
obsolete diagnosis of asymptomatic microscopic parasitemia
A diagnosis of malaria based on positive blood smear with subjective fever or elevated temperature resulting in antimalarial treatment.
diagnosis of symptomatic malaria
A time measurement datum that specifies the date of a clinical visit.
date of clinical visit
Plasmodium asexual stages, by microscopy result
A scalar measurement datum that is the output of a microscopy assay on a specimen and is expressed as a ratio of asexual parasites to either the quantity of specimen or number of leukocytes within it.
Person: Jie Zheng, Chris Stoeckert, John Judkins
asexual parasite density by microscope
An information content entity about dwelling.
A symbol that denotes a specific household.
household identifier
A symbol that denotes a specific human participant under investigation.
human study subject identifier
An information content entity which is about features of a human participant under investigation.
study participant information
elevated temperature or subjective fever
febrile
A function to provide fresh air to a closed space.
A material entity in a dwelling that is designed, built, installed, selected, etc., to serve a specific function affording a convenience or service to people who are living in the dwelling.
A phenotypic abnormality of a subjective fever as reported by the study participant or their parent/guardian
subjective fever
a febrile quality of an abnormally high temperature
A scalar measurement datum that is about temperature.
A ventilation function to provide fresh air to a dwelling.
an organism that is the bearer of a partipant under investigation role
participant under investigation
A role that inheres in a material entity that is realized in a building process in which the material entity will become part of a structure with a roof and walls standing more or less permanently in one place.
building material role
A building material role that inheres in a material entity that is realized in a building process in which the material entity will become part of a roof.
roof material role
A building material role that inheres in a material entity that is realized in a building process in which the material entity will become part of a wall.
wall material role
A building material role that inheres in a material entity that is realized in a building process in which the material entity will become part of a floor.
floor material role
A role that inheres in a material entity that is realized in a process that provides a convenience or service to people who are living in a dwelling.
A temperature measurement datum that is about an organism.
obsolete organismal body temperature measurement datum
A processed material shaped a small rectangular block typically made of clay mixed with sand and fired in a kiln or baked by the sun, used in building floor construction.
An age since birth measurement datum at the time of a clinical visit.
Person: Jie Zheng, Chris Stoeckert, Shon cade, Grant Dorsey
obsolete age since birth at time of visit
An average value of asexual parasites counted per microliter of blood (i.e. malaria parasite density) across mulitiple clinical visits of a participant who was diagnosed with asymptomatic microscopic parasitemia.
average asexual parasite density of a participant with asymptomatic microscopic parasitemia
An average value of asexual parasites counted per microliter of blood (i.e. malaria parasite density) across mulitiple clinical visits of a participant who was diagnosed with malaria.
average asexual parasite density of a participant with malaria
An average value of female Anopheles mosquitoes collected across multiple collections (e.g. from one or more households on a number of nights).
average number of female Anopheles per night
An average value of Anopheles mosquitoes tested for sporozoites across multiple collections (e.g. from a given household across CDC light trap collections) in a given period.
average number of female Anopheles tested for sporozoite
An average value of sporozoite positive female Anopheles mosquitoes across multiple collections (e.g. from a given household over a number of nights of collections).
average number of sporozoite-positive female Anopheles
An average percentage value of female Anopheles mosquitoes tested as sporozoites-positive in all female mosquitoes tested for sporozoites across multiple collections.
average percent of female Anopheles with Plasmodium sporozoites
An age since birth measurement datum at the time of subject enrollment.
obsolete age since birth at time of enrollment
A data item of the total number of clinical visits by a participant in an investigation.
number of clinical visits
A data item of the number of clinical visits during which the participant was diagnosed with malaria
number of clinical visits resulting in a malaria diagnosis
Total visits with microscopic parasitemia
A data item of the number of clinical visits during which the participant was diagnosed with asymptomatic microscopic parasitemia.
number of clinical visits resulting in an asymptomatic microscopic parasitemia diagnosis
A data item of the total number of clinical visits which were not sheduled routine visits.
obsolete number of non-routine clinical visits
obsolete number of routine clinical visits
An information content entity that is about the type of sample/specimen collected during a clinical visit.
A blood specimen that is located on a filter paper.
Peripheral blood mononuclear cell sample
A processed specimen that is extracted from whole blood using gradient centrifugation that separates the blood into a layer of peripheral blood mononuclear cell under the top layer of plasma. It contains lymphocytes, monocytes or macrophages that are critical components in the immune system.
peripheral blood mononuclear cell specimen
A processed specimen consisting of red blood cells isolated from whole blood by centrifugation.
An average value for female Anopheles mosquitoes tested positive for carrying Plasmodium parasites across multiple collections (e.g. from a given household across CDC light trap collections) in a given period.
obsolete average number of Plasmodium parasite-positive female Anopheles
An average value for female Anopheles mosquitoes tested for carrying Plasmodium parasites across multiple collections (e.g. from a given household across CDC light trap collections) in a given period.
obsolete average number of female Anopheles tested for Plasmodium parasite
An average percentage value for female Anopheles mosquitoes carrying Plasmodium parasites in all female mosquitoes tested for carrying Plasmodium parasites across multiple collections.
obsolete average percent of Plasmodium parasite-positive female Anopheles
A count of Anopheles mosquitoes collections performed (e.g. from a given household) in a given period.
number of Anopheles collections
A sum value for all species of female Anopheles mosquitoes in a given collections.
sum number of female Anopheles in a collection
A sum value for all female Anopheles funestus mosquitoes in a given collections.
sum number of female Anopheles funestus in a collection
A sum value for all female Anopheles gambiae mosquitoes in a given collections.
sum number of female Anopheles gambiae in a collection
A time datum for the duration of a patients participation in an investigation.
duration of observation of study participant
An average value for the number of clinical visits of a patient based on calendar years
average number of clinical visits per year
An average value for the number of clinical visits of a patient with asymptomatic microscopic parasitemia based on calendar years.
average number of clinical visits with asymptomatic microscopic parasitemia diagnosis per year
An average value for the number of clinical visits of a patient with malaria based on calendar years
average number of clinical visits with malaria diagnosis per year
A clinical visit date that specifies the date/time period of a routine clinical visit.
A data item about a household's cumulative living standard represented in a categorical datum. The wealth index is calculated using data on a household's ownership of selected assets, such as televisions and bicycles; materials used for housing construction; and types of water access and sanitation facilities.
Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey
categorical household wealth index
An information content entity about items that a household owns such as a car, funiture, etc.
household asset information
An information content entity indicating whether a person was given antimalarial therapy outside the study since last seen as part of the study.
obsolete antimalarial therapy given outside the study since last seen information
An information content entity indicating the cause of death for a participant in the study.
A clinical visit occuring because of a sickness.
A covered pit latrine that does not have a latrine slab.
obsolete covered pit latrine without slab
A time measurement datum specifying the date of death
date of death
A time measurement datum that specified the date of participant first enrolled in a study
date of participant first enrolled in a study
A time measurement datum that specified the date of participant last seen in a study
date of participant last seen in a study
A time measurement datum measuring the number of days since a clinical visit took place which resulted in a malaria diagnosis.
obsolete days since a clinical visit with a malaria diagnosis
A time measurement datum that measures the duration of having abdominal pain.
duration of abdominal pain
A time measurement datum that measures the duration of having anorexia.
duration of anorexia
A time measurement datum that measures the duration of having a cough.
duration of cough
A time measurement datum that measures the duration of having diarrhea.
duration of diarrhea
A time measurement datum that measures the duration of having fatigue.
duration of fatigue
A time measurement datum that measures the duration of having a headache.
duration of headache
A time measurement datum that measures the duration of having jaundice.
duration of jaundice
A time measurement datum that measures the duration of having joint pains.
duration of joint pains
A time measurement datum that measures the duration of having muscle aches.
duration of muscle aches
A time measurement datum that measures the duration of having seizures.
duration of seizures
A time measurement datum that measures the duration of having subjective fever.
duration of subjective fever
A time measurement datum that measures the duration of having vomiting.
duration of vomiting
A household asset information indicating whether a member of a household has or owns an animal-drawn cart.
Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey, John Judkins
indicator of household having animal-drawn cart
A household asset information indicating whether a member of a household has a bank account.
indicator of household having bank account
A household asset information indicating whether a household has a bed.
A household asset information indicating whether a member of a household has or owns a bicycle.
A household asset information indicating whether a member of a household has or owns a boat without a motor.
indicator of household having boat without a motor
A household asset information indicating whether a member of a household has or owns a car or truck.
indicator of household having car
A household asset information indicating whether a household has a cassette player.
obsolete household cassette player asset
A household asset information indicating whether a household has a chair.
A household asset information indicating whether a household has a clock.
A household asset information indicating whether a household has a cupboard.
A household asset information indicating whether a household has electricity in their dwelling.
A household asset information indicating whether a household has a land line or fixed location phone.
A household asset information indicating whether a household has a mobile phone.
A household asset information indicating whether a member of a household has or owns a boat with a motor.
indicator of household having motorboat
A household asset information indicating whether a member of a household has or owns a motorcycle or motor scooter.
obsolete household motorcycle or scooter asset
A household asset information indicating whether a household has a radio.
A household asset information indicating whether a household has a refrigerator.
A household asset information indicating whether a household has a sofa.
A household asset information indicating whether a household has a table.
A household asset information indicating whether a household has a television.
A household asset information indicating whether a member of a household has or owns a watch.
indicator of household having watch
An information content entity indicating whether a malaria episode occurred
obsolete incident of malaria episode information
A material entity where a clinical visit took place.
A material entity where a death occurred.
An information content entity indicating whether medical care occurred outside the study clinic since last seen as part of the study.
obsolete medical care outside the study clinic since last seen information
A time measurement datum of the interval from participant enrollment in a study until the current visit.
duration of study participation from enrollment to current visit
A measurement datum of the number of female Anopheles funestus with a recent blood meal in a given collection
number of fed female Anopheles funestus in a collection
A measurement datum of the number of female Anopheles gambiae with a recent blood meal in a given collection
number of fed female Anopheles gambiae in a collection
A measurement datum of the number of female Anopheles dissected for parity in a given collection.
number of female Anopheles dissected for parity in a collection
A measurement datum of the number of female Anopheles that have never layed eggs in a given collection.
number of female null parous Anopheles in a collection
A measurement datum of the number of female Anopheles that have layed eggs before or are pregnant in a given collection.
number of female parous Anopheles in a collection
A measurement datum of the number of gravid or semi-gravid female Anopheles funestus in a given collection
number of gravid or semi-gravid Anopheles funestus in a collection
A measurement datum of the number of gravid or semi-gravid female Anopheles gambiae in a given collection
number of gravid or semi-gravid female Anopheles gambiae in a collection
An average value for the number of insecticide treated mosquito net(s) per person.
obsolete number of insecticide treated mosquito net(s) per person
A measurement datum of the number of female Anopheles that are not gambiae nor funestus in a given collection.
number of non-gambiae or funestus female Anopheles species in a collection
A data item of the number of sleeping spaces in a dwelling.
number of sleeping places in dwelling with a household
Unable to assess Anopheles funestus count
A measurement datum of the number of Anopheles funestus that could not be accessed in a given collection
number of unassessable Anopheles funestus in a collection
Unable to assess Anopheles gambiae count
A measurement datum of the number of Anopheles gambiae that could not be assessed in a given collection
number of unassessable Anopheles gambiae in a collection
A measurement datum of the number of female Anopheles funestus without a recent blood meal in a given collection
number of unfed female Anopheles funestus in a collection
A measurement datum of the number of female Anopheles gambiae without a recent blood meal in a given collection
number of unfed female Anopheles gambiae in a collection
An information content entity that indicates whether a plasma sample is lost or not.
A Plasmodium gametocytes in blood by microscopy assay datum that specifies whether gametocytes were detected.
presence of Plasmodium gametocyte in blood by microscopy assay
An information content entity indicating the reason why a participant withdrew from a study.
reason for participant withdrawal
An information content entity that indicates whether a redraw of a symptom occurred after a clinical visit.
obsolete redraw of a symptom after clinical visit information
A routine clinical visit in which a blood specimen was collected for a T-cell study.
obsolete routine clinical visit for T-cell study
A routine clinical visit in which a blood specimen was collected by finger prick and sent for lab testing (e.g., blood smear, hemoglobin level measurement).
obsolete routine clinical visit with finger prick
A routine clinical visit in which a blood specimen was collected using venipuncture and sent for lab testing (e.g., blood smear, hemoglobin level measurement).
obsolete routine clinical visit with venipuncture
A routine clinical visit in which no routine assessment was done during the visit.
obsolete routine clinical visit without any routine assessment done
An air brick with a screen that can prevent some insects get in the dwelling.
An anemia with hemoglobin levels less than 5 gm/dL.
severe anemia
An information content entity indicating whether a person slept in an insecticide treated net the previous night.
slept in an insecticide treated net last night information
A sum value for all female Anopheles examined for sporozoites in a given collection.
sum number of female Anopheles examined for sporozoites in a collection
A sum value for all female Anopheles with Plasmodium sporozoites in a given collection.
sum number of female Anopheles with Plasmodium sporozoites in a collection
An information content entity indicating whether enrollment of a human study subject occurred at the beginning of a study or during the study.
indicator of enrollment timing
A pit latrine that is not sheltered by an outhouse but has a latrine slab.
obsolete uncovered pit latrine with slab
A pit latrine that is not sheltered by an outhouse and does not have a latrine slab.
obsolete uncovered pit latrine without slab
An air brick without a screen to prevent insects from enetering the dwelling.
Pain perceived to originate in the muscle.
A light source that light is produced from solar energy.
drinking water that is obtained from a publicly accessible water well without a constructed barrier built around it to limit movement of waste or runoff into it
obsolete drinking water from open public well
drinking water that is obtained from a water well with a constructed barrier built around it to limit movement of waste or runoff into the well and the well is located in the yard of a dwelling
obsolete drinking water from open well in yard
drinking water accessed through a plumbing fixture located inside a human dwelling
drinking water from pipe into dwelling
drinking water obtained through a plumbing fixture located in the yard of a human dwelling
drinking water from pipe into yard
obsolete drinking water from protected public well
obsolete drinking water from freshwater spring
obsolete drinking water from protected well in yard
drinking water that is obtained from a freshwater spring without a constructed barrier built around it that would limit movement of waste or runoff into it
obsolete drinking water from unprotected freshwater spring
obsolete drinking water from water truck
A centrally registered identifier symbol assigned by the American Type Culture Collection (ATCC).
half life datum (t 1/2) for cleaning parasite
parasite clearance half life
a rate measurement datum that represents the number of parasite organisms removed from the bearer of a host role by means of the biological processes of the bearer of the host role
parasite clearance rate
a time measurement datum that is the result of measuring the time it takes for the biological processes of the bearer of a host role to remove parasite organisms within it, until such time as the organisms cannot be detected
duration of parasite clearance
was in EuPathDB/PlasmoDB, no longer used
obsolete pyrimethamine and chloroquine resistant
obsolete pyrimethamine, mefloquine and chloroquine resistant
obsolete pyrimethamine resistant, chloroquine sensitive
obsolete pyrimethamine,chloroquine, and mefloquine resistant
obsolete sodium antimony gluconate resistant
was EuPathDB/PlasmoDB term, no longer used
obsolete sodium antimony gluconate sensitive
obsolete no malaria parasite infection diagnosis
A population of people who share a common ancestor on the patrilineal or matrilineal line.
haplogroup
a time measurement datum that represents the beginning of the first process in which a parasitemia is realized
time parasitemia started
an information content entity that describes the success, failure, or indeterminacy of a treatment
treatment outcome information
Shannon Takala Harrison: Also not sure about LF, it could either be late failure or lost to follow-up.
Term need for annotation NIH-10K experiment, treatment outcome
Shannon Takala Harrison: LOSS probably also means the patient was lost to follow-up.
Shannon Takala Harrison: Not sure what NULL means; it could also indicate lost to follow-up.
obsolete have a subsequent P. vivax infection
obsolete summary information about a dwelling
an information content entity that is about a process in which a human being occupying a dwelling participates. It either specifies the bearer of the function that is realized in the process, or it specifies that the process does not occur in the dwelling or its yard.
information on dwelling facilities
a information content entity that is about a part of a dwelling
information on dwelling physical characteristics
an information content entity that is about a household and is an estimator of capabilities of household members to participate in processes that maintain their health, social status, and economic freedom
socioeconomic factor
a data item that is about an investigation and is the specified output of a data transformation that has only clinical visit data as input
aggregated clinical visit information
a genotype information that is about the genetic material of a human being
human genotype information
an information content entity that is about a part of a study design execution that is part of an investigation under which a human being is a participant
information on participant study details
an information content entity that is about a part of a health care encounter that occurs in a hospital facility
hospitalization information
an information content entity that is about a sign or symptom of a patient
This should stay consistent w/OGMS's definitions, so this definition may need to be changed if OGMS changes their definitions of sign and symptom to information content entities.
symptom or sign information
an information content entity that is about a clinical visit
information on observation details
an information content entity that specifies whether a clinical visit is scheduled or unscheduled
clinical visit type information
an entomological data item that results from either (a) counting insect collections from multiple catches of live specimens or (b) an averaging data transformation that has single catch entomological measurement data as input
aggregated entomological measurement data
aggregated entomological data item
an entomological data item that is the specified output of an assay that has a collection of insect specimens as specified input; this collection is the specified output of exactly one catch of live specimens
obsolete single catch entomological measurement datum
a clinical visit that realizes the concretization of a protocol specifying the time of the visit
a clinical visit that occurs at a time that is not mentioned in a protocol that directs the time of the visit
an information content entity that is about a malaria diagnosis and describes the severity of the disease or the basis for the diagnosis
obsolete malaria severity and basis information
A diagnosis that is an assertion that a patient, who is the subject of a diagnostic process, has a disease other than malaria.
diagnosis of disease other than malaria
an information content entity that is about a participant under investigation and specifies the hospital admitting the participant
hospital admission information
a time measurement datum that is about a human being who bears a patient role and specifies the date of the patient's admission to a hospital
date of hospital admission
a time measurement datum that is about a human being who bears a patient role and specifies the date of the patient's discharge from a hospital
date of hospital discharge
A diagnosis that is documented during the patient discharge process.
diagnosis at patient discharge
an information content entity that is about a collection of Anopheles funestus
Anopheles funestus related information
an information content entity that is about a collection of Anopheles gambiae sensu lato
Anopheles gambiae sensu lato related information
an information content entity that is about a number of mosquitos that have given birth
mosquito parity information
an entomological data item that is the specified output of an analyte assay to determine whether a sporozoite is present in any insect in a collection of insects
sporozoite testing information
a data item that is the specified output of a data transformation that has only sporozoite testing information as input
aggregated sporozoite testing information
a data item that is about a collection of insects
One dimensional cartesian spatial coordinate datum refers to eastward-measured distance (or the x-coordinate). The terms easting and northing are geographic Cartesian coordinates for a point. Easting and northing coordinates are commonly measured in meters from a horizontal datum.
obsolete easting coordinate measurement datum
One dimensional cartesian spatial coordinate datum refers to the northward-measured distance (or the y-coordinate). The terms easting and northing are geographic Cartesian coordinates for a point. Easting and northing coordinates are commonly measured in meters from a horizontal datum.
obsolete northing coordinate measurement datum
A human waste disposal in a household.
human waste disposal in a household
A count of the total number of non-scheduled clinical visits in an investigation.
number of non-scheduled visits
A count of the total number of scheduled clinical visits in an investigation.
number of scheduled visits
An information content entity that is about malaria diagnosis and parasite status testing by blood smear or LAMP.
Values for this class: Symptomatic malaria Blood smear positive, no malaria Blood smear negative, LAMP positive Blood smear negative, LAMP negative Blood smear negative, LAMP not done Blood smear indicated but not done Blood smear not indicated
Person: Jie Zheng, Grant Dorsey, John Judkins
information on malaria diagnosis and parasite status
A dwelling information about animal living in a human dwelling.
An information content entity that is about human traveling.
An information content entity that is about vector control intervention towards interruption of transmission of infectious diseases.
vector control intervention information
An information content entity that is about employment.
employment information
An organism that raised by people and lives in a human dwelling.
domesticated animal in a human dwelling
An information content entity that is about when the bed net is last treated.
information on when bed net last treated
An information content entity that is about the highest level of schooling that a person has reached.
Lifetime Plasmodium vivax infections count
A count of the total times of a person who infected with P. vivax in his lifetime.
number of infections with P. vivax in lifetime
Plasmodium vivax infections last year count
A count of the total times of a person who infected with P. vivax last year.
number of infections with P. vivax in the last year
Lifetime Plasmodium falciparum infections count
A count of the total times of a person who infected with P. falciparum in his lifetime.
number of infections with P. falciparum in lifetime
Plasmodium falciparum infections last year count
A count of the total times of a person who infected with P. falciparum last year.
number of infections with P. falciparum in the last year
A measurement datum of days per week spent in one's primary occupation.
days per week at primary occupation
A measurement datum of days per week spent in one's secondary occupation.
days per week at secondary occupation
A human social role realized in a process that often performed in exchange for payment. Many people have multiple job roles, such as those of parent, homemaker, and employee.
A planned process that a person participates in exchange for payment. The job role born by the person is realized in the process.
An economic activity that a person is involved in primarily.
An occupation that a person is not involved in primarily.
secondary occupation
A textual entity that describes a person's primary economic activity.
obsolete primary economic activity description
A textual entity that describes a person's secondary economic activity.
obsolete secondary economic activity description
An information content entity about secondary economic activity a person participates in the last month.
secondary economic activity in last month
An information content entity that is about an activity that realizes a social role and is often performed for payment.
occupation
A time measurement datum about the pay period of primary economic activity.
primary economic activity pay period
A time measurement datum about the pay period of secondary economic activity.
secondary economic activity pay period
An information content entity about whether a person received payment from primary economic activity.
indicator of whether person received payment from primary economic activity
An information content entity about whether a person received payment from secondary economic activity.
indicator of whether person received payment from secondary economic activity
A data item of salary of primary job.
salary of primary economic activity
A data item of salary of other job.
salary of secondary economic activity
A measurement datum of hours in one's primary occupation per day spent in that occupation.
hours per day at primary occupation
A measurement datum of hours in one's secondary occupation per day spent in that occupation.
hours per day at secondary occupation
An environmental feature for disposing garbage.
A textual entity about community where a person is living.
A textual entity about community where a study taken place.
A malaria medication that is generally taken for initial treatment of malaria.
"A malaria medication that is given when first-line medication doesn't work, or stops working."
obsolete information of whether malaria medication is given
a categorical value specification that is about a human being and specifies whether that human being is joined to another human being in marriage
EuPathDB, BFO's 'relational quality' examples
marital status
a categorical value specification that specifies whether a human being plans to change within two years the dwelling which that human being occupies
indicator of whether person plans to move
An information content entity that specifies the relationship between a person and the head of their household.
relationship to head of household
a time measurement datum that represents the time a human being resides in a human dwelling
duration of residence in dwelling
A time measurement datum of the time interval that a human being has lived in a geographic location where the inhabitants share a common trait.
duration of residence in community
a count of the number of instances of a site, within a human dwelling and its yard, to which any resident of the dwelling has access
number of common areas in a dwelling
a scalar measurement datum that has the square meter as its measurement label and is the result of a measurement of area that is covered by a roof
covered area measured in square meter
An information content entity about where the kitchen is located inside or outside of a dwelling.
information on kitchen location
A scalar measurement datum that is the result of a measurement of area.
area measurement datum
a categorical value specification that is about a dwelling and specifies whether (a) it is owned by an occupant of the dwelling or (b) a rental agreement exists such that an occupant has an obligation to pay rent to someone who does not occupy the dwelling
information on whether occupant owns or pays rent on dwelling
obsolete information of whether ship is taken during a trip
an information content entity that is about a geographic location in which part of a journey occurs
obsolete information on place visited during a trip
An information content entity about travel to any place more than 10 km away from where a person lives.
information on travel in the last month
an information content entity that is about a patient diagnosed with malaria and describes geographic locations the patient visited
information on travel before malaria
A material entity that is used to make bed net.
bed net material
a time measurement datum that is about a human dwelling and specifies the most recent date on which the dwelling was fumigated, i.e. filled with pesticide
date of last fumigation
an information content entity that specifies the organization that administers insecticide to a collection of bed nets
information on organization responsible for treating bed nets
An information content entity that specifies whether a human participant under investigation is a contact for malaria, based on the partipant's association with sites in which malaria infections are known to occur.
information on contact with malaria
an information content entity that is about a human participant under investigation and specifies whether the person is present for a scheduled clinical visit
obsolete information on participant status at visit
obsolete information of whether address has changed
a count of the number of instances of a domesticated animal that is raised in an agricultural setting to produce labor and commodities
number of livestock
a count of the number of instances of a domesticated animal that is kept for pleasure rather than utility
number of pets
a count of the number of instances of a bed net to which insecticide was applied in the past six months
number of insecticide-treated bed nets treated less than 6 months ago
a count of the number of instances of a bed net to which insecticide was applied before the previous six months
number of insecticide-treated bed nets treated more than 6 months ago
a count of the number of instances of bed net to which long last insecticide is administered
number of long last insecticide-treated bed nets
a count of the number of instances of a bed net to which insecticide has not been applied
number of untreated bed net
obsolete blood pressure measurement datum
A categorical measurement datum about proximity to case dwelling.
obsolete proximity to case dwelling datum
obsolete information of whether a census form filled at enrollment
an organization that administrates a medical care center that provides healthcare services on an outpatient basis
A geographic location where the clinic is located.
A second-order administrative region of India.
district of India
A textual entity about a 'division' or 'ward' being a sub-division of a city.
a categorical value specification that specifies whether a patient complies with a dose specification that specifies the dose of malaria medication to self-administer
indicator of whether participant taking antimalarial drugs as advised
an information content entity that specifies whether a participant under investigation self-administered antimalarial drugs in the past 2 weeks
indicator of whether participant taking antimalarial drugs in last 2 weeks
an information content entity that is about a human participant under investigation that has a disease and specifies the disease
information on existing illness
an information content entity that is about a human participant under investigation and specifies whether the participant has a disease
indicator of whether participant having existing illness
a categorical value specification that is about a health care provider role that is realized in a treatment to alleviate symptoms of a fever. It either specifies whether this role is borne by a hospital or clinic, private practice, or the patient, or it specifies that this information is missing.
fever treatment provider information
A time measurement datum that measures the duration of having febrile.
duration of being febrile
obsolete information of whether a person is family head
an information content entity that specifies whether a human being is manifesting a disease
indicator of whether person is sick now
"An information content entity is about who are indoor residents, such as only human, or human and animals."
indoor residents information
a measurement datum that approximates the temporal interval between applications of larvicide at the same site
frequency of larvicide in use
an information content entity that specifies any locations in which a diagnostic process has occurred in the past twelve months that resulted in a diagnosis of malaria
obsolete information on where malaria diagnosed in last 12 months
a count of the number of instances of a parasite in a life cycle stage in which reproduction is asexual
EuPathDB, Centers for Disease Control and Prevention
A data item of which parasite species detected in a blood specimen.
parasite species information
A country name denote where a person was born.
birth country name
an information content entity that is part of a diagnosis of malaria, resulting from a diagnostic process that occurred within the past year, and specifies the species of the infectious agent causing the malaria
information on malaria parasite infection diagnosis past year
Malaria diagnoses in the past year count
A count of malaria diagnosis past year.
number of malaria diagnosis past year
A time measurement datum of the time since the most recent diagnosis of malaria.
duration since last diagnosis of malaria
An information content entity about whether antimalarial drug treated last year
indicator of whether participant treated antimalarial drugs last year
A time measurement datum about when the antimalarial drug used last year
date antimalarial drug used
An information content entity about what antimalarial drug used last year
information on antimalarial drug used last year
An information about who treated malaria last year
information on who treated malaria last year
A specimen that is used for DNA extraction and following PCR assay.
specimen used for DNA PCR
An organism identification assay that identifies the species of parasites by PCR.
obsolete parasite species identification by PCR assay
A textual entity that denotes the public health clinic/hospital that the human subject normally uses (for non malaria illness).
A data item of income level issued annually by the Department of Health and Human Services. Federal poverty levels are used to determine your eligibility for certain programs and benefits.
poverty line
An information that specifies a person has no illness.
obsolete information that there is no illness
A laboratory test that can quickly establishing the diagnosis of P. falciparum or P. vivax malaria infection by detecting the antigens in a person's blood.
A laboratory test that is a rapid, sensitive malaria test that is able to differentiate between P. falciparum and other malaria parasites.
obsolete optimal-IT rapid diagnostic test
A material entity that a person uses to deter mosquitoes from approaching or settling.
personal mosquito repellent
"An information content entity about a person's resident status, permanent or temporary."
resident status information
An information content entity about repellent sprayed in last 12 months in a dwelling.
information on mosquito repellent sprayed in last 12 months
A text entity denotes to a state where a person was born.
state name of birth
An information content entity that is about whether a person take fever suppressant.
take fever suppressant information
A third-order administrative region of India.
taluk of India
A country name denote a geographic location that a person has visited.
visited country name
A text entity denotes to a district that a person has visited.
visited district name
A text entity denotes to a state that a person has visited.
visited state name
A taluk name denote a geographic location that a person has visited.
visited taluk name
A village name denote a geographic location that a person has visited.
visited village name
An information content entity about whether a person travelled in last 14 days.
traveled information in last 14 days
public, private, or community funded health care
Health care information that specifies the source of funding for a health care process.
indicator of health care source
A first-order administrative region of Mali.
region of Mali
A text entity of a zone number denotes to a geographic location.
a data item that is about a sequencing assay and is the ratio of the count of mapped reads to the total count of reads
obsolete unstranded unique average mapping coverage
obsolete unstranded unique proportion mapped reads
obsolete unstranded unique number mapped reads
obsolete unstranded unique average read length
obsolete unstranded non unique average mapping coverage
obsolete unstranded non unique proportion mapped reads
obsolete unstranded non unique number mapped reads
obsolete unstranded non unique average read length
obsolete first strand unique average mapping coverage
obsolete first strand unique proportion mapped reads
obsolete first strand unique number mapped reads
obsolete first strand unique average read length
obsolete first strand non unique unstranded unique average mapping coverage
obsolete first strand non unique unstranded unique proportion mapped reads
obsolete first strand non unique unstranded unique number mapped reads
obsolete first strand non unique unstranded unique average read length
obsolete second strand unique unstranded non unique average mapping coverage
obsolete second strand unique unstranded non unique proportion mapped reads
obsolete second strand unique unstranded non unique number mapped reads
obsolete second strand unique unstranded non unique average read length
obsolete second strand non unique first strand unique average mapping coverage
obsolete second strand non unique first strand unique proportion mapped reads
obsolete second strand non unique first strand unique number mapped reads
obsolete second strand non unique first strand unique average read length
A diagnosis based on parasites detected by microscopy (parasite density > 0) or LAMP assay (LAMP result is positive) in the absence of febrile (subjective fever and temperature>=38).
obsolete diagnosis of asymptomatic parasitemia
A diagnosis based on presence of parasites by LAMP assay when microscopy result was negative in the absence of subjective fever or documented elevated temperature.
obsolete diagnosis of submicroscopic parasitemia
A data item of the number of clinical visits during which the participant was diagnosed with asymptomatic parasitemia.
Person: Jie Zheng, Shon cade, Grant Dorsey
number of clinical visits resulting in an asymptomatic parasitemia diagnosis
A eukaryota in blood datum that specifies whether Plasmodium was detected by loop-mediated isothermal amplification.
presence of Plasmodium in blood by loop-mediated isothermal amplification
An information content entity is about blood smear not performed.
obsolete information on blood smear not performed
A presence of parasite that indicates that no parasite was detected in a specimen, either by loop-mediated isothermal amplification or blood smear.
obsolete negative blood smear and negative LAMP
An information content entity is about parasite status with negative blood smear and LAMP test is not performed.
information on negative blood smear and LAMP not done
An average value for the number of clinical visits of a patient with asymptomatic parasitemia based on calendar years.
average number of clinical visits with asymptomatic parasitemia diagnosis per year
A count of the number of courses of antibiotics received by the human or animal.
number of courses of antibiotics given
A symbol that denotes a specific family, rather than the physical home in which they live.
family identifier
A symbol denotes a physical structure/home/dwelling, rather than the human inhabitants.
dwelling identifier
An information content entity that idicates whether the hive was treated with tetracyline to prevent infection with the bacterial pathogen Paenibacillus larvae.
obsolete information on whether hive treated with tetracyline
An information indicates that samples from child or from the mother, or both.
obsolete information on whether specimen from mother or child
A number of courses of antibiotics given to a mother during delivery.
number of courses of antibiotics received by mom prior to delivery
A region of the 16S rRNA gene that was PCR amplified and sequenced.
obsolete 16S rRNA gene region for sequencing
An organism that realizes host role in laboratory.
lab host
obsolete bronchoalveolar lavage fluid specimen
A textual entity refers to a taxon or organism that is based on the normal language of everyday life; this kind of name is often contrasted with the scientific name for the same organism, which is Latinized.
An information content entity specify any molecular data associated with specimen source is available.
information on availability of molecular data
An information content entity indicates whether the specimen collection is original collection or follow up collection from same study subject.
information on original or follow up specimen collection
An information content entity specifies whether study subject signed informed consent for data collection and usage.
information on informed consent for data collection and usage
A categorical measurement datum that indicates whether Plasmodium falciparum were present in a specimen.
presence of Plasmodium falciparum
A categorical measurement datum that indicates whether gametocyte were present in a specimen.
presence of gametocyte
A categorical measurement datum that indicates whether Plasmodium knowlesi were present in a specimen.
presence of Plasmodium knowlesi
A categorical measurement datum that indicates whether Plasmodium malariae were present in a specimen.
presence of Plasmodium malariae
A categorical measurement datum that indicates whether Plasmodium ovale were present in a specimen.
presence of Plasmodium ovale
A categorical measurement datum that indicates whether parasite were present in a specimen.
presence of parasite
A categorical measurement datum that indicates whether Plasmodium vivax were present in a specimen.
presence of Plasmodium vivax
A time measurement datum measuring the time interval from the first specimen collection to the current specimen collection from the same study subject.
duration of study participation from first to current specimen collection
A scalar measurement datum that is about gametocyte density measured using microscopy.
gametocyte density by microscope
Plasmodium gametocytes, by RT-PCR result
A scalar measurement datum that is about gametocyte density measured by RT-PCR.
gametocyte density by RT-PCR
An assay that detects parasite gametocyte in a specimen.
A protocol that specifies how to measure the density of parasite gametocyte.
gametocyte detection protocol
a site in which a global positioning system receiver produces a data item specifying the location of the site
location where GPS coordinates were taken
An information content entity specify any host genetics data associated with specimen source is available.
information on availabilty of host genetics data
An information content entity specify any immune response data associated with specimen source is available.
information on availability of immune response data
An information content entity specify any parasite genetics data associated with specimen source is available.
information on availability of parasite genetics data
An information content entity specify any molecular data other than host genetics, parasite genetics, and immune response, associated with specimen source is available.
information on availability of other molecular data
A centrally registered identifier symbol assigned to a research project by Institutional Review Board (IRB). The IRB is a committee established to review and approve applications for research projects involving human subjects. The primary purpose of the IRB is to protect the rights and welfare of the human subjects.
IRB number
A scalar measurement datum that is about parasite density measured by PCR.
parasite density by PCR
A eukaryota in blood datum that is the output of a microscopy assay and is used to determine the presence of Plasmodium in the specimen.
Plasmodium in blood by microscopy assay datum
An assay that detects parasite in a specimen.
An assay that detects parasite in a specimen using PCR.
obsolete parasite detection by PCR assay
A categorical measurement datum that indicates whether asexual parasite were present in a specimen using PCR.
presence of asexual parasite by PCR
A categorical measurement datum that is the result of rapid diagnosis test using a value of positive or negative.
rapid diagnosis test result as positive or negative
The site where specimen collection taken place.
location of specimen collection
a research organization that is located in an area where malaria is endemic and is one of many centers established by the National institute of Allergy and Infectious Diseases with the following aims: to design and conduct multidisciplinary research on the epidemiology, transmission, and pathogenesis of malaria in its specific region, to design and conduct special projects to capitalize on new opportunities and emerging public health needs, and to build clinical research capacity and improve malaria control and prevention
National Institute of Allergy and Infectious Diseases
ICEMR organization
An assay that detects body temperature of an organism.
obsolete organismal body temperature measurement assay
An assay that is quick and easy in the diagnosis of malaria by detecting evidence of malaria parasites (antigens) in human blood.
Plasmodium falciparum gametocytes, by microscopy result
gametocyte density by microscope that is the output of an assay that realizes a measurand role that inheres in Plasmodium falciparum
Plasmodium falciparum gametocyte density by microscope
Plasmodium vivax gametocytes, by microscopy result
gametocyte density by microscope that is the output of an assay that realizes a measurand role that inheres in Plasmodium vivax
Plasmodium vivax gametocyte density by microscope
Plasmodium vivax gametocytes, by RT-PCR result
A gametocyte density by RT-PCR that is about Plasmodium vivax.
Plasmodium vivax gametocyte density by RT-PCR
Plasmodium vivax asexual stages, by PCR result
parasite density by PCR that is the output of an assay that realizes a measurand role that inheres in Plasmodium vivax
Plasmodium vivax parasite density by PCR
Plasmodium falciparum asexual stages, by microscopy result
parasite density by microscope that is the output of an assay that realizes a measurand role that inheres in Plasmodium falciparum
Plasmodium falciparum parasite density by microscope
Plasmodium vivax asexual stages, by microscopy result
parasite density by microscope that is the output of an assay that realizes a measurand role that inheres in Plasmodium vivax
Plasmodium vivax parasite density by microscope
Plasmodium falciparum asexual stages, by PCR result
parasite density by PCR that is the output of an assay that realizes a measurand role that inheres in Plasmodium falciparum
Plasmodium falciparum parasite density by PCR
An information content entity specifies whether study subject signed informed consent for future use of specimen.
information on informed consent for future use of specimen
A genotype information of parasite organism.
parasite organism genotype information
a data item that is about some virulence and is the count of infectious agents that kill half of a collection of human beings infected with the agents
virulence score (LDt50)
a data item that is about some virulence and is the proportion of the number of human beings with a disease (caused by the bearer of the virulence) that die of the disease
virulence score (slope)
A centrally registered identifier symbol assigned by the BEI Resources (https://www.beiresources.org/) to cultures and reagents for microbiology and infectious diseases research.
BEI repository identifier
A measurement datum of vertical distance below local surface, e.g. for sediment or soil samples depth is measured from sediment or soil surface, respectivly.
vertical distance below a surface measurement datum
An age since birth measurement datum measured in days.
age since birth in days
An information content entity about whether child exposed to antibiotics.
indicator of whether child exposed to antibiotics
a health care encounter in which a health care provider assists a mother in the birth of a child
baby delivery
A medication material that is used in the treatment and prevention of bacterial infections. It may either kill or inhibit the growth of bacteria.
antibiotics
An information content entity about whether bee colony treated with tetracycline.
indicator of whether bee colony treated with tetracycline
main source of nutrition for a child
child's diet
main source of nutrition for a child for each month
child's diet by month
An information content entity about any drug used by a participant under investigation and the frequency of usage.
drug usage information
An information content entity about environmental material, environmental feature, environmental system, etc.
environment information
household information that specifies whether the household relocated during its time under investigation
indicator of whether a family moved
an information content entity that is about the bearer of a host role
host information
the diet of an animal that is the bearer of a host role
type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types
host's diet
An organism that has host role
host organism
a categorical value specification that is about a collection of bee larvae and specifies whether tetracycline was administered to the larvae
indicator of whether bee larvae treated with tetracycline
mass measurement datum is about a host that measured at specimen collection process
host mass measurement datum at specimen collection
An information content entity which indicates that samples are from the child or from the mother, or both.
indicator of whether specimen from mother or child
a count that is about a dwelling and is also the result of counting the instances of a child that occupies the dwelling
number of child occupants in a dwelling
An information content entity about disposal of human excreta material.
information on disposal of human excreta material
a ratio that is about a dwelling, is expressed as a percent, has a count of adult occupants of the dwelling as the numerator, and has a count of all occupants of the dwelling as the denominator
percent adult occupants in a dwelling
a ratio that is about a dwelling, is expressed as a percent, has a count of male occupants of the dwelling as the numerator, and has a count of all occupants of the dwelling as the denominator
percent male occupants in a dwelling
a categorical value specification that specifies whether a mother received an antimicrobial agent
indicator of whether antibiotics given to mother of participant
an information content entity that is about an antimicrobial agent given to a mother and specifies the agent by chemical compound
information on class of antibiotics given to mom
an information content entity that specifies the trimester of a pregnancy for which a mother receives an antimicrobial agent
information on trimester antibiotics given to mom
An information content entity about presence of pets or farm animals in the environment of subject, if yes the animals should be specified; can include multiple animals present.
environmental pets or farm animals information
a protocol that, when concretized, is realized in an assay that uses chemical or biological means to infer the sequence of a biomaterial
An information content entity about In which batch were samples sequenced together.
sequencing batch information
an information content entity that is about an investigation and has as parts only the most significant information content entities that result from the investigation
summary information of investigation
a symbol that denotes the bearer of a participant under investigation role
an information content entity that is about weight loss occurring in a three-month period
information on weight loss in last three months
a protocol such that, if it is concretized and its concretization is realized, its concretization is realized in a planned process that has as its objective collecting a specimen
an information content entity about the bearer of a specimen role
specimen information
symptom or sign information that results from an examination of either the skin of the patient or a process in which the skin participates
skin symptom or sign information
an information content entity that is about a specimen collection process
specimen source information
an information content entity that specifies whether an animal is also human
information specifying human or animal
a specimen collection time measurement datum that is the measure of a time when specimens are collected after an infection starts
obsolete specimen collection time post infection
skin symptom or sign information that is about the thickness of the ear of the patient
ear thickness
skin symptom or sign information that specifies the rate at which water passes through the epidermis of the patient into the air
transepidermal water loss
a categorical measurement datum that is about the skin of a human being and specifies whether the skin is either dry, moist, or sebaceous
skin type swabbed
a categorical value specification that is about a portion of skin that has a disorder hypothesized to be clinically significant. It specifies the degree to which a portion of skin is clinically abnormal.
skin pathology score
a count of the number of instances of a treatment
number of treatments
skin symptom or sign information that is about increased thickness of the skin
degree of skin thickening
skin symptom or sign information that specifies the size of a disorder on the skin of a patient
lesion size
skin symptom or sign information that is about a lesion on the axilla of a patient and specifies the extent of damage to the tissue before a treatment to alleviate the lesion
axillary lesion score before treatment
skin symptom or sign information that is about a lesion on the axilla of a patient and specifies the extent of damage to the tissue during a treatment to alleviate the lesion
axillary lesion score during treatment
skin symptom or sign information that is about a lesion on the axilla of a patient and specifies the extent of damage to the tissue that remains after a treatment to alleviate the lesion
axillary lesion score after treatment
skin symptom or sign information that is about a lesion on the groin of a patient and specifies the extent of damage to the tissue before a treatment to alleviate the lesion
groin lesion score before treatment
skin symptom or sign information that is about a lesion on the groin of a patient and specifies the extent of damage to the tissue during a treatment to alleviate the lesion
groin lesion score during treatment
skin symptom or sign information that is about a lesion on the groin of a patient and specifies the extent of damage to the tissue that remains after a treatment to alleviate the lesion
groin lesion score after treatment
skin symptom or sign information that is about a lesion on a pinna of a patient and specifies the extent of damage to the tissue before a treatment to alleviate the lesion
pinna lesion score before treatment
skin symptom or sign information that is about a lesion on a pinna of a patient and specifies the extent of damage to the tissue during a treatment to alleviate the lesion
pinna lesion score during treatment
skin symptom or sign information that is about a lesion on a pinna of a patient and specifies the extent of damage to the tissue that remains after a treatment to alleviate the lesion
pinna lesion score after treatment
treatment outcome information that specifies whether the treatment of a skin lesion was successful
information on whether skin lesion cured after treatment
a time measurement datum that represents the time interval between the first appearance of a skin lesion and the time it is swabbed for specimen collection
skin lesion duration
a categorical value specification that specifies the degree of erythema
degree of skin redness
skin symptom or sign information that specifies the area of a part of a patient's skin that participates in an inflammation process
degree of skin inflammation
a measurement datum that is a measurement of the hydration of the outer epidermis
Pubmed 2459872 & https://academic.oup.com/jn/article/134/8/2110S/4688890
corneometry
an information content entity that specifies the degree to which alopecia has been realized in a patient
degree of hairloss
a skin symptom or sign information that specifies whether the patient has atopic dermatitis
information on whether affected by atopic dermatitis
A diagnosis that is documented during the hospital admission process.
diagnosis at hospital admission
a population that is the bearer of a study group role
study group
a symbol that denotes a cage that has the function to keep an animal that is the bearer of a participant under investigation role
animal cage number for experiment
a symbol that denotes a cage that has the function to keep a mouse that is the bearer of a participant under investigation role
A z-score of the divergence of an experimental BMI measurement from the average BMI value for an organism of the same age.
BMI-for-age z-score
Household information that specifies a planned process with the objective to maintain health and prevent the spread of disease.
This IRI was previously mistakenly assigned to 'antimalarial'.
household hygiene information
An information content entity about disposal of excreta material produced by a child.
information on disposal of child excreta material
Assay that subjects a feces specimen to a test for microorganisms.
Person: Cristian Cocos, Jie Zheng, Chris Stoeckert
An information content entity that is about the water usage of a household.
information on household water
A biological process that breeds a plant or animal by natural processes from the parent stock.
Term added for annotation of a Crypto SNP dataset but the term is not used.
A genotype information which is about cluster of differentiation 36 (CD36) gene, which encodes an integral membrane protein in many cell types and a member of the scavenger receptor family that imports fatty acids into cells (Canton et al., 2013). CD36 is also an endothelial receptor for binding of erythrocytes infected with P. falciparum.
Grant Dorsey: The human CD36 antigen is an integral membrane protein in many cell types and a member of the scavenger receptor family that imports fatty acids into cells (Canton et al., 2013). CD36 is also an endothelial receptor for binding of erythrocytes infected with P. falciparum; this cytoadhesion is believed to be an important feature of the virulence of falciparum malaria, due both to its prevention of clearance of infected erythrocytes by the spleen and to local effects of cytoadhering parasites (Newbold et al., 1999). Importantly, expression of CD36 is low in the brain, even in the setting of cerebral malaria (Silamut et al., 1999), suggesting that binding to CD36 is most relevant in non-cerebral forms of severe malaria. CD36 is also believed to be an important macrophage pattern recognition receptor that mediates innate recognition and clearance of infected erythrocytes (Cabrera et al., 2014). Considering our current understanding, CD36 expression might be seen to contribute to malaria severity, by mediating cytoadherence, or to help control malaria, via immune effects. Results with murine malaria models have been complex; mice with decreased CD36-mediated cytoadherence had decreased growth of P. berghei (Fonager et al., 2012), but CD36-deficient mice had increased risk of fatal P. chabaudi malaria (Patel et al., 2007). Considering human populations, many CD36 polymorphisms, including nonsense mutations that prevent production of the molecule, are common, particularly in African populations (Aitman et al., 2000). However, attempts to identify associations between common polymorphisms and malaria risk have led to inconsistent results, with evidence for enhancement of(Aitman et al., 2000; Omi et al., 2002), no effect (Fry et al., 2009), or protection from (Das et al., 2009; Omi et al., 2003; Pain et al., 2001; Sinha et al., 2008) severe malaria with different polymorphisms. CD3T188G is a polymophism on the human CD36 gene.
cluster of differentiation 36 genotype
An information content entity is about a process.
information on process
A planned process that an organism exposed to that are not one of the variables under study.
A treatment to alleviate the signs and symptoms associated with malaria.
malaria treatment
A time measurement datum of duration of an individual acquires, develops, or first experiences a condition or symptoms of a disease or disorder.
time to onset
A time measurement datum that specifies when the DNA was extracted
date of DNA extraction
The measurement datum generated by Inverse polymerase chain reaction (Inverse PCR).
iPCR datum
A time measurement datum of duration of the observation at the end of an observation period.
duration of observation period
A time measurement datum of a person first diagnosed as malaria
time to first malaria diagnosis
A time measurement datum of the duration for reinfection.
time to reinfection
A genotype information about 60 kDa glycoprotein (gp60) gene.
gp60 genotype
A specimen collection time measurement datum in year.
specimen collection time in year
An information content entity of multiple blood smear results during an observation period.
information on blood smear result
A quality inheres in parasite organism.
parasite phenotype
A genotype information of fungus.
fungal organism genotype information
A Fungus that is bred to have some uniform behavioral, morphological, physiological, or genetic characteristics with similarly bred Fungus
fungal strain
A Candida albicans that is bred to have some uniform behavioral, morphological, physiological, or genetic characteristics with similarly bred Candida albicans
A parasite that is bred to have some uniform behavioral, morphological, physiological, or genetic characteristics with similarly bred parasite organisms
parasite strain
A data item that indicates whether some organism is present in a specimen.
"Present" in this definition means 'located in' or 'part of' the specimen.
presence of organism in specimen
An information content entity that is about some quality, risk, or access to health care that inheres in a human being and is deemed clinically significant by the World Health Organization, which uses this entity to categorize each of their individual core health indicators, based on the type of quality, risk, or access.
WHO 2018 Global Reference List of 100 Core Health Indicators
World Health Organization core health indicator subdomain
An information content entity that is about data collected at the household level on multiple occasions.
household repeated measure
Skin symptom or sign information that is about a lesion on the groin of a patient and specifies the extent of damage to the tissue.
groin lesion score
Skin symptom or sign information that is about a lesion on an axilla of a patient and specifies the extent of damage to the tissue.
axillary lesion score
Skin symptom or sign information that is about a lesion on a pinna of a patient and specifies the extent of damage to the tissue.
pinna lesion score
A mosquito feeds on a human whereby the human acquires the blood host role for the mosquito blood meal.
A role borne by an organism that is gained during a process in which another organism ingests blood as food from the organism.
A time measurement datum that is about the duration of exposure to an insecticide that results in the death of 50% of a population of insects.
lethal insecticide time 50
A clinical finding of a death that has been confirmed to be likely caused by COVID-19.
finding of death from COVID-19
An information content entity that is about a treatment.
treatment information
An information content entity identifying an assay and specifying whether it was performed.
information on whether assay performed
An assay that detects parasite organisms in a specimen that are in the sporozoite stage.
An information content entity about the groups of participants that are randomized to receive an intervention in a trial.
study cluster information
A blood microbiology datum that indicates whether some organism was detected.
presence of organism in blood
A cerebrospinal fluid microbiology datum that indicates whether some organism was detected.
presence of organism in cerebrospinal fluid
A endotracheal tube aspirate microbiology datum that indicates whether some organism was detected.
presence of organism in endotracheal aspirate
A feces microbiology datum that indicates whether some organism was detected.
presence of organism in feces
A induced sputum microbiology datum that indicates whether some organism was detected.
presence of organism in induced sputum
A lung microbiology datum that indicates whether some organism was detected.
presence of organism in lung
A nasopharyngeal or oropharyngeal swab microbiology datum that indicates whether some organism was detected.
presence of organism in nasopharynx or oropharynx
A pleural fluid microbiology datum that indicates whether some organism was detected.
presence of organism in pleural fluid
A umbilical cord blood microbiology datum that indicates whether some organism was detected.
presence of organism in umbilical cord blood
A urine microbiology datum that indicates whether some organism was detected.
presence of organism in urine
A 16S rRNA sequencing assay in which primers target the V1-V2 portion of the 16s gene.
16S rRNA sequencing assay targeting V1-V2 region
16S rRNA sequencing assay in which primers target the V1-V3 portion of the 16s gene
16S rRNA sequencing assay targeting V1-V3 region
16S rRNA sequencing assay in which primers target the V2 portion of the 16s gene
16S rRNA sequencing assay targeting V2 region
16S rRNA sequencing assay in which primers target the V3-V4 portion of the 16s gene
16S rRNA sequencing assay targeting V3-V4 region
16S rRNA sequencing assay in which primers target the V3-V5 portion of the 16s gene
16S rRNA sequencing assay targeting V3-V5 region
16S rRNA sequencing assay in which primers target the V4 portion of the 16s gene
16S rRNA sequencing assay targeting V4 region
A placental blood microbiology datum that indicates whether some organism was detected.
presence of organism in placental blood
A data transformation that uses data from a whole metagenome sequencing assay and CORRAL (for Clustering Of Related Reference ALignments) software to specify taxa of Eukaryota in a specimen.
eukaryote detection and abundance analysis using CORRAL software
An information content entity that is about a health care process.
health care information
A participant under investigation that is the female biological parent of a participant under investigation.
maternal participant under investigation
A collecting specimen from organism in which the organism is a maternal participant under investigation.
maternal specimen collection process
A participant under investigation that is an offspring of a participant under investigation.
offspring participant under investigation
A collecting specimen from organism in which the organism is an offspring participant under investigation.
offspring specimen collection process
A data item that is the specified output of a maternal urine microbiology assay.
maternal urine microbiology datum
A urine specimen that is the specified output of a maternal specimen collection process.
maternal urine specimen
A saliva specimen that is the specified output of a maternal specimen collection process.
maternal saliva specimen
A feces specimen that is the specified output of a maternal specimen collection process.
maternal feces specimen
A feces assay that has a maternal feces specimen as evaluant.
maternal feces assay
a time measurement datum specifying the date of a clinical visit scheduled for sixty days after a treatment
date of 60-day follow-up
A parasitemia measurement in which the number of parasitized erythrocytes is divided by the number of all erythrocytes in a specified sample of blood, and the result presented as a ratio, fraction, quotient or percentage.
Christian Stoeckert https://orcid.org/0000-0002-5714-991X
John Judkins https://orcid.org/0000-0001-6595-0902
parasitized erythrocyte count to total erythrocyte count ratio
Metagenome pathway and function analysis
A data transformation of metagenome input sequence data involving mapping to genes with full Enzyme Commision (EC) number enzyme classifications and calculation of pathways.
A data item that is the output of a metagenome pathway and function analysis for the number of copies of genes annotated at the finest (4th level) EC classification.
4th level EC metagenome abundance data
Metagenome enzyme pathway abundance data
A data item that is the output of a metagenome pathway and function analysis for the number of copies of a pathway defined by EC classifications.
A data item that is the output of a metagenome pathway and function analysis for gene coverage in a pathway defined by EC classifications.
metagenome enzyme pathway coverage data
A data transformation of input sequence data to obtain the fraction of relative abundance of organisms.
relative taxonomic abundance analysis
A data item that is the output of a relative taxonomic abundance analysis for organisms grouped at the level of kingdom.
relative abundance of kingdom data
A data item that is the output of a relative taxonomic abundance analysis for organisms grouped at the level of phylum.
relative abundance of phylum data
A data item that is the output of a relative taxonomic abundance analysis for organisms grouped at the level of class.
relative abundance of class data
A data item that is the output of a relative taxonomic abundance analysis for organisms grouped at the level of order.
relative abundance of order data
A data item that is the output of a relative taxonomic abundance analysis for organisms grouped at the level of family.
relative abundance of family data
A data item that is the output of a relative taxonomic abundance analysis for organisms grouped at the level of genus.
relative abundance of genus data
A data item that is the output of a relative taxonomic abundance analysis for organisms grouped at the level of species.
relative abundance of species data
A data transformation of input sequence data to obtain a mean species diversity.
alpha diversity taxonomic analysis
A data item that is the output of an alpha diversity taxonomic analysis based on the Shannon index of diversity.
Shannon-indexed alpha diversity data
inverse Simpson-indexed alpha diversity data
A data item that is the output of an alpha diversity taxonomic analysis based on the inverse Simpson index of diversity.
A taxon detected by sequence match that indicates whether a plant taxon was detected.
plant taxon detected by sequence match
A taxon detected by sequence match that indicates whether an animal taxon was detected.
animal taxon detected by sequence match
Protist taxon detected by sequence match
A taxon detected by sequence match that indicates whether a protist taxon was detected.
A data item that indicates whether a method applied to data coming from a sequencing assay of the sample has detected a taxon through identifying sequences associated with organisms of a particular taxonomic grouping.
taxon detected by sequence match
A taxon detected by sequence match that indicates whether a fungal taxon was detected.
fungal taxon detected by sequence match
A data item of the normalized number of sequences that match a specific taxon.
normalized number of taxon-specific sequence matches
A data transformation of input sequence data to obtain the absolute abundance of organisms.
absolute taxonomic abundance analysis
A data item that is the output of an absolute taxonomic abundance analysis for organisms grouped at the level of kingdom.
absolute abundance of kingdom data
A data item that is the output of an absolute taxonomic abundance analysis for organisms grouped at the level of phylum.
absolute abundance of phylum data
A data item that is the output of an absolute taxonomic abundance analysis for organisms grouped at the level of class.
absolute abundance of class data
A data item that is the output of an absolute taxonomic abundance analysis for organisms grouped at the level of order.
absolute abundance of order data
A data item that is the output of an absolute taxonomic abundance analysis for organisms grouped at the level of family.
absolute abundance of family data
A data item that is the output of an absolute taxonomic abundance analysis for organisms grouped at the level of genus.
absolute abundance of genus data
A data item that is the output of an absolute taxonomic abundance analysis for organisms grouped at the level of species.
absolute abundance of species data
Antibiotic administration before stool collection
A planned process in which a feces specimen is collected from an organism after the administration of an antibiotic to the organism, in order to determine effects of the antibiotic.
antibiotic administration preceding feces collection
An information content entity that is about a subject pairing of two participants for a case-control study design
information on case matching
A clinical history that is about a treatment for diarrhea.
previous diarrheal treatment datum
an information content entity that is about a realization of diarrhea
information on diarrheal episode
Treatment whose aim is to restore the normal hydration state of a living organism.
rehydration treatment
environmental system associated with the dwelling used by humans.
environment associated with human dwelling
study participant information that specifies details of the study design execution in which the human participant under investigation is participating
study participant administrative information
An information content entity that mentions an eligiblity criterion
information on eligibility criterion
an information content entity that is about a human being in the community of a human participant under investigation and identifies the relationship between them both
information on relation to participant
A data item that is about a quality of a fecal specimen
fecal specimen quality data item
Specimen collection process aimed at collecting a feces specimen.
feces specimen collection process
Antibiotic administered before stool collection
an information content entity that specifies an antibiotic that is administered to a human participant under investigation, which precedes stool collection from the participant
information specifying antibiotic administered before stool collection
Organization that undertakes a clinical study at some point in time.
A participant identifier that denotes the bearer of a case-control study case role.
case participant identifier
Site where a human life process ended.
location of death
A mass measurement datum that is the result of measuring the combined mass of a human participant under investigation and a caregiver of that participant.
caregiver and participant combined mass measurement datum
A mass measurement datum that is the result of measuring the mass of a caregiver of a human participant under investigation.
caregiver of participant mass measurement datum
A length measurement datum that is the result of the first in a series of assays measuring the height of the same material entity.
first height measurement datum
A length measurement datum that is the result of the second in a series of assays measuring the height of the same material entity.
second height measurement datum
A length measurement datum that is the result of the third in a series of assays measuring the height of the same material entity.
third height measurement datum
an average value that is the specified output of a data transformation that has as input only length measurement data about height
mean height
A center value that is the specified output of a median calculation that has as input only length measurement data about height
median height
a length measurement datum that is the result of the first in a series of assays measuring the length around the same upper arm, such that the measurement is taken midway along the upper arm
The Mother and Child Health and Education Trust
first mid-upper arm circumference datum
a length measurement datum that is the result of the second in a series of assays measuring the length around the same upper arm, such that the measurement is taken midway along the upper arm
second mid-upper arm circumference datum
A length measurement datum that is the result of the third in a series of assays measuring the length around the same upper arm, such that the measurement is taken midway along the upper arm
third mid-upper arm circumference datum
An average value of two or more mid-upper arm circumference data of the same human participant under investigation
mean mid-upper arm circumference
A center value of one or more mid-upper arm circumference data of the same human participant under investigation
median mid-upper arm circumference
A temperature measurement datum that is about the temperature of an axilla
obsolete axillary temperature measurement datum
a rate measurement datum that is about a human participant under investigation and is the specified output of the first of a series of countings of instances of the participant's respiration
first respiratory rate measurement datum
a rate measurement datum that is about a human participant under investigation and is the specified output of the second of a series of countings of instances of the participant's respiration
second respiratory rate measurement datum
an average value that is the specified output of a data transformation that has two or more respiratory rates of the same human participant under investigation as specified input
average respiratory rate
Container used by humans to drink water.
water container
Information Content entity that is a boolean-valued measurement datum, outcome of a chlorine testing assay that aims at testing a body of drinking water for a specified minimum concentration of Chlorine.
chlorine test result
Site where humans wash their hands.
location of hand washing
An information content entity that specifies whether a human participant under investigation is currently a medication-taking patient
indicator of whether participant receiving medication
A time measurement datum of the date encompassing a defecation
date of defecation
a quality of water composition, shape, or structure that inheres in fecal material
stool consistency
A time measurement datum of the date of the first in a series of antibiotic administrations to a human participant under investigation
date of first antibiotic administration
A time measurement datum of the time of the first in a series of antibiotic administrations to a human participant under investigation
time of first antibiotic administration to human participant under investigation
A time measurement datum that is the result of measuring the duration of a diarrheal episode
duration of diarrheal episode
A measurement datum that results from measuring the volume of feces excreted during an instance of defecation.
Person: Cristian Cocos, Jie Zheng, Chris Stoeckert, John Judkins
feces volume measurement datum
a time measurement datum of the date at which a dehydration treatment is administered
date of rehydration
a time measurement datum of the time of day at which a dehydration treatment is administered
time of rehydration
A time measurement datum of the duration of a health care encounter occuring in a hospital facility.
duration of hospitalization
A symptom at enrollment information about a symptom that was experienced within seven days prior to the time of enrollment
symptom in last seven days information
A symptom or sign information that is about a symptom experienced after a disease course has started
symptom since illness began information
Process of feeding of babies and young children with milk from a woman's breast.
Child study subject identifier received upon enrolling into a healthcare study for the first time.
child study subject identifier at first enrollment
An information content entity that is about a treatment for diarrhea that precedes any treatment for diarrhea given to the same person during a clinical visit.
information on diarrhea treatment before clinical visit
an information content entity that specifies how the money was raised to cover the cost of a health care encounter
information on raising money for health care encounter
A previous diarrheal treatment datum that is about the person or place from which the treatment is sought
information on where diarrheal treatment sought
A categorical value specification that specifies whether the value of an anthropometric information content entity lies outside a specified range
anthropometric value range specification
Diarrhea treatment given in health center
An information content entity that is about a treatment for diarrhea that is administered in a health care facility
information on diarrhea treatment in health care facility
Diarrhea treatment by prescription at home
An information content entity that is about a treatment provided by a health care prescription for a human participant under investigation for diarrhea
information on diarrhea treatment by prescription
Previous diagnosis noted at 60 day follow-up visit
A diagnosis of a human participant under investigation, two months before the participant's follow-up visit.
diagnosis previous to two month follow-up
Information on case matching that denotes the sex of the case subject
information on sex of matched case
The date of birth of a case subject in a case-control study
date of birth of matched case
Current diarrhea episode began within the last 7 days
An eligibility criterion indicating an episode of diarrhea starting within the past seven days.
eligibility criterion of diarrhea episode starting with past 7 days
A categorical value specification that specifies whether a human participant under investigation meets requirements for human subject enrollment
indicator of whether participant eligible for enrollment
a categorical measurement datum that is about a maximum fever temperature in Celsius and specifies whether its value is at least 37.5
presence of maximum fever temperature of at least 37.5 degrees
a categorical value specification that specifies whether an enzyme linked immunosorbent assay was performed with the objective of determining whether a specimen contains Adenovirus
indicator of whether Adenovirus ELISA performed
a categorical value specification that specifies whether an enzyme linked immunosorbent assay was performed with the objective of determining whether a specimen contains Astrovirus
indicator of whether Astrovirus ELISA performed
a categorical value specification that specifies whether an enzyme linked immunosorbent assay was performed with the objective of determining whether a specimen contains Rotavirus
indicator of whether Rotavirus ELISA performed
Modified acid stain microscopy performed
a categorical value specification that specifies whether a modified acid fast staining method was performed
modified acid fast staining method performed
indicator of whether modified acid fast staining method performed
A count of feces assays evaluating the same specimen.
number of feces assays
a categorical value specifiction that specifies whether a reverse transcription polymerase chain reaction assay was performed with the objective of determining whether a specimen contains Norovirus
indicator of whether Norovirus RT-PCR performed
a categorical value specification that specifies whether an enzyme linked immunosorbent assay was performed with the objective of determining whether a specimen contains Cryptosporidium
indicator of whether Cryptosporidium ELISA performed
a categorical value specification that specifies whether an enzyme linked immunosorbent assay was performed with the objective of determining whether a specimen contains Entamoeba histolytica
indicator of whether Entamoeba histolytica ELISA performed
a categorical value specification that specifies whether an enzyme linked immunosorbent assay was performed with the objective of determining whether a specimen contains Giardia
indicator of whether Giardia ELISA performed
A eukaryota in feces datum by enzyme-linked immunosorbent assay datum that specifies whether the virus was detected.
presence of Adenoviridae in feces by enzyme-linked immunosorbent assay
An Aeromonas in feces datum that specifies whether Aeromonas was detected, without specifying the taxon further.
presence of Aeromonas unspecified in feces
A eukaryota in feces datum in feces that specifies whether Ascaris lumbricoides was detected by microscopy assay.
presence of Ascaris lumbricoides in feces by microscopy assay
An Astrovirus in feces by enzyme-linked immunosorbent assay datum that specifies whether the virus was detected.
presence of Astrovirus in feces by enzyme-linked immunosorbent assay
A eukaryota in feces datum that specifies whether Trichuris trichiura was detected by microscopy assay.
presence of Trichuris trichiura in feces by microscopy assay
A eukaryota in feces datum that specifies whether Balantioides cf. coli was detected by microscopy assay.
presence of Balantioides coli in feces by microscopy assay
A bacteria in feces datum that is used to determine the presence of Aeromonas in the specimen.
Aeromonas in feces datum
A bacteria in feces datum that is the output of an enzyme-linked immunosorbent assay and is used to determine the presence of Campylobacter in the specimen.
Campylobacter in feces by enzyme-linked immunosorbent assay datum
A bacteria in feces datum that is used to determine the presence of Campylobacter in the specimen.
Campylobacter in feces datum
Escherichia coli, by bacteriology result
A bacteria in feces datum that is used to determine the presence of Escherichia coli in the specimen.
Escherichia coli in feces datum
A bacteria in feces datum that is used to determine the presence of Salmonella in the specimen.
Salmonella in feces datum
A bacteria in feces datum that is used to determine the presence of Shigella in the specimen.
Shigella in feces datum
A bacteria in feces datum that is used to determine the presence of Vibrio in the specimen.
Vibrio in feces datum
A eukaryota in feces datum that specifies whether Chilomastix mesnili was detected by microscopy assay.
presence of Chilomastix mesnili in feces by microscopy assay
A eukaryota in feces datum that specifies whether Cyclospora was detected by microscopy assay.
presence of Cyclospora in feces by microscopy assay
A Entamoeba histolytica in feces by enzyme-linked immunosorbent assay datum that specifies whether the organism was detected.
presence of Entamoeba histolytica in feces by enzyme-linked immunosorbent assay
A eukaryota in feces datum that specifies whether Endolimax nana was detected by microscopy assay.
presence of Endolimax nana in feces by microscopy assay
A eukaryota in feces datum that specifies whether Enterobius vermicularis was detected by microscopy assay.
presence of Enterobius vermicularis in feces by microscopy assay
A virus in feces datum that is the output of an enzyme-linked immunosorbent assay and is used to determine the presence of Adenovirus in the specimen.
Adenovirus in feces by enzyme-linked immunosorbent assay datum
A virus in feces datum that is the output of an enzyme-linked immunosorbent assay and is used to determine the presence of Astrovirus in the specimen.
Astrovirus in feces by enzyme-linked immunosorbent assay datum
A eukaryota in feces datum that specifies whether Hymenolepis diminuta was detected by microscopy assay.
presence of Hymenolepis diminuta in feces by microscopy assay
A eukaryota in feces datum that specifies whether Rodentolepis nana was detected by microscopy assay.
presence of Rodentolepis nana in feces by microscopy assay
A eukaryota in feces datum that specifies whether Ancylostomatoidea was detected by microscopy assay.
presence of Ancylostomatoidea in feces by microscopy assay
A eukaryota in feces datum that specified whether Iodamoeba butschlii was detected by microscopy assay.
presence of Iodamoeba butschlii by microscopy assay
A eukaryota in feces datum that specifies whether Entamoeba coli was detected by microscopy assay
presence of Entamoeba coli in feces by microscopy assay
A virus in feces datum that specifies whether Norovirus was detected by real time polymerase chain reaction assay.
presence of Norovirus in feces by real time polymerase chain reaction assay
A virus in feces datum that specifies whether Norovirus GI was detected by real time polymerase chain reaction assay.
presence of Norovirus GI in feces by real time polymerase chain reaction assay
A virus in feces datum that specifies whether Norovirus GII was detected by real time polymerase chain reaction assay.
presence of Norovirus GII in feces by real time polymerase chain reaction assay
The threshold cycle that is the specified output of a multiplex real time polymerase chain reaction assay that has the objective of determining the number of Norovirus GII in a feces specimen.
multiplex qPCR threshold cycle for Norovirus GII in feces
The threshold cycle that is the specified output of a multiplex real time polymerase chain reaction assay that has the objective of determining the number of Norovirus GI in a feces specimen.
multiplex qPCR threshold cycle for Norovirus GI in feces
The threshold cycle that is the specified output of a multiplex real time polymerase chain reaction assay that has the objective of determining the number of Norovirus in a feces specimen.
multiplex qPCR threshold cycle for Norovirus in feces
A eukaryota in feces datum that is the output of an enzyme-linked immunosorbent assay and is used to determine the presence of Cryptosporidium in the specimen.
Cryptosporidium in feces by enzyme-linked immunosorbent assay datum
a categorical measurement datum that specifies whether Entamoeba histolytica was detected by an enzyme-linked immunosorbent assay
obsolete presence of Entamoeba histolytica by ELISA
A eukaryota in feces datum that is the output of an enzyme-linked immunosorbent assay and is used to determine the presence of Giardia in the specimen.
Giardia in feces by enzyme-linked immunosorbent assay datum
Plesiomonas shigelloides, by bacteriology
A bacteria in feces datum that specifies whether Plesiomonas shigelloides was detected.
presence of Plesiomonas shigelloides in feces
A virus in feces datum that specifies whether Rotavirus was detected by enzyme-linked immunosorbent assay.
presence of Rotavirus in feces by enzyme-linked immunosorbent assay
A Salmonella in feces datum that specifies whether Salmonella was detected, without specifying the taxon further.
presence of Salmonella unspecified in feces
A eukaryota in feces datum that specifies whether Schistosoma was detected by microscopy assay.
presence of Schistosoma in feces by microscopy assay
A Shigella in feces datum that specifies whether Shigella was detected, without specifying the taxon further.
presence of Shigella unspecified in feces
Strongyloides stercoralis, by microscopy
A eukaryota in feces datum that specifies whether Strongyloides stercoralis was detected by microscopy assay.
presence of Strongyloides stercoralis in feces by microscopy assay
An Escherichia coli in feces datum that specifies whether Escherichia coli was detected by polymerase chain reaction assay.
presence of Escherichia coli in feces by polymerase chain reaction assay
A eukaryota in feces datum that specifies whether Taenia was detected by microscopy assay.
presence of Taenia in feces by microscopy assay
A Vibrio in feces datum that specifies whether Vibrio was detected, withou specifying the taxon further.
presence of Vibrio unspecified in feces
Yersinia enterocolitica, by bacteriology
A bacteria in feces datum that specifies whether Yersinia enterocolitica was detected.
presence of Yersinia enterocolitica in feces
A bacteria in feces datum that specifies whether bacteria were detected, without further specifying the taxon or assay.
presence of unspecified bacteria in feces by unspecified assay
A feces microbiology datum that specifies whether a parasite organism was detected, without further specifying the taxon or assay.
presence of unspecified parasite organism in feces by unspecified assay
A feces microbiology datum that specifies whether a pathogen was detected, without further specifying the taxon or assay.
presence of unspecified pathogen in feces by unspecified assay
Any pathogen (excluding NRV), by any method
A feces microbiology datum that specifies whether a pathogen excluding Norovirus was detected by an unspecified assay.
presence of any pathogen excluding Norovirus in feces by unspecified assay
A count of species of bacteria in a feces specimen.
number of bacteria species in feces specimen
A count of species of parasite organisms in a feces specimen.
number of parasite organism species in feces specimen
Pathogen count, analysis monthly and per protocol diarrheal stools
A count of species of pathogen in a feces specimen.
number of pathogen species in feces specimen
A count of species of virus in a feces specimen.
number of virus species in feces specimen
A feces microbiology datum that specifies whether a virus was detected, without further specifying the taxon or assay.
presence of unspecified virus in feces by unspecified assay
Any virus (excluding NRV), by any method
A virus in feces datum that specifies whether a virus excluding Norovirus was detected.
presence of virus excluding Norovirus in feces
Any parasites, by modified acid stain microscopy
A feces microbiology datum that specifies whether a parasite organism was detected by modified acid-fast stain microscopy assay.
presence of parasite organism in feces by modified acid-fast stain microscopy assay
A Campylobacter in feces datum that specifies whether the organism was detected by polymerase chain reaction assay.
presence of Campylobacter in feces by polymerase chain reaction assay
A Campylobacter in feces by enzyme-linked immunosorbent assay datum that specifies whether the organism was detected.
presence of Campylobacter in feces by enzyme-linked immunosorbent assay
A Cryptosporidium in feces by enzyme-linked immunosorbent assay datum that specifies whether the organism was detected.
presence of Cryptosporidium in feces by enzyme-linked immunosorbent assay
Cryptosporidium, by modified acid stain microscopy result
A eukaryota in feces datum that is the output of a modified acid-fast stain microscopy and is used to determine the presence of Cryptosporidium in the specimen.
Cryptosporidium in feces by modified acid-fast stain microscopy datum
Entamoeba histolytica, by microscopy result
A eukaryota in feces datum that is the output of a microscopy assay and is used to determine the presence of Entamoeba histolytica in the specimen.
Entamoeba histolytica in feces by microscopy assay datum
A Giardia in feces by enzyme-linked immunosorbent assay datum that specifies whether the organism was detected.
presence of Giardia in feces by enzyme-linked immunosorbent assay
A eukaryota in feces datum that is the output of a microscopy assay and is used to determine the presence of Giardia lamblia in the specimen.
Giardia lamblia in feces by microscopy assay datum
A eukaryota in feces datum that specifies whether Isospora was detected by microscopy assay.
presence of Isospora in feces by microscopy assay
A feces assay datum of the concentration of myeloperoxidase.
feces myeloperoxidase concentration
A collecting specimen from organism that has the objective to obtain a blood specimen.
blood specimen collection process
An information content entity that specifies whether a dairy food product was consumed by a study participant yesterday.
indicator of dairy food product consumption yesterday
Information on process that is about suckling behavior.
Person: John Judkins and Chris Stoeckert
information on suckling behavior
Any measurement of the calories (usually large calories, kilogram calories, dietary calories, or nutritional calories) consumed by an organism. a large calorie is the amount of energy needed to raise the temperature of one kilogram of water by one degree celsius, a measure of the energy which an organism can derive by metabolizing the source of those calories, i.e., a food, a drink, or both.
calorie intake measurement
A feces assay that measures some material entity, the amount of which could indicate the occurence of an inflammatory reponse in the organism from which the specimen was collected.
feces assay to detect inflammation
An information content entity that is about an acute manifestation of a lower respiratory tract disease
information on acute lower respiratory tract disease
A laboratory test that has a blood specimen as specified input.
A laboratory test that has a urine specimen as specified input.
An information content entity that is about a microscopy assay
obsolete information on microscopy assay
A blood assay datum of the concentration of ferritin.
blood ferritin concentration
The threshold cycle that is the specified output of a fluorogenic PCR assay that has the objective of determining the number of Blastocystis in a feces specimen.
TaqMan threshold cycle for Blastocystis in feces
The threshold cycle that is the specified output of a fluorogenic PCR assay that has the objective of determining the number of Clostridioides difficile in a feces specimen.
TaqMan threshold cycle for Clostridioides difficile in feces
The threshold cycle that is the specified output of a fluorogenic PCR assay that has the objective of determining the number of Entamoeba in a feces specimen.
TaqMan threshold cycle for Entamoeba in feces
The threshold cycle that is the specified output of a fluorogenic PCR assay that has the objective of determining the number of Rodentolepis nana in a feces specimen.
TaqMan threshold cycle for Rodentolepis nana in feces
Mycobacterium tuberculosis, by TAC result
The threshold cycle that is the specified output of a fluorogenic PCR assay that has the objective of determining the number of Mycobacterium tuberculosis in a feces specimen.
TaqMan threshold cycle for Mycobacterium tuberculosis in feces
The threshold cycle that is the specified output of a fluorogenic PCR assay that has the objective of determining the number of Norovirus GI.1 in a feces specimen.
TaqMan threshold cycle for Norovirus GI.1 in feces
The threshold cycle that is the specified output of a fluorogenic PCR assay that has the objective of determining the number of Norovirus GII.4 in a feces specimen.
TaqMan threshold cycle for Norovirus GII.4 in feces
The threshold cycle that is the specified output of a fluorogenic PCR assay that has the objective of determining the number of Plesiomonas in a feces specimen.
TaqMan threshold cycle for Plesiomonas in feces
The threshold cycle that is the specified output of a fluorogenic PCR assay that has the objective of determining the number of Schistosoma in a feces specimen.
TaqMan threshold cycle for Schistosoma in feces
A blood assay datum of the concentration of retinol.
blood retinol concentration
A eukaryota in feces datum that is the output of an enzyme-linked immunosorbent assay and is used to determine the presence of Entamoeba histolytica in the specimen.
Entamoeba histolytica in feces by enzyme-linked immunosorbent assay datum
A bacteria in feces datum that specifies whether Vibrio was detected.
presence of Vibrio in feces
A virus in feces datum that specifies whether a virus was detected.
presence of virus in feces
A bacteria in feces datum that specifies whether Yersinia was detected.
presence of Yersinia in feces
A bacteria in feces datum that specifies whether Aeronomas was detected.
presence of Aeromonas in feces
A bacteria in feces datum that specifies whether bacteria were detected.
presence of bacteria in feces
A bacteria in feces datum that specifies whether Campylobacter was detected.
presence of Campylobacter in feces
A bacteria in feces datum that specifies whether Escherichia was detected.
presence of Escherichia in feces
A bacteria in feces datum that specifies whether Plesiomonas was detected.
presence of Plesiomonas in feces
A bacteria in feces datum that specifies whether Salmonella was detected.
presence of Salmonella in feces
A bacteria in feces datum that specifies whether Shigella was detected.
presence of Shigella in feces
A virus in feces datum that specifies whether Norovirus GI was detected by real time reverse-transcription polymerase chain reaction assay.
presence of Norovirus GI in feces by real time reverse-transcription polymerase chain reaction assay
A virus in feces datum that specifies whether Norovirus GII was detected by real time reverse-transcription polymerase chain reaction assay.
presence of Norovirus GII in feces by real time reverse-transcription polymerase chain reaction assay
Charcoal as a cooking fuel
charcoal cooking fuel
An information content entity that mentions drinking water piped into a dwelling
obsolete information on drinking water piped into dwelling
An information content entity that mentions drinking water obtained through a plumbing fixture located in the yard of a human dwelling
obsolete information on drinking water piped into yard
drinking water that is derived from rainwater
drinking water derived from rainwater
Drinking water that is derived from bore hole water
drinking water derived from bore hole water
A symptom since illness began information that mentions respiratory distress
respiratory distress since illness began information
A symptom since illness began information that mentions convulsion
convulsion since illness began information
Information on diarrhea treatment before clinical visit that mentions an oral rehydration product as the treatment.
information on oral rehydration for diarrhea before visit
information on raising money for health care encounter that specifies that less money was spent on food to cover healthcare costs
information on cutting food expenses to pay for health care
information on raising money for health care encounter that specifies that less money was spent on goods or services other than food to cover healthcare costs
information on cutting non-food expenses to pay for health care
information on raising money for health care encounter that specifies that the money to cover healthcare costs was derived from savings
information on using savings to pay for health care
information on raising money for health care encounter that specifies that the money to cover healthcare costs was borrowed
information on borrowing to pay for health care
information on raising money for health care encounter that specifies that the money to cover healthcare costs derived from money obtained through the sale of assets
information on selling assets to pay for health care
Asking for donations outside the household
information on raising money for health care encounter that specifies that the money to cover healthcare costs was donated but not by any member of the patient's household
information on asking for donations outside the household to pay for health care
information on raising money for health care encounter that specifies that the money to cover healthcare costs was donated by a friend or relative of the patient
information on health care paid for by relative or friend
A symptom or sign information that mentions rectal prolapse
rectal prolapse information
A symptom or sign information that mentions bipedal edema
bipedal edema symptom or sign information
A symptom or sign information that mentions flaky paint dermatosis
flaky paint dermatosis information
A diagnosis at patient discharge that is an assertion that a patient has diarrhea.
diagnosis of diarrhea at patient discharge
A diagnosis at patient discharge that is an assertion that a patient has dysentery.
diagnosis of dysentery at patient discharge
Pneumonia or lower respiratory infection
A diagnosis at patient discharge that is an assertion that a patient has pneumonia or lower respiratory tract disease.
diagnosis of pneumonia of lower repiratory tract disease at patient discharge
A diagnosis at patient discharge that is an assertion that a patient has malaria.
diagnosis of malaria at patient discharge
A diagnosis at patient discharge that is an assertion that a patient has nutritional deficiency disease.
diagnosis of nutritional deficiency disease at patient discharge
A diagnosis at patient discharge that is an assertion that a patient has typhoid fever.
diagnosis of typhoid fever at patient discharge
A virus in feces datum that specifies whether Human mastadenovirus F was detected by enzyme-linked immunosorbent assay.
presence of Human mastadenovirus F in feces by enzyme-linked immunosorbent assay
A virus in feces datum that specifies whether Adenoviridae excluding human mastadenovirus F were detected by enzyme-linked immunosorbent assay
presence of Adenoviridae excluding human mastadenovirus F in feces by enzyme-linked immunosorbent assay
A Vibrio in feces datum that specifies whether Vibrio cholerae O1 was detected.
presence of Vibrio cholerae O1 in feces
Vibrio cholerae O1 Inaba, by bacteriology
A Vibrio in feces datum that specifies whether Vibrio cholerae serotype Inaba was detected.
presence of Vibrio cholerae serotype Inaba in feces
Vibrio cholerae O1 Ogawa, by bacteriology
A Vibrio in feces datum that specifies whether Vibrio cholerae serotype Ogawa was detected.
presence of Vibrio cholerae serotype Ogawa in feces
A Vibrio in feces datum that specifies whether Vibrio cholerae O139 was detected.
presence of Vibrio cholerae O139 in feces
A Salmonella in feces datum that specifies whether Salmonella enterica subsp. enterica serovar Typhi was detected.
presence of Salmonella enterica subsp. enterica serovar Typhi in feces
A Salmonella in feces datum that specifies whether Salmonella enterica enterica other than Typhi was detected.
presence of Salmonella enterica enterica other than Typhi
A virus in feces datum that specifies whether Sapovirus was detected by reverse transcription polymerase chain reaction assay.
presence of Sapovirus in feces by reverse transcription polymerase chain reaction assay
Campylobacter (non-jejuni or coli), by bacteriology
A Campylobacter in feces datum that specifies whether Campylobacter other than coli or jejuni was detected.
presence of Campylobacter non-(jejuni or coli) in feces
Campylobacter (non-speciated), by bacteriology
A Campylobacter in feces datum that specifies whether Campylobacter was detected, without specifying the taxon further.
presence of Campylobacter unspecified in feces
Shigella flexneri serotype 4B, by bacteriology
A Shigella in feces datum that specifies whether Shigella flexneri, serovar 4b was detected.
presence of Shigella flexneri, serovar 4b in feces
Shigella flexneri serotype 5B, by bacteriology
A Shigella in feces datum that specifies whether Shigella flexneri 5b was detected.
presence of Shigella flexneri 5b in feces
Shigella flexneri serotype 6, by bacteriology
A Shigella in feces datum that specifies whether Shigella flexneri 6 was detected.
presence of Shigella flexneri 6 in feces
Shigella flexneri non-typeable, by bacteriology result
A bacteria in feces datum that is used to determine the presence of non-typeable Shigella flexneri in the specimen.
Shigella flexneri non-typeable in feces datum
A Shigella in feces datum that specifies whether Shigella non-typeable was detected.
presence of Shigella non-typeable in feces
A Vibrio in feces datum that specifies whether Vibrio cholerae was detected.
presence of Vibrio cholerae in feces
Vibrio cholerae non-O1/O139, by bacteriology
A Vibrio in feces datum that specifies whether Vibrio cholerae non-(O1 or O139) was detected.
presence of Vibrio cholerae non-(O1 or O139) in feces
A Vibrio in feces datum that specifies whether Vibrio other than cholerae or parahaemolyticus was detected.
presence of Vibrio non-(cholerae or parahaemolyticus) in feces
A Campylobacter in feces datum that specifies whether Campylobacter coli was detected, without specifying the taxon further.
presence of Campylobacter coli in feces
A Campylobacter in feces datum that specifies whether Campylobacter jejuni was detected.
presence of Campylobacter jejuni in feces
A Shigella in feces datum that specifies whether Shigella flexneri was detected.
presence of Shigella flexneri in feces
A Shigella in feces datum that specifies whether Shigella boydii was detected.
presence of Shigella boydii in feces
A Shigella in feces datum that specifies whether Shigella dysenteriae was detected.
presence of Shigella dysenteriae in feces
Vibrio parahaemolyticus, by bacteriology
A Vibrio in feces datum that specifies whether Vibrio parahaemolyticus was detected.
presence of Vibrio parahaemolyticus in feces
A Shigella in feces datum that specifies whether Shigella sonnei was detected.
presence of Shigella sonnei in feces
Shigella flexneri serotype 4A, by bacteriology
A Shigella in feces datum that specifies whether Shigella flexneri 4a was detected.
presence of Shigella flexneri 4a in feces
Shigella flexneri serotype 4C, by bacteriology
A Shigella in feces datum that specifies whether Shigella flexneri 4c was detected.
presence of Shigella flexneri 4c in feces
Shigella flexneri serotype 5A, by bacteriology
A Shigella in feces datum that specifies whether Shigella flexneri 5a was detected.
presence of Shigella flexneri 5a in feces
Shigella flexneri serotype X, by bacteriology
A Shigella in feces datum that specifies whether Shigella flexneri X variant was detected.
presence of Shigella flexneri X variant in feces
Shigella flexneri serotype Y, by bacteriology
A Shigella in feces datum that specifies whether Shigella flexneri Y was detected.
presence of Shigella flexneri Y in feces
A virus in feces datum that specifies whether Astrovirus was detected by reverse transcription polymerase chain reaction assay.
presence of Astrovirus in feces by reverse transcription polymerase chain reaction assay
The threshold cycle that is the specified output of a fluorogenic PCR assay that has the objective of determining the number of Adenoviridae in a feces specimen.
TaqMan threshold cycle for Adenoviridae in feces
The threshold cycle that is the specified output of a fluorogenic PCR assay that has the objective of determining the number of Aeromonas in a feces specimen.
TaqMan threshold cycle for Aeromonas in feces
The threshold cycle that is the specified output of a fluorogenic PCR assay that has the objective of determining the number of Ancylostoma in a feces specimen.
TaqMan threshold cycle for Ancylostoma in feces
The threshold cycle that is the specified output of a fluorogenic PCR assay that has the objective of determining the number of Ascaris in a feces specimen.
TaqMan threshold cycle for Ascaris in feces
The threshold cycle that is the specified output of a fluorogenic PCR assay that has the objective of determining the number of Astroviridae in a feces specimen.
TaqMan threshold cycle for Astroviridae in feces
The threshold cycle that is the specified output of a fluorogenic PCR assay that has the objective of determining the number of Bacteroides fragilis in a feces specimen.
TaqMan threshold cycle for Bacteroides fragilis in feces
The threshold cycle that is the specified output of a fluorogenic PCR assay that has the objective of determining the number of Campylobacter in a feces specimen.
TaqMan threshold cycle for Campylobacter in feces
The threshold cycle that is the specified output of a fluorogenic PCR assay that has the objective of determining the number of Cryptosporidium in a feces specimen.
TaqMan threshold cycle for Cryptosporidium in feces
The threshold cycle that is the specified output of a fluorogenic PCR assay that has the objective of determining the number of Cryptosporidium hominis in a feces specimen.
TaqMan threshold cycle for Cryptosporidium hominis in feces
The threshold cycle that is the specified output of a fluorogenic PCR assay that has the objective of determining the number of Cryptosporidium parvum in a feces specimen.
TaqMan threshold cycle for Cryptosporidium parvum in feces
The threshold cycle that is the specified output of a fluorogenic PCR assay that has the objective of determining the number of Cyclospora in a feces specimen.
TaqMan threshold cycle for Cyclospora in feces
The threshold cycle that is the specified output of a fluorogenic PCR assay that has the objective of determining the number of Enterocytozoon bieneusi in a feces specimen.
TaqMan threshold cycle for Enterocytozoon bieneusi in feces
The threshold cycle that is the specified output of a fluorogenic PCR assay that has the objective of determining the number of Entamoeba histolytica in a feces specimen.
TaqMan threshold cycle for Entamoeba histolytica in feces
Encephalitozoon intestinalis, by TAC result
The threshold cycle that is the specified output of a fluorogenic PCR assay that has the objective of determining the number of Encephalitozoon intestinalis in a feces specimen.
TaqMan threshold cycle for Encephalitozoon intestinalis in feces
The threshold cycle that is the specified output of a fluorogenic PCR assay that has the objective of determining the number of Giardia intestinalis assemblage A in a feces specimen.
TaqMan threshold cycle for Giardia intestinalis assemblage A in feces
The threshold cycle that is the specified output of a fluorogenic PCR assay that has the objective of determining the number of Giardia intestinalis assemblage B in a feces specimen.
TaqMan threshold cycle for Giardia intestinalis assemblage B in feces
The threshold cycle that is the specified output of a fluorogenic PCR assay that has the objective of determining the number of Giardia in a feces specimen.
TaqMan threshold cycle for Giardia in feces
The threshold cycle that is the specified output of a fluorogenic PCR assay that has the objective of determining the number of Helicobacter pylori in a feces specimen.
TaqMan threshold cycle for Helicobacter pylori in feces
The threshold cycle that is the specified output of a fluorogenic PCR assay that has the objective of determining the number of Isospora in a feces specimen.
TaqMan threshold cycle for Isospora in feces
The threshold cycle that is the specified output of a fluorogenic PCR assay that has the objective of determining the number of Necator in a feces specimen.
TaqMan threshold cycle for Necator in feces
The threshold cycle that is the specified output of a fluorogenic PCR assay that has the objective of determining the number of Norovirus GI in a feces specimen.
TaqMan threshold cycle for Norovirus GI in feces
The threshold cycle that is the specified output of a fluorogenic PCR assay that has the objective of determining the number of Norovirus GII in a feces specimen.
TaqMan threshold cycle for Norovirus GII in feces
The threshold cycle that is the specified output of a fluorogenic PCR assay that has the objective of determining the number of Rotavirus in a feces specimen.
TaqMan threshold cycle for Rotavirus in feces
The threshold cycle that is the specified output of a fluorogenic PCR assay that has the objective of determining the number of Rotavirus G10 in a feces specimen.
TaqMan threshold cycle for Rotavirus G10 in feces
The threshold cycle that is the specified output of a fluorogenic PCR assay that has the objective of determining the number of Rotavirus G12 in a feces specimen.
TaqMan threshold cycle for Rotavirus G12 in feces
The threshold cycle that is the specified output of a fluorogenic PCR assay that has the objective of determining the number of Rotavirus G1 in a feces specimen.
TaqMan threshold cycle for Rotavirus G1 in feces
The threshold cycle that is the specified output of a fluorogenic PCR assay that has the objective of determining the number of Rotavirus G2 in a feces specimen.
TaqMan threshold cycle for Rotavirus G2 in feces
The threshold cycle that is the specified output of a fluorogenic PCR assay that has the objective of determining the number of Rotavirus G3 in a feces specimen.
TaqMan threshold cycle for Rotavirus G3 in feces
The threshold cycle that is the specified output of a fluorogenic PCR assay that has the objective of determining the number of Rotavirus G4 in a feces specimen.
TaqMan threshold cycle for Rotavirus G4 in feces
The threshold cycle that is the specified output of a fluorogenic PCR assay that has the objective of determining the number of Rotavirus G8 in a feces specimen.
TaqMan threshold cycle for Rotavirus G8 in feces
The threshold cycle that is the specified output of a fluorogenic PCR assay that has the objective of determining the number of Rotavirus G9 in a feces specimen.
TaqMan threshold cycle for Rotavirus G9 in feces
The threshold cycle that is the specified output of a fluorogenic PCR assay that has the objective of determining the number of Rotavirus A P4 in a feces specimen.
TaqMan threshold cycle for Rotavirus A P4 in feces
The threshold cycle that is the specified output of a fluorogenic PCR assay that has the objective of determining the number of Human rotavirus P6 in a feces specimen.
TaqMan threshold cycle for Human rotavirus P6 in feces
The threshold cycle that is the specified output of a fluorogenic PCR assay that has the objective of determining the number of Rotavirus A P8 in a feces specimen.
TaqMan threshold cycle for Rotavirus A P8 in feces
The threshold cycle that is the specified output of a fluorogenic PCR assay that has the objective of determining the number of Salmonella in a feces specimen.
TaqMan threshold cycle for Salmonella in feces
The threshold cycle that is the specified output of a fluorogenic PCR assay that has the objective of determining the number of Sapovirus in a feces specimen.
TaqMan threshold cycle for Sapovirus in feces
The threshold cycle that is the specified output of a fluorogenic PCR assay that has the objective of determining the number of Strongyloides in a feces specimen.
TaqMan threshold cycle for Strongyloides in feces
The threshold cycle that is the specified output of a fluorogenic PCR assay that has the objective of determining the number of Trichuris trichiura in a feces specimen.
TaqMan threshold cycle for Trichuris trichiura in feces
The threshold cycle that is the specified output of a fluorogenic PCR assay that has the objective of determining the number of Vibrio cholerae in a feces specimen.
TaqMan threshold cycle for Vibrio cholerae in feces
A eukaryota in feces datum that specifies whether Ancylostoma duodenale was detected by real time polymerase chain reaction assay.
presence of Ancylostoma duodenale in feces by real time polymerase chain reaction assay
A eukaryota in feces datum that specifies whether Ascaris lumbricoides was detected by real time polymerase chain reaction assay.
presence of Ascaris lumbricoides in feces by real time polymerase chain reaction assay
A eukaryota in feces datum that is the output of a reverse transcription polymerase chain reaction assay and is used to determine the presence of Ascaris lumbricoides in the specimen.
Ascaris lumbricoides in feces by reverse transcription polymerase chain reaction assay datum
A bacteria in feces datum that is the output of a reverse transcription polymerase chain reaction assay and is used to determine the presence of Bacteroides fragilis in the specimen.
Bacteroides fragilis in feces by reverse transcription polymerase chain reaction assay datum
a categorical measurement datum that specifies whether Escherichia coli was detected by differential medium assay
obsolete presence of Escherichia coli by differential medium assay
A bacteria in feces datum that specifies whether Helicobacter pylori was detected by immunoassay.
presence of Helicobacter pylori in feces by immunoassay
A eukaryota in feces datum that specifies whether Ancylostomatoidea was detected by real time polymerase chain reaction assay.
presence of Ancylostomatoidea in feces by real time polymerase chain reaction assay
A eukaryota in feces datum that specifies whether Necator americanus was detected by real time polymerase chain reaction assay.
presence of Necator americanus in feces by real time polymerase chain reaction assay
Shigella dysenteriae serotype 1, by bacteriology result
A bacteria in feces datum that is used to determine the presence of Shigella dysenteriae 1 in the specimen.
Shigella dysenteriae 1 in feces datum
Shigella flexneri serotype 7, by bacteriology result
A bacteria in feces datum that is used to determine the presence of Shigella flexneri serotype 7 in the specimen.
Shigella flexneri 7 in feces datum
Shigella flexneri serotype 1A, by bacteriology
A Shigella in feces datum that specifies whether Shigella flexneri 1a was detected.
presence of Shigella flexneri 1a in feces
Shigella flexneri serotype 1B, by bacteriology
A Shigella in feces datum that specifies whether Shigella flexneri 1b was detected.
presence of Shigella flexneri 1b in feces
Shigella flexneri serotype 2A, by bacteriology
A Shigella in feces datum that specifies whether Shigella flexneri 2a was detected.
presence of Shigella flexneri 2a in feces
Shigella flexneri serotype 2B, by bacteriology
A Shigella in feces datum that specifies whether Shigella flexneri 2b was detected.
presence of Shigella flexneri 2b in feces
Shigella flexneri serotype 3A, by bacteriology
A Shigella in feces datum that specifies whether Shigella flexneri 3a was detected.
presence of Shigella flexneri 3a in feces
Shigella flexneri serotype 3B, by bacteriology
A Shigella in feces datum that specifies whether Shigella flexneri 3b was detected.
presence of Shigella flexneri 3b in feces
A Shigella in feces datum that specifies whether Shigella flexneri, serovar 3c was detected.
presence of Shigella flexneri, serovar 3c in feces
A Shigella in feces datum that specifies whether Shigella flexneri 7a was detected.
presence of Shigella flexneri 7a in feces
A mass measurement datum of the mass of a feces specimen.
feces specimen mass measurement datum
Strongyloides stercoralis, by RT-PCR result
A eukaryota in feces datum that is the output of a reverse transcription polymerase chain reaction assay and is used to determine the presence of Strongyloides stercoralis in the specimen.
Strongyloides stercoralis in feces by reverse transcription polymerase chain reaction assay datum
A Strongyloides stercoralis in feces by reverse transcription polymerase chain reaction assay datum that specifies whether the organism was detected.
presence of Strongyloides stercoralis in feces by reverse transcription polymerase chain reaction assay
A time measurement datum of the date encompassing a feces microbiology assay
date of feces microbiology assay
A Bacteroides fragilis in feces by reverse transcription polymerase chain reaction assay datum that specifies whether the organism was detected.
presence of Bacteroides fragilis in feces by polymerase chain reaction assay
Vibrio cholerae O1 El Tor, by bacteriology result
A bacteria in feces datum that is used to determine the presence of Vibrio cholerae O1 biovar El Tor in the specimen.
Vibrio cholerae O1 biovar El Tor in feces datum
Vibrio cholerae O1, by bacteriology result
A bacteria in feces datum that is used to determine the presence of Vibrio cholerae O1 in the specimen.
Vibrio cholerae O1 in feces datum
Vibrio cholerae O139, by bacteriology result
A bacteria in feces datum that is used to determine the presence of Vibrio cholerae O139 in the specimen.
Vibrio cholerae O139 in feces datum
Vibrio cholerae Inaba or Ogawa, by bacteriology result
A bacteria in feces datum that is used to determine the presence of Vibrio cholerae Inaba or Ogawa in the specimen.
Vibrio cholerae Inaba or Ogawa in feces datum
A treatment information that mentions a medication that treats diarrhea.
information on diarrhea treatment
A bacteria in feces datum that specifies whether Bacteroides was detected.
presence of Bacteroides in feces
A bacteria in feces datum that specifies whether Clostridioides was detected.
presence of Clostridioides in feces
A bacteria in feces datum that specifies whether Helicobacter was detected.
presence of Helicobacter in feces
An information content entity that is about a dead human participant under investigation and specifies the process which caused the death of the participant
information on cause of death
A data item that is the specified output of a data transformation that has multiple clinical data items as input.
aggregated clinical data item
A eukaryota in blood datum that is the output of a real time polymerase chain reaction assay and is used to determine the presence of Plasmodium in the specimen.
Plasmodium in blood by real time polymerase chain reaction assay datum
A Plasmodium in blood by microscopy assay datum that specifies whether Plasmodium ovale was detected by microscopy assay.
presence of Plasmodium ovale in blood by microscopy assay
a domesticated animal that is raised in an agricultural setting to produce labor and commodities
livestock animal
a categorical value specification that specifies that a bed net is not used
no use of bed net
a categorical value specification that specifies that a bed net is used, but it is not treated with insecticide
bed net not treated
a categorical value specification that specifies that a bed net is used, but it was last treated earlier than six months ago
bed net treated over six months ago
a categorical value specification that specifies that a bed net is used, and it was last treated more recently than six months previous
bed net treated within past six months
a categorical value specification that specifies that a bed net is used, and it was treated with long last insecticide
bed net treated with long last insecticide
an information content entity that is about a human participant under investigation and specifies that the participant received treatment, for a fever, that was provided at a clinic within the past two weeks
information specifying fever treated at clinic in past 2 weeks
an information content entity that is about a human participant under investigation and specifies that the participant received treatment, for a fever, that was provided by a self-employed health care provider within the past two weeks
information specifying fever treated by private practicioner in past 2 weeks
an information content entity that is about a human participant under investigation and specifies that the participant received treatment, for a fever, that was self-provided within the past two weeks
information specifying fever self-treated in past 2 weeks
an information content entity that is about a human participant under investigation and specifies that the participant had a fever within the past two weeks but did not receive treatment for the fever
information specifying untreated fever in past two weeks
a data item that is the specified output of a microscopy assay that has a sample of blood as specified input and indicates that the sample does not contain Plasmodium
(Plasmodium species, by microscopy) Negative
no Plasmodium by microscopy
A Plasmodium in blood by microscopy assay datum that specifies whether Plasmodium falciparum was detected by microscopy assay.
presence of Plasmodium falciparum in blood by microscopy assay
A Plasmodium in blood by microscopy assay datum that specifies whether Plasmodium vivax was detected by microscopy assay.
presence of Plasmodium vivax by microscopy assay
A Plasmodium in blood by microscopy assay datum that specifies whether Plasmodium malariae was detected by microscopy assay.
presence of Plasmodium malariae by microscopy assay
a categorical value specification that specifies whether a microscopy assay was performed
indicator of whether microscopy assay performed
an information content entity that is about a human participant under investigation and specifies that the participant remembers being diagnosed, within the past year, with a disease by Plasmodium falciparum
(Plasmodium species in last year) Plasmodium falciparum
Plasmodium falciparum diagnosis within past year
an information content entity that is about a human participant under investigation and specifies that the participant remembers being diagnosed, within the past year, with a disease by Plasmodium vivax
(Plasmodium species in last year) Plasmodium vivax
Plasmodium vivax diagnosis within past year
an information content entity that is about a human participant under investigation and specifies that the participant remembers being diagnosed, within the past year, with a disease by Plasmodium malariae
(Plasmodium species in last year) Plasmodium malariae
Plasmodium malariae diagnosis within past year
an information content entity that is about a human participant under investigation and specifies that the participant remembers being diagnosed, within the past year, with a disease by Plasmodium, but does not remember the species of Plasmodium
(Plasmodium species in last year) Can't remember
forgot which Plasmodium species in diagnosis within past year
information on antimalarial drug used last year that specifies artesunate as the drug administered as the most recent treatment
information specifying Artesunate as antimalarial drug as most recent treatment within past year
an information content entity that is about a human participant under investigation who, within one year previous, was administered an antimalarial drug to alleviate symptoms of malaria. This information content entity specifies that the participant does not remember which drug was administered.
(Antimalarial medications used) Can't remember
forgot which antimalarial in most recent treatment
information on antimalarial drug used last year that specifies a combination of aretesunate, pyrimethamine, and sulphadox as the drugs administered as the most recent treatment
artesunate/pyrimethamine/sulphadoxine combination as most recent malaria treatment
information on antimalarial drug used last year that specifies chloroquine or primaquine as the drugs administered as the most recent treatment
chloroquine or primaquine as most recent malaria treatment
information on antimalarial drug used last year that specifies pyrimethamine or sulphadoxine as the drugs administered as the most recent treatment
pyrimethamine or sulphadoxine as most recent malaria treatment
information on antimalarial drug used last year that specifies quinine or quinidine as the drugs administered as the most recent treatment
quinine or quinidine as most recent malaria treatment
information on antimalarial drug used last year that specifies tetracycline or doxycycline as the drugs administered as the most recent treatment
tetracycline or doxycycline as most recent malaria treatment
an information content entity that is about a human participant under investigation and specifies that the participant received treatment for malaria in a clinic, within the past year
indicator of whether treated in clinic
a categorical value specification that specifies whether the bearer of an organization health care role, which administered a treatment to alleviate an episode of malaria, was a private practice
indicator of whether treated by private practice
A categorical value specification that specifies whether a treatment to alleviate an episode of malaria was self-administered
indicator of whether malaria self-treated
an information content entity that is about a human participant under investigation who, within one year previous, was administered an antimalarial drug to alleviate symptoms of malaria. This information content entity specifies that the participant does not remember the geographic location where this treatment was provided.
indicator of whether participant forgot treatment location within past year
a presence of parasite that is the specified output of a parasite detection by PCR assay, has a blood specimen as specified input, and specifies that no Plasmodium was detected
no Plasmodium by blood sample PCR
a presence of Plasmodium falciparum that is the specified output of a parasite detection by PCR assay, has a blood specimen as specified input, and specifies that Plasmodium falciparum was detected
(Plasmodium species, by qPCR) Plasmodium falciparum
presence of Plasmodium falciparum by blood sample PCR
a presence of Plasmodium falciparum that is the specified output of a parasite detection by PCR assay, has a blood specimen as specified input, and specifies that Plasmodium vivax was detected
(Plasmodium species, by qPCR) Plasmodium vivax
presence of Plasmodium vivax by blood sample PCR
a presence of Plasmodium malariae that is the specified output of a parasite detection by PCR assay, has a blood specimen as specified input, and specifies that Plasmodium malariae was detected
(Plasmodium species, by qPCR) Plasmodium malariae
presence of Plasmodium malariae by blood sample PCR
a presence of Plasmodium ovale that is the specified output of a parasite detection by PCR assay, has a blood specimen as specified input, and specifies that Plasmodium ovale was detected
presence of Plasmodium ovale by blood sample PCR
a presence of Plasmodium falciparum that is the specified output of a falcivax rapid diagnostic test and specifies that Plasmodium falciparum was detected
(Plasmodium species, by FalciVax RDT) Plasmodium falciparum
presence of Plasmodium falciparum by falcivax
a presence of Plasmodium vivax that is the specified output of a falcivax rapid diagnostic test and specifies that Plasmodium vivax was detected
(Plasmodium species, by FalciVax RDT) Plasmodium vivax
presence of Plasmodium vivax by falcivax
a presence of parasite that is the specified output of a falcivax rapid diagnostic test and indicates that no Plasmodium was detected
(Plasmodium species, by FalciVax RDT) Negative
no presence of Plasmodium by falcivax
a categorical value specification that specifies whether a falcivax rapid diagnostic test was performed
indicator of whether falcivax performed
a presence of Plasmodium falciparum that is the specified output of a optimal-IT rapid diagnostic test and specifies that Plasmodium falciparum was detected
(Plasmodium species, by OptiMAL RDT) Plasmodium falciparum
presence of Plasmodium falciparum by optimal-IT
a presence of parasite that is the specified output of a optimal-IT rapid diagnostic test and specifies that an antigen common to multiple Plasmodium species was detected
presence of pan-Plasmodium antigen by optimal-IT
a presence of parasite that is the specified output of an optimal-IT rapid diagnostic test and specifies that no Plasmodium was detected
(Plasmodium species, by OptiMAL RDT) Negative
no Plasmodium by optimal-IT
a categorical value specification that specifies whether an optimal-IT rapid diagnostic test was performed
indicator of whether optimal-IT performed
an information content entity that is about a human participant under investigation and specifies that the participant does not remember using a personal mosquito repellent
(Personal mosquito repellent) Can't remember
information on participant forgetting whether used personal mosquito repellent
an information content entity that specifies that a human participant under investigation does not remember whether insecticide was applied in the previous 12 months
(Sprayed in the last 12 months) Can't remember
no knowledge of insecticide spraying in last 12 months
healthcare information that specifies that the organization that typically provides the healthcare is funded by a government rather than funded independently
public healthcare information
healthcare information that specifies that the organization that typically provides the healthcare is funded independently of any government
EuPathDB, New Oxford American Dictionary entry for 'private'
private healthcare information
water accessed through a plumbing fixture located inside a human dwelling
water piped into dwelling
water derived from water that is part of either a stream or a river
stream water
A blood specimen that is located in a vacutainer.
A household asset information indicating whether a household has electricity.
indicator of household having electricity
a time measurement datum of the day that encompasses a process that has as specified output a data item about a household
date of household data collection
a categorical value specification that specifies whether there exists some quality of a patient, material entity that is part of a patient, or processual entity that a patient participates in, that is both observed in a physical examination and deemed by the clinician to be of clinical significance
EuPathDB, based on definition for 'sign' in OGMS
indicator of whether participant has sign
a categorical value specification that specifies whether there exists some quality of a patient that is observed by the patient or some processual entity experienced by the patient that is hypothesized by the patient to be a realization of a disease
indicator of whether participant has symptom
a categorical value specification that specifies whether a human participant under investigation was febrile in the previous 48 hours
indicator of whether participant had fever in last 48 hours
a categorical value specification that specifies whether medication to treat malaria was administered in the past two weeks to a human participant under investigation
information on whether given malaria medication in past 2 weeks
A first-order administrative region of India.
state of India
a categorical value specification that specifies whether a human participant under investigation was febrile in the previous two weeks
indicator of whether participant had fever in last two weeks
a clinical history that is about a human participant under investigation and contains only statements about health-relevant qualities that come into existence after the enrollment of the participant in the study
An information content entity that specifies whether medication material was administered during a health care encounter.
indicator of medication administered during health care encounter
A bacteria in blood datum that specifies whether a typhus group virus was detected.
presence of typhus group in blood
A virus in blood datum that specifies whether the Chikungunya virus was detected.
presence of Chikungunya virus in blood
A virus in blood datum that specifies whether the Dengue virus was detected.
presence of Dengue virus in blood
A virus in blood datum that specifies whether Orthohepadnavirus was detected.
presence of Orthohepadnavirus in blood
A bacteria in blood datum that specifies whether Salmonella enterica subsp. enterica serovar Typhi was detected by polymerase chain reaction assay.
presence of Salmonella enterica subsp. enterica serovar Typhi in blood by polymerase chain reaction assay
A blood assay datum of the concentration of alanine aminotransferase.
blood alanine aminotransferase concentration
A blood assay datum of the concentration of alkaline phosphatase.
blood alkaline phosphatase concentration
A diagnosis at patient discharge that is an assertion that a patient has chikungunya.
diagnosis of chikungunya at patient discharge
A virus in blood datum that specifies whether Chikungunya virus was detected, by an unspecified assay.
presence of Chikungunya virus in blood by unspecified assay
A diagnosis at patient discharge that is an assertion that a patient has dengue disease.
diagnosis of dengue disease at patient discharge
A virus in blood datum that specifies whether Dengue virus was detected by an unspecified assay.
presence of Dengue virus in blood by unspecified assay
A diagnosis at patient discharge that is an assertion that a patient has a gastrointestinal infection.
diagnosis of gastrointestinal infection at patient discharge
A virus in blood datum that specifies whether Hepacivirus C was detected by an unspecified assay.
presence of Hepacivirus C in blood by unspecified assay
A virus in blood datum that specifies whether Hepatitis B virus was detected by HBV surface antigen assay.
presence of Hepatitis B virus in blood by surface antigen assay
A virus in blood datum that specifies whether Human immunodeficiency virus 1 was detected by an unspecified assay.
presence of Human immunodeficiency virus 1 in blood by unspecified assay
A diagnosis at patient discharge that is an assertion that a patient has leptospirosis.
diagnosis of leptospirosis at patient discharge
A blood assay datum of the concentration of phosphate.
blood phosphate concentration
A diagnosis at patient discharge that is an assertion that a patient has scrub typhus.
diagnosis of scrub typhus at patient discharge
A blood assay datum of the concentration of urea.
blood urea concentration
A blood assay datum of the concentration of uric acid.
blood uric acid concentration
A diagnosis at patient discharge that is an assertion that a patient has viral hepatitis.
diagnosis of viral hepatitis at patient discharge
A virus in blood datum that specifies whether Lentivirus was detected.
presence of Lentivirus in blood
A virus in blood datum that specifies whether Hepacivirus was detected.
presence of Hepacivirus in blood
a geographic location that is either a city or an area containing settlements where the inhabitants share a common trait
community
a wall material used to build an exterior wall
external wall material
a wall material used to build a wall between rooms
internal wall material
a count of the number of beds in the dwelling of a household that have a bed net hung over them
number of beds with bednet
A household asset information indicating whether a household has a freezer.
indicator of household having freezer
A household asset information indicating whether a household has an electrical appliance that has the function of mixing food or drink.
indicator of household having blender
A household asset information indicating whether a household has an appliance that has a heating element as part and has the function of heating food or drink.
indicator of household having electric stove
A household asset information indicating whether a household has an appliance that has the function of heating food or drink through the combustion of natural gas.
indicator of household having gas stove
A household asset information indicating whether a household has an appliance that has the function of heating food or drink through the combustion of kerosene.
indicator of household having kerosene stove
A household asset information indicating whether a household has an appliance that has the function of heating food or drink through the combustion of coal.
indicator of household having coal stove
A household asset information indicating whether a household has a television set that is capable of producing grayscale images but not color images.
indicator of household having black and white television
A household asset information indicating whether a household has a television set that is capable of producing color images.
indicator of household having color television
A household asset information indicating whether a household has a device capable of playing a DVD.
indicator of household having DVD player
A household asset information indicating whether a household has a sound system.
indicator of household having sound system
A household asset information indicating whether a household has any cows.
indicator of household having cow
A household asset information indicating whether a household has a goat.
indicator of household having goat
A household asset information indicating whether a household has any sexually immature domesticated birds.
indicator of household having chick
A household asset information indicating whether a household has a domesticated female bird.
indicator of household having hen
A household asset information indicating whether a household has a rooster.
indicator of household having roosters
A household asset information indicating whether a household has a turkey.
indicator of household having turkeys
A household asset information indicating whether a household has a duck.
indicator of household having duck
A household asset information indicating whether a household has a small parrot with a long tail.
indicator of household having parakeet
A household asset information indicating whether a household has a parrot.
indicator of household having parrot
A household asset information indicating whether a household has a monkey.
indicator of household having monkey
A household asset information indicating whether a household has a pig.
indicator of household having pig
A household asset information indicating whether a household has a rabbit.
indicator of household having rabbits
A household asset information indicating whether a household has a dog.
indicator of household having dog
A household asset information indicating whether a household has a cat.
indicator of household having cat
A household asset information indicating whether a household has a turtle.
indicator of household having turtles
Traveled in the 2 weeks before most recent malaria episode
a categorical value specification that specifies whether a human participant under investigation had traveled within the two weeks previous to the time of the participant's most recent malaria episode
traveled within two weeks earlier than most recent malaria episode
Traveled in the 2 weeks before 2nd most recent malaria episode
a categorical value specification that specifies whether a human participant under investigation had traveled within the two weeks previous to the time of the participant's second most recent malaria episode
Traveled in the 2 weeks before second most recent malaria episode
traveled within two weeks earlier than second most recent malaria episode
Traveled in the 2 weeks before 3rd most recent malaria episode
a categorical value specification that specifies whether a human participant under investigation had traveled within the two weeks previous to the time of the participant's third most recent malaria episode
Traveled in the 2 weeks before third most recent malaria episode
traveled within two weeks earlier than third most recent malaria episode
Traveled in the 2 weeks before 4th most recent malaria episode
a categorical value specification that specifies whether a human participant under investigation had traveled within the two weeks previous to the time of the participant's fourth most recent malaria episode
Traveled in the 2 weeks before fourth most recent malaria episode
traveled within two weeks earlier than fourth most recent malaria episode
a time measurement datum of the duration of the most recent journey of a human participant under investigation
duration of most recent trip
a time measurement datum of the duration of the second most recent journey of a human participant under investigation
Length of second most recent trip (days)
duration of second most recent trip
a time measurement datum of the duration of the third most recent journey of a human participant under investigation
duration of third most recent trip
a time measurement datum of the duration of the fourth most recent journey of a human participant under investigation
Length of fourth most recent trip (days)
duration of fourth most recent trip
an information content entity that specifies which rivers were visited during the most recent journey of a human participant under investigation
rivers traveled on most recent trip
human traveling information that specifies the community to which a human participant under investigation has most recently traveled
community visited on most recent trip
Settlement visited on 2nd most recent trip
human traveling information that specifies the community to which a human participant under investigation has traveled the second most recently
community visited on second most recent trip
Settlement visited on 3rd most recent trip
human traveling information that specifies the community to which a human participant under investigation has traveled the third most recently
community visited on third most recent trip
Settlement visited on 4th most recent trip
human traveling information that specifies the community to which a human participant under investigation has traveled the fourth most recently
community visited on fourth most recent trip
a time measurement datum of the time since the beginning of the most significant occupation of a human participant under investigation
duration of current main occupation
a time measurement datum of the time since the beginning of the second most significant occupation of a human participant under investigation
duration of current secondary occupation
a categorical value specification that specifies whether a human participant under investigation was on the property of the participant's household at the time of a scheduled clinical visit
indicator of whether participant present for clinical visit
human travel informaton that is about a human participant under investigation and specifies both method and geographic location of the most recent journey taken by the participant
information on most recent travel
human travel information that is about a human participant under investigation and specifies both method and geographic location of the second most recent journey taken by the participant
information on second most recent travel
a categorical value specification that specifies whether the collection of a specimen from a human participant under investigation was prompted by a sign that the participant was febrile
information on whether specimen collection prompted by sign of fever
an information content entity that is about a human participant under investigation from which the collection of a specimen was not prompted by a sign that the partipant was febrile. This information content entity specifies that which prompted the specimen collection
reason besides fever for specimen collection
The threshold cycle that is the specified output of a real time polymerase chain reaction assay that has the objective of determining the number of Plasmodium vivax in a blood specimen.
qPCR threshold cycle for Plasmodium vivax in blood
The threshold cycle that is the specified output of a real time polymerase chain reaction assay that has the objective of determining the number of Plasmodium falciparum in a blood specimen.
qPCR threshold cycle for Plasmodium falciparum in blood
a time measurement datum of the last time insecticide was applied to the bednets used by a household
time of most recent bednet treatment
A eukaryota in feces datum that specifies whether a parasite organism was detected by microscopy assay.
presence of parasite organism in feces by microscopy assay
A eukaryota in blood datum that specifies whether a Plasmodium gametocyte was detected by real time polymerase chain reaction assay.
presence of Plasmodium gametocyte in blood by real time polymerase chain reaction assay
A household asset information indicating whether a household has a shotgun.
indicator of household having shotgun
A measurement datum of the total area of a land lot on which a dwelling is built.
dwelling lot area measurement datum
an information content entity that is about the relocation of the household of a human participant under investigation
relocation information
a time measurement datum of the time point at which a human subject enrollment is complete
time of participant first enrolled in a study
A bacteria in blood datum that specifies whether bacteria were detected by microscopy assay.
presence of bacteria in blood by microscopy assay
A blood assay datum of the concentration of hydrogencarbonate.
blood hydrogencarbonate concentration
A data item that is about a child infected with malaria and is the sum of the blantyre coma eye movement score, the blantyre coma motor response score, and the blantyre coma verbal response score for the same child during the same infection
Blantyre coma score sum
A scalar measurement datum of the concentration of urea nitrogen in blood that is the specified output of a blood test.
blood urea nitrogen concentration
A blood assay datum of the concentration of creatinine.
blood creatinine concentration
a categorical value specification that specifies whether a human participant under investigation was administered malaria medication a second time while in hospital
indicator of whether participant taking second antimalarial medication
a categorical value specification that specifies whether a human participant under investigation was discharged from hospital
indicator of whether participant discharged from hospital
Plasmodium gametocytes, by microscopy result
A eukaryota in blood datum that is the output of a microscopy assay and is used to determine the presence of Plasmodium gametocytes in the specimen.
Plasmodium gametocytes in blood by microscopy assay datum
a categorical value specification that specifies whether a human participant under investigation was administered malaria medication a third time while in hospital
indicator of whether participant taking third antimalarial medication
A hemoglobin level in g per dl that is the specified output of an assay that occurs in a hospital facility
hemoglobin concentration measured in hospital
a categorical value specification that specifies whether a human participant under investigation moved to a different dwelling in the previous twelve months
indicator of whether participant moved in past twelve months
a categorical value specification that specifies whether a human participant under investigation moved to a different dwelling in the previous month
indicator of whether participant moved in past month
Plasmodium falciparum parasitemia (%), by microscopy result
A parasitemia measurement that is the specified output of a microscopy assay in which a blood specimen is evaluated to determine the fraction of red blood cells infected with plasmodium falciparum
Plasmodium falciparum parasitemia measurement datum
Plasmodium malariae parasitemia (%), by microscopy result
A parasitemia measurement that is the specified output of a microscopy assay in which a blood specimen is evaluated to determine the fraction of red blood cells infected with plasmodium malariae
Plasmodium malariae parasitemia measurement datum
Plasmodium vivax parasitemia (%), by microscopy result
A parasitemia measurement that is the specified output of a microscopy assay in which a blood specimen is evaluated to determine the fraction of red blood cells infected with plasmodium vivax
Plasmodium vivax parasitemia measurement datum
Plasmodium species, by FalciVax RDT at hospital
a falcivax rapid diagnostic test that occurs in a hospital facility
Parasite species, FalciVax RDT from hospital
falcivax rapid diagnostic test in hospital
Plasmodium species, by thick smear microscopy
A eukaryota in blood datum that specifies whether Plasmodium was detected by thick smear microscopy assay.
presence of Plasmodium in blood by thick smear microscopy assay
Plasmodium species, by thin smear microscopy
A eukaryota in blood datum that specifies whether Plasmodium was detected by thin smear microscopy assay.
presence of Plasmodium in blood by thin smear microscopy assay
A specimen collection time measurement datum that specifies the time of day without the date.
specimen collection time of day measurement datum
a categorical value specification that specifies whether a human participant under investigation is receiving treatment to alleviate symptoms of malaria
indicator of whether participant taking initial antimalarial medication
A relocation information on a human participant under investigation who moved to a different dwelling within one month previous. this information specifies the subnational region from which the participant moved.
subnational region relocated from within past month
human traveling information that specifies which subnational regions a human participant under investigation had visited within one month previous
subnational region visited within past month
A relocation information on a human participant under investigation who moved to a different dwelling within twelve months previous. this information specifies subnational regions from which the participant moved.
subnational region relocated from within past 12 months
a categorical value specification that specifies whether a human participant under investigation was administered malaria medication a fourth time while in hospital
indicator of whether participant taking fourth antimalarial medication
a categorical value specification that specifies whether a human participant under investigation was administered malaria medication a fifth time while in hospital
indicator of whether participant taking fifth antimalarial medication
human traveling information that specifies which subnational regions a human participant under investigation had visited within twelve months previous
subnational region visited within past 12 months
a time measurement datum of the date during which a treatment starts
date treatment started
a time measurement datum of the time point at which a treatment starts
time treatment started
a time measurement datum specifying the time (of day) of a clinical visit scheduled for sixty days after a treatment
time of 60-day follow up
A blood assay datum of the concentration of bilirubin IXalpha.
blood bilirubin IXalpha concentration
a categorical value specification that is about a human participant under investigation and specifies whether the participant had traveled within twelve months previous
information on participant travel in the last twelve months
a categorical value specification that specifies whether a human participant under investigation self-identifies as a member of a tribe
indicator of whether participant is member of tribe
a categorical value specification that specifies whether the life-death temporal boundary of a human participant under investigation occurred during a health care encounter in a hospital facility
indicator of whether participant died in hospital
Time since last personal bednet treatment
A time measurement datum of the duration since the last application of pesticide to a bed net.
duration since bed net treatment
A time measurement datum of the duration a human being has owned a bed net.
duration of bed net ownership
A diagnosis that is an assertion that a patient has diarrhea.
diagnosis of diarrhea
A diagnosis that is an assertion that a patient has pneumonia.
diagnosis of pneumonia
A diagnosis that is an assertion that a patient has upper respiratory tract disease.
diagnosis of upper respiratory tract disease
The first mention of a medication that is administered as part of a treatment.
first medication in treatment
A Plasmodium in blood by real time polymerase chain reaction assay datum that specifies whether the organism was detected.
presence of Plasmodium in blood by real time polymerase chain reaction assay
A diagnosis that is an assertion that a patient has malaria.
diagnosis of malaria
Time since last personal bednet treatment categorization
A data item that specifies which group a value for 'duration since bed net treatment' belongs to when the data are grouped by range of values.
categorical duration since bed net treatment
Time owned personal bednet categorization
A data item that specifies which group a value for 'duration of bed net ownership' belongs to when the data are grouped by range of values.
categorical duration of bed net ownership
A third-order administrative region of Thailand.
subdistrict of Thailand
A second-order administrative region of Thailand.
district of Thailand
A first-order administrative region of Thailand.
province of Thailand
A Plasmodium in blood by microscopy assay datum that specifies whether the organism was detected.
presence of Plasmodium in blood by microscopy assay
A fifth-order administrative region of Uganda.
parish of Uganda
Assay that subjects a urine specimen to a test for microorganisms.
A eukaryota in feces datum that specifies whether a eukaryote was detected.
presence of eukaryote in feces
A eukaryota in feces datum that specifies whether Schistosoma mansoni was detected by microscopy assay.
presence of Schistosoma mansoni in feces by microscopy assay
A eukaryota in urine datum that specifies whether Schistosoma was detected.
presence of Schistosoma in urine
A eukaryota in urine datum that specifies whether Schistosoma haematobium was detected by microscopy assay.
presence of Schistosoma haematobium in urine by microscopy assay
A eukaryota in urine datum that specifies whether a eukaryote was detected.
presence of eukaryote in urine
Assay that subjects an induced sputum specimen to a test for microorganisms.
obsolete induced sputum microbiology assay
A bacteria in induced sputum datum that specifies whether bacteria were detected.
presence of bacteria in induced sputum
A eukaryota in induced sputum datum that specifies whether a eukaryote was detected.
presence of eukaryote in induced sputum
A virus in induced sputum datum that specifies whether a virus was detected.
Assay that subjects a pleural fluid specimen to a test for microorganisms.
obsolete pleural fluid microbiology assay
A bacteria in pleural fluid datum that specifies whether bacteria were detected.
presence of bacteria in pleural fluid
A eukaryota in pleural fluid datum that specifies whether a eukaryote was detected.
presence of eukaryote in pleural fluid
A virus in pleural fluid datum that specifies whether a virus was detected.
presence of virus in pleural fluid
A bacteria in lung datum that specifies whether bacteria were detected.
presence of bacteria in lung
A eukaryota in lung datum that specifies whether a eukaryote was detected.
presence of eukaryote in lung
A virus in lung datum that specifies whether a virus was detected.
presence of virus in lung
Bacteria in nasopharyngeal/oropharyngeal swabs
A bacteria in nasopharyngeal or oropharyngeal swab datum that specifies whether bacteria were detected.
presence of bacteria in nasopharynx or oropharynx
Eukaryota in nasopharyngeal/oropharyngeal swabs
A eukaryota in nasopharyngeal or oropharyngeal swab datum that specifies whether a eukaryote was detected.
presence of eukaryote in nasopharynx or oropharynx
Virus in nasopharyngeal/oropharyngeal swabs
A virus in nasopharyngeal or oropharyngeal swab datum that specifies whether a virus was detected.
presence of virus in nasopharynx or oropharynx
Assay that subjects a endotracheal aspirate specimen to a test for microorganisms.
obsolete endotracheal aspirate microbiology assay
A bacteria in lung datum that specifies whether Haemophilus was detected.
presence of Haemophilus in lung
A bacteria in lung datum that specifies whether Moraxella was detected.
presence of Moraxella in lung
A bacteria in lung datum that specifies whether Staphylococcus was detected.
presence of Staphylococcus in lung
A bacteria in lung datum that specifies whether Streptococcus was detected.
presence of Streptococcus in lung
A bacteria in blood datum that specifies whether Acinetobacter was detected, without specifying the taxon further.
presence of Acinetobacter unspecified in blood
A bacteria in blood datum that specifies whether unspecified bacteria were detected.
presence of unspecified bacteria in blood
A bacteria in blood datum that specifies whether Enterobacter cloacae was detected.
presence of Enterobacter cloacae in blood
A bacteria in blood datum that specifies whether Enterobacteriaceae was detected.
presence of Enterobacteriaceae in blood
A bacteria in blood datum that specifies whether Enterococcus faecium was detected.
presence of Enterococcus faecium in blood
A bacteria in blood datum that specifies whether Escherichia coli was detected.
presence of Escherichia coli in blood
A bacteria in blood datum that specifies whether Haemophilus influenzae was detected.
presence of Haemophilus influenzae in blood
A bacteria in blood datum that specifies whether Klebsiella pneumoniae was detected.
presence of Klebsiella pneumoniae in blood
Moraxella catarrhalis (Branhamella catarrhalis), by bacteriology
A bacteria in blood datum that specifies whether Moraxella catarrhalis was detected.
presence of Moraxella catarrhalis in blood
A bacteria in blood datum that specifies whether Neisseria meningitidis was detected.
presence of Neisseria meningitidis in blood
A bacteria in blood datum that specifies whether Pseudomonas aeruginosa was detected.
presence of Pseudomonas aeruginosa in blood
A bacteria in blood datum that specifies whether Salmonella enterica enterica serovar Paratyphi A was detected.
presence of Salmonella enterica enterica serovar Paratyphi A in blood
Salmonella except Paratyphi A or Typhi, by bacteriology
A bacteria in blood datum that specifies whether Salmonella enterica enterica other than serovars Typhi or Paratyphi A were detected.
presence of Salmonella enterica enterica non-(Typhi or Paratyphi-A) in blood
A bacteria in blood datum that specifies whether Salmonella enterica enterica serovar Typhi was detected.
presence of Salmonella enterica enterica serovar Typhi in blood
A bacteria in blood datum that specifies whether Salmonella was detected, without specifying the taxon further.
presence of Salmonella unspecified in blood
A bacteria in blood datum that specifies whether Staphylococcus aureus was detected.
presence of Staphylococcus aureus in blood
Streptococcus group A (Streptococcus pyogenes), by bacteriology
A bacteria in blood datum that specifies whether Staphylococcus group A was detected.
presence of Staphylococcus group A in blood
Streptococcus pneumoniae, by bacteriology
A bacteria in blood datum that specifies whether Streptococcus pneumoniae was detected.
presence of Streptococcus pneumoniae in blood
Acinetobacter baumannii, by bacteriology
An Acinetobacter baumannii in induced sputum datum that specifies whether the organism was detected.
presence of Acinetobacter baumannii in induced sputum
Acinetobacter calcoaceticus, by bacteriology
An Acinetobacter calcoaceticus in induced sputum datum that specifies whether the organism was detected.
presence of Acinetobacter calcoaceticus in induced sputum
An Acinetobacter in induced sputum datum that specifies whether Acinetobacter lwoffii was detected.
presence of Acinetobacter lwoffii in induced sputum
An Acinetobacter in induced sputum datum that specifies whether the organism was detected.
presence of Acinetobacter in induced sputum
An Aeromonas hydrophila in induced sputum datum that specifies whether the organism was detected.
presence of Aeromonas hydrophila in induced sputum
Agregattibacter aphrophilus (Haemophilus aphrophilus), by bacteriology
An Aggregatibacter aphrophilus in induced sputum datum that specifies whether the organism was detected.
presence of Aggregatibacter aphrophilus in induced sputum
Alpha-hemolytic Streptococcus (viridans), by bacteriology
An Alpha-Hemolytic Streptococcus in induced sputum datum that specifies whether the organism was detected.
presence of Alpha-Hemolytic Streptococcus in induced sputum
Any noncontaminant bacteria, by multiplexed qPCR
A bacteria in induced sputum datum that specifies whether bacteria were detected by multiplex real time polymerase chain reaction assay.
presence of bacteria in induced sputum by multiplex real time polymerase chain reaction assay
Beta-hemolytic Streptococcus, by bacteriology
A Beta-Hemolytic Streptococcus in induced sputum datum that specifies whether the organism was detected.
presence of Beta-Hemolytic Streptococcus in induced sputum
Bordetella pertussis, by multiplexed qPCR
A bacteria in induced sputum datum that specifies whether Bordetella pertussis was detected by multiplex real time polymerase chain reaction assay.
presence of Bordetella pertussis in induced sputum by multiplex real time polymerase chain reaction assay
A Burkholderia cepacia in induced sputum datum that specifies whether the organism was detected.
presence of Burkholderia cepacia in induced sputum
Chlamydophila pneumoniae, by multiplexed qPCR
A bacteria in induced sputum datum that specifies whether Chlamydia pneumoniae was detected by multiplex real time polymerase chain reaction assay.
presence of Chlamydia pneumoniae in induced sputum by multiplex real time polymerase chain reaction assay
A Citrobacter braakii in induced sputum datum that specifies whether the organism was detected.
presence of Citrobacter braakii in induced sputum
A Citrobacter freundii in induced sputum datum that specifies whether the organism was detected.
presence of Citrobacter freundii in induced sputum
Coagulase-negative Staphylococcus, by bacteriology
A Coagulase-Negative Staphylococcus in induced sputum datum that specifies whether the organism was detected.
presence of Coagulase-Negative Staphylococcus in induced sputum
A bacteria in induced sputum datum that specifies whether Coliform bacilli was detected.
presence of Coliform bacilli in induced sputum
A Corynebacterium in induced sputum datum that specifies whether the organism was detected.
presence of Corynebacterium in induced sputum
Cronobacter sakazakii (Enterobacter sakazakii), by bacteriology
A Cronobacter sakazakii in induced sputum datum that specifies whether the organism was detected.
presence of Cronobacter sakazakii in induced sputum
A Enterobacter asburiae in induced sputum datum that specifies whether the organism was detected.
presence of Enterobacter asburiae in induced sputum
A Enterobacter cloacae in induced sputum datum that specifies whether the organism was detected.
presence of Enterobacter cloacae in induced sputum
An Enterobacter in induced sputum datum that specifies whether the organism was detected.
presence of Enterobacter in induced sputum
A Enterobacter in induced sputum datum that specifies whether Enterococcus faecalis was detected.
presence of Enterococcus faecalis in induced sputum
An Enterococcus in induced sputum datum that specifies whether the organism was detected.
presence of Enterococcus in induced sputum
A Escherichia coli in induced sputum datum that specifies whether the organism was detected.
presence of Escherichia coli in induced sputum
Haemophilus haemolyticus, by bacteriology
A Haemophilus haemolyticus in induced sputum datum that specifies whether the organism was detected.
presence of Haemophilus haemolyticus in induced sputum
Haemophilus influenzae type B, by bacteriology
A Haemophilus influenzae serotype b in induced sputum datum that specifies whether the organism was detected.
presence of Haemophilus influenzae serotype b in induced sputum
Haemophilus influenzae type B, by multiplexed qPCR
A Haemophilus influenzae serotype b in induced sputum datum that specifies whether the organism was detected by multiplex real time polymerase chain reaction assay.
presence of Haemophilus influenzae serotype b in induced sputum by multiplex real time polymerase chain reaction assay
A Haemophilus influenzae in induced sputum datum that specifies whether the organism was detected.
presence of Haemophilus influenzae in induced sputum
Haemophilus influenzae, by multiplexed qPCR
A Haemophilus influenzae in induced sputum datum that specifies whether the organism was detected by multiplex real time polymerase chain reaction assay.
presence of Haemophilus influenzae in induced sputum by multiplex real time polymerase chain reaction assay
Haemophilus parahaemolyticus, by bacteriology
A Haemophilus parahaemolyticus in induced sputum datum that specifies whether the organism was detected.
presence of Haemophilus parahaemolyticus in induced sputum
Haemophilus parahaemolyticus, by multiplexed qPCR
A Haemophilus parahaemolyticus in induced sputum datum that specifies whether the organism was detected by multiplex real time polymerase chain reaction assay.
presence of Haemophilus parahaemolyticus in induced sputum by multiplex real time polymerase chain reaction assay
Haemophilus parainfluenzae, by bacteriology
A Haemophilus parainfluenzae in induced sputum datum that specifies whether the organism was detected.
presence of Haemophilus parainfluenzae in induced sputum
A Haemophilus in induced sputum datum that specifies whether the organism was detected.
presence of Haemophilus in induced sputum
A Kingella in induced sputum datum that specifies whether the organism was detected.
presence of Kingella in induced sputum
Klebsiella aerogenes (Enterobacter aerogenes), by bacteriology
A Klebsiella aerogenes in induced sputum datum that specifies whether the organism was detected.
presence of Klebsiella aerogenes in induced sputum
A Klebsiella oxytoca in induced sputum datum that specifies whether the organism was detected.
presence of Klebsiella oxytoca in induced sputum
A Klebsiella pneumoniae in induced sputum datum that specifies whether the organism was detected.
presence of Klebsiella pneumoniae in induced sputum
A Klebsiella in induced sputum datum that specifies whether the organism was detected.
presence of Klebsiella in induced sputum
A bacteria in induced sputum datum that specifies whether Legionella was detected by multiplex real time polymerase chain reaction assay.
presence of Legionella in induced sputum by multiplex real time polymerase chain reaction assay
Mixed gram-negative rods, by bacteriology
A bacteria in induced sputum datum that specifies whether Mixed gram-negative rods was detected.
presence of Mixed gram-negative rods in induced sputum
A Moraxella catarrhalis in induced sputum datum that specifies whether the organism was detected.
presence of Moraxella catarrhalis in induced sputum
Moraxella catarrhalis (Branhamella catarrhalis), by multiplexed qPCR
A bacteria in induced sputum datum that specifies whether Moraxella catarrhalis was detected by multiplex real time polymerase chain reaction assay.
presence of Moraxella catarrhalis in induced sputum by multiplex real time polymerase chain reaction assay
Moraxella nonliquefaciens, by bacteriology
A Moraxella nonliquefaciens in induced sputum datum that specifies whether the organism was detected.
presence of Moraxella nonliquefaciens in induced sputum
A Moraxella in induced sputum datum that specifies whether the organism was detected.
presence of Moraxella in induced sputum
Mycoplasma pneumoniae, by multiplexed qPCR
A bacteria in induced sputum datum that specifies whether Mycoplasmoides pneumoniae was detected by multiplex real time polymerase chain reaction assay.
presence of Mycoplasmoides pneumoniae in induced sputum by multiplex real time polymerase chain reaction assay
A Neisseria meningitidis in induced sputum datum that specifies whether the organism was detected.
presence of Neisseria meningitidis in induced sputum
A Proteus mirabilis in induced sputum datum that specifies whether the organism was detected.
presence of Proteus mirabilis in induced sputum
A Pseudomonas aeruginosa in induced sputum datum that specifies whether the organism was detected.
presence of Pseudomonas aeruginosa in induced sputum
Pseudomonas fluorescens, by bacteriology
A Pseudomonas fluorescens in induced sputum datum that specifies whether the organism was detected.
presence of Pseudomonas fluorescens in induced sputum
A Pseudomonas in induced sputum datum that specifies whether the organism was detected.
presence of Pseudomonas in induced sputum
A Stutzerimonas stutzeri in induced sputum datum that specifies whether the organism was detected.
presence of Stutzerimonas stutzeri in induced sputum
A Salmonella in induced sputum datum that specifies whether the organism was detected.
presence of Salmonella in induced sputum
A Salmonella in induced sputum datum that specifies whether Salmonella was detected by multiplex real time polymerase chain reaction assay.
presence of Salmonella in induced sputum by multiplex real time polymerase chain reaction assay
A Salmonella in induced sputum datum that specifies whether Salmonella enterica subsp. enterica serovar Typhi was detected.
presence of Salmonella enterica subsp. enterica serovar Typhi in induced sputum
A Serratia marcescens in induced sputum datum that specifies whether the organism was detected.
presence of Serratia marcescens in induced sputum
A Serratia in induced sputum datum that specifies whether the organism was detected.
presence of Serratia in induced sputum
A Staphylococcus aureus in induced sputum datum that specifies whether the organism was detected.
presence of Staphylococcus aureus in induced sputum
Staphylococcus aureus, by multiplexed qPCR
A Staphylococcus aureus in induced sputum datum that specifies whether Staphylococcus aureus was detected by multiplex real time polymerase chain reaction assay.
presence of Staphylococcus aureus in induced sputum by multiplex real time polymerase chain reaction assay
Staphylococcus epidermidis, by bacteriology
A Staphylococcus epidermidis in induced sputum datum that specifies whether the organism was detected.
presence of Staphylococcus epidermidis in induced sputum
Stenotrophomonas maltophilia, by bacteriology
A Stenotrophomonas maltophilia in induced sputum datum that specifies whether the organism was detected.
presence of Stenotrophomonas maltophilia in induced sputum
Streptococcus anginosus group (Streptococcus milleri group), by bacteriology
A Streptococcus anginosus group in induced sputum datum that specifies whether the organism was detected.
presence of Streptococcus anginosus group in induced sputum
A Streptococcus sp. group A in induced sputum datum that specifies whether the organism was detected.
presence of Streptococcus group A in induced sputum
A Streptococcus sp. group C in induced sputum datum that specifies whether the organism was detected.
presence of Streptococcus group C in induced sputum
A Streptococcus sp. group G in induced sputum datum that specifies whether the organism was detected.
presence of Streptococcus group G in induced sputum
A laboratory test that has an induced sputum specimen as specified input.
A laboratory test that has a endotracheal aspirate specimen as specified input.
A Streptococcus pneumoniae in induced sputum datum that specifies whether the organism was detected.
presence of Streptococcus pneumoniae in induced sputum
Streptococcus pneumoniae, by multiplexed qPCR
A Streptococcus pneumoniae in induced sputum datum that specifies whether the organism was detected by multiplex real time polymerase chain reaction assay.
presence of Streptococcus pneumoniae in induced sputum by multiplex real time polymerase chain reaction assay
A Streptococcus in induced sputum datum that specifies whether the organism was detected.
presence of Streptococcus in induced sputum
Pneumocystis jiroveci, by multiplexed qPCR
A eukaryota in induced sputum datum that specifies whether Pneumocystis jirovecii was detected by multiplex real time polymerase chain reaction assay.
presence of Pneumocystis jirovecii in induced sputum by multiplex real time polymerase chain reaction assay
Acinetobacter baumannii, by bacteriology result
A bacteria in induced sputum datum that is used to determine the presence of Acinetobacter baumannii in the specimen.
Acinetobacter baumannii in induced sputum datum
Acinetobacter calcoaceticus, by bacteriology result
A bacteria in induced sputum datum that is used to determine the presence of Acinetobacter calcoaceticus in the specimen.
Acinetobacter calcoaceticus in induced sputum datum
A bacteria in induced sputum datum that is used to determine the presence of Acinetobacter in the specimen.
Acinetobacter in induced sputum datum
Aeromonas hydrophila, by bacteriology result
A bacteria in induced sputum datum that is used to determine the presence of Aeromonas hydrophila in the specimen.
Aeromonas hydrophila in induced sputum datum
Agregattibacter aphrophilus (Haemophilus aphrophilus), by bacteriology result
A bacteria in induced sputum datum that is used to determine the presence of Aggregatibacter aphrophilus in the specimen.
Aggregatibacter aphrophilus in induced sputum datum
Alpha-hemolytic Streptococcus (viridans), by bacteriology result
A bacteria in induced sputum datum that is used to determine the presence of Alpha-Hemolytic Streptococcus in the specimen.
Alpha-Hemolytic Streptococcus in induced sputum datum
Beta-hemolytic Streptococcus, by bacteriology result
A bacteria in induced sputum datum that is used to determine the presence of Beta-Hemolytic Streptococcus in the specimen.
Beta-Hemolytic Streptococcus in induced sputum datum
Bordetella pertussis, by multiplexed qPCR result
The threshold cycle that is the specified output of a multiplex real time polymerase chain reaction assay that has the objective of determining the number of Bordetella pertussis in an induced sputum specimen.
multiplex qPCR threshold cycle for Bordetella pertussis in induced sputum
Burkholderia cepacia, by bacteriology result
A bacteria in induced sputum datum that is used to determine the presence of Burkholderia cepacia in the specimen.
Burkholderia cepacia in induced sputum datum
Citrobacter braakii, by bacteriology result
A bacteria in induced sputum datum that is used to determine the presence of Citrobacter braakii in the specimen.
Citrobacter braakii in induced sputum datum
Citrobacter freundii, by bacteriology result
A bacteria in induced sputum datum that is used to determine the presence of Citrobacter freundii in the specimen.
Citrobacter freundii in induced sputum datum
Coagulase-negative Staphylococcus, by bacteriology result
A bacteria in induced sputum datum that is used to determine the presence of Coagulase-Negative Staphylococcus in the specimen.
Coagulase-Negative Staphylococcus in induced sputum datum
Coliform bacilli, by bacteriology result
A bacteria in induced sputum datum that is used to determine the presence of Coliform Bacteria in the specimen.
Coliform Bacteria in induced sputum datum
A bacteria in induced sputum datum that is used to determine the presence of Corynebacterium in the specimen.
Corynebacterium in induced sputum datum
Cronobacter sakazakii (Enterobacter sakazakii), by bacteriology result
A bacteria in induced sputum datum that is used to determine the presence of Cronobacter sakazakii in the specimen.
Cronobacter sakazakii in induced sputum datum
Enterobacter asburiae, by bacteriology result
A bacteria in induced sputum datum that is used to determine the presence of Enterobacter asburiae in the specimen.
Enterobacter asburiae in induced sputum datum
Enterobacter cloacae, by bacteriology result
A bacteria in induced sputum datum that is used to determine the presence of Enterobacter cloacae in the specimen.
Enterobacter cloacae in induced sputum datum
A bacteria in induced sputum datum that is used to determine the presence of Enterobacter in the specimen.
Enterobacter in induced sputum datum
A bacteria in induced sputum datum that is used to determine the presence of Enterococcus in the specimen.
Enterococcus in induced sputum datum
A bacteria in induced sputum datum that is used to determine the presence of Escherichia coli in the specimen.
Escherichia coli in induced sputum datum
Haemophilus haemolyticus, by bacteriology result
A bacteria in induced sputum datum that is used to determine the presence of Haemophilus haemolyticus in the specimen.
Haemophilus haemolyticus in induced sputum datum
Haemophilus influenzae, by multiplexed qPCR result
The threshold cycle that is the specified output of a multiplex real time polymerase chain reaction assay that has the objective of determining the number of Haemophilus influenzae in an induced sputum specimen.
multiplex qPCR threshold cycle for Haemophilus influenzae in induced sputum
Haemophilus influenzae type B, by bacteriology result
A bacteria in induced sputum datum that is used to determine the presence of Haemophilus influenzae serotype b in the specimen.
Haemophilus influenzae serotype b in induced sputum datum
Haemophilus influenzae, by bacteriology result
A bacteria in induced sputum datum that is used to determine the presence of Haemophilus influenzae in the specimen.
Haemophilus influenzae in induced sputum datum
Haemophilus parahaemolyticus, by bacteriology result
A bacteria in induced sputum datum that is used to determine the presence of Haemophilus parahaemolyticus in the specimen.
Haemophilus parahaemolyticus in induced sputum datum
Haemophilus parainfluenzae, by bacteriology result
A bacteria in induced sputum datum that is used to determine the presence of Haemophilus parainfluenzae in the specimen.
Haemophilus parainfluenzae in induced sputum datum
A bacteria in induced sputum datum that is used to determine the presence of Haemophilus in the specimen.
Haemophilus in induced sputum datum
A bacteria in induced sputum datum that is used to determine the presence of Kingella in the specimen.
Kingella in induced sputum datum
Klebsiella aerogenes (Enterobacter aerogenes), by bacteriology result
A bacteria in induced sputum datum that is used to determine the presence of Klebsiella aerogenes in the specimen.
Klebsiella aerogenes in induced sputum datum
Klebsiella oxytoca, by bacteriology result
A bacteria in induced sputum datum that is used to determine the presence of Klebsiella oxytoca in the specimen.
Klebsiella oxytoca in induced sputum datum
Klebsiella pneumoniae, by bacteriology result
A bacteria in induced sputum datum that is used to determine the presence of Klebsiella pneumoniae in the specimen.
Klebsiella pneumoniae in induced sputum datum
A bacteria in induced sputum datum that is used to determine the presence of Klebsiella in the specimen.
Klebsiella in induced sputum datum
The threshold cycle that is the specified output of a multiplex real time polymerase chain reaction assay that has the objective of determining the number of Legionella in an induced sputum specimen.
multiplex qPCR threshold cycle for Legionella in induced sputum
Moraxella catarrhalis (Branhamella catarrhalis), by multiplexed qPCR result
The threshold cycle that is the specified output of a multiplex real time polymerase chain reaction assay that has the objective of determining the number of Moraxella catarrhalis in an induced sputum specimen.
multiplex qPCR threshold cycle for Moraxella catarrhalis in induced sputum
Moraxella catarrhalis (Branhamella catarrhalis), by bacteriology result
A bacteria in induced sputum datum that is used to determine the presence of Moraxella catarrhalis in the specimen.
Moraxella catarrhalis in induced sputum datum
Moraxella nonliquefaciens, by bacteriology result
A bacteria in induced sputum datum that is used to determine the presence of Moraxella nonliquefaciens in the specimen.
Moraxella nonliquefaciens in induced sputum datum
A bacteria in induced sputum datum that is used to determine the presence of Moraxella in the specimen.
Moraxella in induced sputum datum
Mycoplasma pneumoniae, by multiplexed qPCR result
The threshold cycle that is the specified output of a multiplex real time polymerase chain reaction assay that has the objective of determining the number of Mycoplasmoides pneumoniae in an induced sputum specimen.
multiplex qPCR threshold cycle for Mycoplasmoides pneumoniae in induced sputum
Neisseria meningitidis, by bacteriology result
A bacteria in induced sputum datum that is used to determine the presence of Neisseria meningitidis in the specimen.
Neisseria meningitidis in induced sputum datum
Proteus mirabilis, by bacteriology result
A bacteria in induced sputum datum that is used to determine the presence of Proteus mirabilis in the specimen.
Proteus mirabilis in induced sputum datum
Pseudomonas aeruginosa, by bacteriology result
A bacteria in induced sputum datum that is used to determine the presence of Pseudomonas aeruginosa in the specimen.
Pseudomonas aeruginosa in induced sputum datum
Pseudomonas fluorescens, by bacteriology result
A bacteria in induced sputum datum that is used to determine the presence of Pseudomonas fluorescens in the specimen.
Pseudomonas fluorescens in induced sputum datum
A bacteria in induced sputum datum that is used to determine the presence of Pseudomonas in the specimen.
Pseudomonas in induced sputum datum
Pseudomonas stutzeri, by bacteriology result
A bacteria in induced sputum datum that is used to determine the presence of Stutzerimonas stutzeri in the specimen.
Stutzerimonas stutzeri in induced sputum datum
The threshold cycle that is the specified output of a multiplex real time polymerase chain reaction assay that has the objective of determining the number of Salmonella in an induced sputum specimen.
multiplex qPCR threshold cycle for Salmonella in induced sputum
A bacteria in induced sputum datum that is used to determine the presence of Salmonella in the specimen.
Salmonella in induced sputum datum
Serratia marcescens, by bacteriology result
A bacteria in induced sputum datum that is used to determine the presence of Serratia marcescens in the specimen.
Serratia marcescens in induced sputum datum
A bacteria in induced sputum datum that is used to determine the presence of Serratia in the specimen.
Serratia in induced sputum datum
Staphylococcus aureus, by multiplexed qPCR result
The threshold cycle that is the specified output of a multiplex real time polymerase chain reaction assay that has the objective of determining the number of Staphylococcus aureus in an induced sputum specimen.
multiplex qPCR threshold cycle for Staphylococcus aureus in induced sputum
Staphylococcus aureus, by bacteriology result
A bacteria in induced sputum datum that is used to determine the presence of Staphylococcus aureus in the specimen.
Staphylococcus aureus in induced sputum datum
Staphylococcus epidermidis, by bacteriology result
A bacteria in induced sputum datum that is used to determine the presence of Staphylococcus epidermidis in the specimen.
Staphylococcus epidermidis in induced sputum datum
Stenotrophomonas maltophilia, by bacteriology result
A bacteria in induced sputum datum that is used to determine the presence of Stenotrophomonas maltophilia in the specimen.
Stenotrophomonas maltophilia in induced sputum datum
Streptococcus anginosus group (Streptococcus milleri group), by bacteriology result
A bacteria in induced sputum datum that is used to determine the presence of Streptococcus anginosus group in the specimen.
Streptococcus anginosus group in induced sputum datum
Streptococcus group A (Streptococcus pyogenes), by bacteriology result
A bacteria in induced sputum datum that is used to determine the presence of Streptococcus sp. group A in the specimen.
Streptococcus sp. group A in induced sputum datum
Streptococcus group C, by bacteriology result
A bacteria in induced sputum datum that is used to determine the presence of Streptococcus sp. group C in the specimen.
Streptococcus sp. group C in induced sputum datum
Streptococcus group G, by bacteriology result
A bacteria in induced sputum datum that is used to determine the presence of Streptococcus sp. group G in the specimen.
Streptococcus sp. group G in induced sputum datum
Streptococcus pneumoniae, by multiplexed qPCR result
The threshold cycle that is the specified output of a multiplex real time polymerase chain reaction assay that has the objective of determining the number of Streptococcus pneumoniae in an induced sputum specimen.
multiplex qPCR threshold cycle for Streptococcus pneumoniae in induced sputum
Streptococcus pneumoniae, by bacteriology result
A bacteria in induced sputum datum that is used to determine the presence of Streptococcus pneumoniae in the specimen.
Streptococcus pneumoniae in induced sputum datum
A bacteria in induced sputum datum that is used to determine the presence of Streptococcus in the specimen.
Streptococcus in induced sputum datum
Pneumocystis jiroveci, by multiplexed qPCR result
The threshold cycle that is the specified output of a multiplex real time polymerase chain reaction assay that has the objective of determining the number of Pneumocystis jirovecii in an induced sputum specimen.
multiplex qPCR threshold cycle for Pneumocystis jirovecii in induced sputum
The threshold cycle that is the specified output of a multiplex real time polymerase chain reaction assay that has the objective of determining the number of Adenoviridae in an induced sputum specimen.
multiplex qPCR threshold cycle for Adenoviridae in induced sputum
Coronavirus 229, by multiplexed qPCR result
The threshold cycle that is the specified output of a multiplex real time polymerase chain reaction assay that has the objective of determining the number of Human coronavirus 229E in an induced sputum specimen.
multiplex qPCR threshold cycle for Human coronavirus 229E in induced sputum
Coronavirus 43, by multiplexed qPCR result
The threshold cycle that is the specified output of a multiplex real time polymerase chain reaction assay that has the objective of determining the number of Human coronavirus OC43 in an induced sputum specimen.
multiplex qPCR threshold cycle for Human coronavirus OC43 in induced sputum
Coronavirus 63, by multiplexed qPCR result
The threshold cycle that is the specified output of a multiplex real time polymerase chain reaction assay that has the objective of determining the number of Human coronavirus NL63 in an induced sputum specimen.
multiplex qPCR threshold cycle for Human coronavirus NL63 in induced sputum
Coronavirus HKU, by multiplexed qPCR result
The threshold cycle that is the specified output of a multiplex real time polymerase chain reaction assay that has the objective of determining the number of Human coronavirus HKU1 in an induced sputum specimen.
multiplex qPCR threshold cycle for Human coronavirus HKU1 in induced sputum
Cytomegalovirus, by multiplexed qPCR result
The threshold cycle that is the specified output of a multiplex real time polymerase chain reaction assay that has the objective of determining the number of Cytomegalovirus in an induced sputum specimen.
multiplex qPCR threshold cycle for Cytomegalovirus in induced sputum
Human bocavirus, by multiplexed qPCR result
The threshold cycle that is the specified output of a multiplex real time polymerase chain reaction assay that has the objective of determining the number of Human bocavirus in an induced sputum specimen.
multiplex qPCR threshold cycle for Human bocavirus in induced sputum
Human metapneumovirus A/B, by multiplexed qPCR result
The threshold cycle that is the specified output of a multiplex real time polymerase chain reaction assay that has the objective of determining the number of Human metapneumovirus in an induced sputum specimen.
multiplex qPCR threshold cycle for Human metapneumovirus in induced sputum
Human respiratory syncytial viruses A/B, by multiplexed qPCR result
The threshold cycle that is the specified output of a multiplex real time polymerase chain reaction assay that has the objective of determining the number of Respiratory syncytial virus in an induced sputum specimen.
multiplex qPCR threshold cycle for Respiratory syncytial virus in induced sputum
The threshold cycle that is the specified output of a multiplex real time polymerase chain reaction assay that has the objective of determining the number of Influenza A virus in an induced sputum specimen.
multiplex qPCR threshold cycle for Influenza A virus in induced sputum
The threshold cycle that is the specified output of a multiplex real time polymerase chain reaction assay that has the objective of determining the number of Influenza B virus in an induced sputum specimen.
multiplex qPCR threshold cycle for Influenza B virus in induced sputum
The threshold cycle that is the specified output of a multiplex real time polymerase chain reaction assay that has the objective of determining the number of Influenza C virus in an induced sputum specimen.
multiplex qPCR threshold cycle for Influenza C virus in induced sputum
Parainfluenza 1, by multiplexed qPCR result
The threshold cycle that is the specified output of a multiplex real time polymerase chain reaction assay that has the objective of determining the number of Human respirovirus 1 in an induced sputum specimen.
multiplex qPCR threshold cycle for Human respirovirus 1 in induced sputum
Parainfluenza 2, by multiplexed qPCR result
The threshold cycle that is the specified output of a multiplex real time polymerase chain reaction assay that has the objective of determining the number of Human orthorubulavirus 2 in an induced sputum specimen.
multiplex qPCR threshold cycle for Human orthorubulavirus 2 in induced sputum
Parainfluenza 3, by multiplexed qPCR result
The threshold cycle that is the specified output of a multiplex real time polymerase chain reaction assay that has the objective of determining the number of Human respirovirus 3 in an induced sputum specimen.
multiplex qPCR threshold cycle for Human respirovirus 3 in induced sputum
Parainfluenza 4, by multiplexed qPCR result
The threshold cycle that is the specified output of a multiplex real time polymerase chain reaction assay that has the objective of determining the number of Human orthorubulavirus 4 in an induced sputum specimen.
multiplex qPCR threshold cycle for Human orthorubulavirus 4 in induced sputum
Parechovirus/Enterovirus, by multiplexed qPCR result
The threshold cycle that is the specified output of a multiplex real time polymerase chain reaction assay that has the objective of determining the number of Enterovirus or Parechovirus in an induced sputum specimen.
multiplex qPCR threshold cycle for Enterovirus or Parechovirus in induced sputum
The threshold cycle that is the specified output of a multiplex real time polymerase chain reaction assay that has the objective of determining the number of Rhinovirus in an induced sputum specimen.
multiplex qPCR threshold cycle for Rhinovirus in induced sputum
A virus in induced sputum datum that specifies whether Adenoviridae were detected by multiplex real time polymerase chain reaction assay.
presence of Adenoviridae in induced sputum by multiplex real time polymerase chain reaction assay
A virus in induced sputum datum that specifies whether a virus was detected by multiplex real time polymerase chain reaction assay.
presence of virus in induced sputum by multiplex real time polymerase chain reaction assay
A virus in induced sputum datum that specifies whether Human coronavirus 229E was detected by multiplex real time polymerase chain reaction assay.
presence of human coronavirus 229E in induced sputum by multiplex real time polymerase chain reaction assay
A virus in induced sputum datum that specifies whether Human coronavirus OC43 was detected by multiplex real time polymerase chain reaction assay.
presence of Human coronavirus OC43 in induced sputum by multiplex real time polymerase chain reaction assay
A virus in induced sputum datum that specifies whether Human coronavirus NL63 was detected by multiplex real time polymerase chain reaction assay.
presence of Human coronavirus NL63 in induced sputum by multiplex real time polymerase chain reaction assay
A virus in induced sputum datum that specifies whether Human coronavirus HKU1 was detected by multiplex real time polymerase chain reaction assay.
presence of Human coronavirus HKU1 in induced sputum by multiplex real time polymerase chain reaction assay
A virus in induced sputum datum that specifies whether Cytomegalovirus was detected by multiplex real time polymerase chain reaction assay.
presence of Cytomegalovirus in induced sputum by multiplex real time polymerase chain reaction assay
A virus in induced sputum datum that specifies whether Human bocavirus was detected by multiplex real time polymerase chain reaction assay.
presence of Human bocavirus in induced sputum by multiplex real time polymerase chain reaction assay
Human metapneumoviruses A/B, by multiplexed qPCR
A virus in induced sputum datum that specifies whether Human metapneumovirus was detected by multiplex real time polymerase chain reaction assay.
presence of Human metapneumovirus in induced sputum by multiplex real time polymerase chain reaction assay
Human respiratory syncytial viruses A/B, by multiplexed qPCR
A virus in induced sputum datum that specifies whether Human orthopneumovirus was detected by multiplex real time polymerase chain reaction assay.
presence of Human orthopneumovirus in induced sputum by multiplex real time polymerase chain reaction assay
A virus in induced sputum datum that specifies whether Influenza A virus was detected by multiplex real time polymerase chain reaction assay.
presence of Influenza A virus in induced sputum by multiplex real time polymerase chain reaction assay
A virus in induced sputum datum that specifies whether Influenza B virus was detected by multiplex real time polymerase chain reaction assay.
presence of Influenza B virus in induced sputum by multiplex real time polymerase chain reaction assay
A virus in induced sputum datum that specifies whether Influenza C virus was detected by multiplex real time polymerase chain reaction assay.
presence of Influenza C virus in induced sputum by multiplex real time polymerase chain reaction assay
A virus in induced sputum datum that specifies whether Human respirovirus 1 was detected by multiplex real time polymerase chain reaction assay.
presence of Human respirovirus 1 in induced sputum by multiplex real time polymerase chain reaction assay
A virus in induced sputum datum that specifies whether Human orthorubulavirus 2 was detected by multiplex real time polymerase chain reaction assay.
presence of Human orthorubulavirus 2 in induced sputum by multiplex real time polymerase chain reaction assay
A virus in induced sputum datum that specifies whether Human respirovirus 3 was detected by multiplex real time polymerase chain reaction assay.
presence of Human respirovirus 3 in induced sputum by multiplex real time polymerase chain reaction assay
A virus in induced sputum datum that specifies whether Human orthorubulavirus 4 was detected by multiplex real time polymerase chain reaction assay.
presence of Human orthorubulavirus 4 in induced sputum by multiplex real time polymerase chain reaction assay
Parechovirus/Enterovirus, by multiplexed qPCR
A virus in induced sputum datum that specifies whether Picornaviridae was detected by multiplex real time polymerase chain reaction assay.
presence of Picornaviridae in induced sputum by multiplex real time polymerase chain reaction assay
A virus in induced sputum datum that specifies whether Rhinovirus was detected by multiplex real time polymerase chain reaction assay.
presence of Rhinovirus in induced sputum by multiplex real time polymerase chain reaction assay
Streptococcus pneumoniae serotype 2, by bacteriology result
A bacteria in induced sputum datum that is used to determine the presence of Streptococcus pneumoniae serotype 2 in the specimen.
Streptococcus pneumoniae serotype 2 in induced sputum datum
A bacteria in lung datum that specifies whether bacteria were detected by multiplex real time polymerase chain reaction assay.
presence of bacteria in lung by multiplex real time polymerase chain reaction assay
A bacteria in lung datum that specifies whether Bordetella pertussis was detected by multiplex real time polymerase chain reaction assay.
presence of Bordetella pertussis in lung by multiplex real time polymerase chain reaction assay
A bacteria in lung datum that specifies whether Chlamydia pneumoniae was detected by multiplex real time polymerase chain reaction assay.
presence of Chlamydia pneumoniae in lung by multiplex real time polymerase chain reaction assay
A bacteria in lung datum that specifies whether Coagulase-Negative Staphylococcus was detected.
presence of Coagulase-Negative Staphylococcus in lung
A bacteria in lung datum that specifies whether Haemophilus influenzae serotype b was detected by multiplex real time polymerase chain reaction assay.
presence of Haemophilus influenzae serotype b in lung by multiplex real time polymerase chain reaction assay
A bacteria in lung datum that specifies whether Haemophilus influenzae was detected.
presence of Haemophilus influenzae in lung
A bacteria in lung datum that specifies whether Haemophilus influenzae was detected by multiplex real time polymerase chain reaction assay.
presence of Haemophilus influenzae in lung by multiplex real time polymerase chain reaction assay
A bacteria in lung datum that specifies whether Haemophilus parahaemolyticus was detected by multiplex real time polymerase chain reaction assay.
presence of Haemophilus parahaemolyticus in lung by multiplex real time polymerase chain reaction assay
A bacteria in lung datum that specifies whether Legionella was detected by multiplex real time polymerase chain reaction assay.
presence of Legionella in lung by multiplex real time polymerase chain reaction assay
A bacteria in lung datum that specifies whether Moraxella catarrhalis was detected.
presence of Moraxella catarrhalis in lung
A bacteria in lung datum that specifies whether Moraxella catarrhalis was detected by multiplex real time polymerase chain reaction assay.
presence of Moraxella catarrhalis in lung by multiplex real time polymerase chain reaction assay
A bacteria in lung datum that specifies whether Mycoplasmoides pneumoniae was detected by multiplex real time polymerase chain reaction assay.
presence of Mycoplasmoides pneumoniae in lung by multiplex real time polymerase chain reaction assay
A bacteria in lung datum that specifies whether Salmonella was detected by multiplex real time polymerase chain reaction assay.
presence of Salmonella in lung by multiplex real time polymerase chain reaction assay
A bacteria in lung datum that specifies whether Staphylococcus aureus was detected.
presence of Staphylococcus aureus in lung
A bacteria in lung datum that specifies whether Staphylococcus aureus was detected by multiplex real time polymerase chain reaction assay.
presence of Staphylococcus aureus in lung by multiplex real time polymerase chain reaction assay
A bacteria in lung datum that specifies whether Streptococcus pneumoniae was detected.
presence of Streptococcus pneumoniae in lung
A bacteria in lung datum that specifies whether Streptococcus pneumoniae was detected by multiplex real time polymerase chain reaction assay.
presence of Streptococcus pneumoniae in lung by multiplex real time polymerase chain reaction assay
A eukaryota in lung datum that specifies whether Pneumocystis jirovecii was detected by multiplex real time polymerase chain reaction assay.
presence of Pneumocystis jirovecii in lung by multiplex real time polymerase chain reaction assay
The threshold cycle that is the specified output of a multiplex real time polymerase chain reaction assay that has the objective of determining the number of Bordetella pertussis in an lung specimen.
multiplex qPCR threshold cycle for Bordetella pertussis in lung
Chlamydophila pneumoniae, by multiplexed qPCR result
The threshold cycle that is the specified output of a multiplex real time polymerase chain reaction assay that has the objective of determining the number of Chlamydia pneumoniae in an lung specimen.
multiplex qPCR threshold cycle for Chlamydia pneumoniae in lung
The threshold cycle that is the specified output of a multiplex real time polymerase chain reaction assay that has the objective of determining the number of Haemophilus influenzae in an lung specimen.
multiplex qPCR threshold cycle for Haemophilus influenzae in lung
The threshold cycle that is the specified output of a multiplex real time polymerase chain reaction assay that has the objective of determining the number of Legionella in an lung specimen.
multiplex qPCR threshold cycle for Legionella in lung
The threshold cycle that is the specified output of a multiplex real time polymerase chain reaction assay that has the objective of determining the number of Moraxella catarrhalis in an lung specimen.
multiplex qPCR threshold cycle for Moraxella catarrhalis in lung
The threshold cycle that is the specified output of a multiplex real time polymerase chain reaction assay that has the objective of determining the number of Mycoplasmoides pneumoniae in an lung specimen.
multiplex qPCR threshold cycle for Mycoplasmoides pneumoniae in lung
The threshold cycle that is the specified output of a multiplex real time polymerase chain reaction assay that has the objective of determining the number of Salmonella in an lung specimen.
multiplex qPCR threshold cycle for Salmonella in lung
The threshold cycle that is the specified output of a multiplex real time polymerase chain reaction assay that has the objective of determining the number of Staphylococcus aureus in an lung specimen.
multiplex qPCR threshold cycle for Staphylococcus aureus in lung
The threshold cycle that is the specified output of a multiplex real time polymerase chain reaction assay that has the objective of determining the number of Streptococcus pneumoniae in an lung specimen.
multiplex qPCR threshold cycle for Streptococcus pneumoniae in lung
The threshold cycle that is the specified output of a multiplex real time polymerase chain reaction assay that has the objective of determining the number of Pneumocystis jirovecii in an lung specimen.
multiplex qPCR threshold cycle for Pneumocystis jirovecii in lung
The threshold cycle that is the specified output of a multiplex real time polymerase chain reaction assay that has the objective of determining the number of Adenoviridae in an lung specimen.
multiplex qPCR threshold cycle for Adenoviridae in lung
The threshold cycle that is the specified output of a multiplex real time polymerase chain reaction assay that has the objective of determining the number of Human coronavirus 229E in an lung specimen.
multiplex qPCR threshold cycle for Human coronavirus 229E in lung
The threshold cycle that is the specified output of a multiplex real time polymerase chain reaction assay that has the objective of determining the number of Human coronavirus OC43 in an lung specimen.
multiplex qPCR threshold cycle for Human coronavirus OC43 in lung
The threshold cycle that is the specified output of a multiplex real time polymerase chain reaction assay that has the objective of determining the number of Human coronavirus NL63 in an lung specimen.
multiplex qPCR threshold cycle for Human coronavirus NL63 in lung
The threshold cycle that is the specified output of a multiplex real time polymerase chain reaction assay that has the objective of determining the number of Human coronavirus HKU1 in an lung specimen.
multiplex qPCR threshold cycle for Human coronavirus HKU1 in lung
The threshold cycle that is the specified output of a multiplex real time polymerase chain reaction assay that has the objective of determining the number of Cytomegalovirus in an lung specimen.
multiplex qPCR threshold cycle for Cytomegalovirus in lung
The threshold cycle that is the specified output of a multiplex real time polymerase chain reaction assay that has the objective of determining the number of Human bocavirus in an lung specimen.
multiplex qPCR threshold cycle for Human bocavirus in lung
Human metapneumonoviruses A/B, by multiplexed qPCR result
The threshold cycle that is the specified output of a multiplex real time polymerase chain reaction assay that has the objective of determining the number of Human metapneumovirus in an lung specimen.
multiplex qPCR threshold cycle for Human metapneumovirus in lung
The threshold cycle that is the specified output of a multiplex real time polymerase chain reaction assay that has the objective of determining the number of Respiratory syncytial virus in an lung specimen.
multiplex qPCR threshold cycle for Respiratory syncytial virus in lung
The threshold cycle that is the specified output of a multiplex real time polymerase chain reaction assay that has the objective of determining the number of Influenza A virus in an lung specimen.
multiplex qPCR threshold cycle for Influenza A virus in lung
The threshold cycle that is the specified output of a multiplex real time polymerase chain reaction assay that has the objective of determining the number of Influenza B virus in an lung specimen.
multiplex qPCR threshold cycle for Influenza B virus in lung
The threshold cycle that is the specified output of a multiplex real time polymerase chain reaction assay that has the objective of determining the number of Influenza C virus in an lung specimen.
multiplex qPCR threshold cycle for Influenza C virus in lung
The threshold cycle that is the specified output of a multiplex real time polymerase chain reaction assay that has the objective of determining the number of Human respirovirus 1 in an lung specimen.
multiplex qPCR threshold cycle for Human respirovirus 1 in lung
The threshold cycle that is the specified output of a multiplex real time polymerase chain reaction assay that has the objective of determining the number of Human orthorubulavirus 2 in an lung specimen.
multiplex qPCR threshold cycle for Human orthorubulavirus 2 in lung
The threshold cycle that is the specified output of a multiplex real time polymerase chain reaction assay that has the objective of determining the number of Human respirovirus 3 in an lung specimen.
multiplex qPCR threshold cycle for Human respirovirus 3 in lung
The threshold cycle that is the specified output of a multiplex real time polymerase chain reaction assay that has the objective of determining the number of Human orthorubulavirus 4 in an lung specimen.
multiplex qPCR threshold cycle for Human orthorubulavirus 4 in lung
The threshold cycle that is the specified output of a multiplex real time polymerase chain reaction assay that has the objective of determining the number of Enterovirus or Parechovirus in an lung specimen.
multiplex qPCR threshold cycle for Enterovirus or Parechovirus in lung
The threshold cycle that is the specified output of a multiplex real time polymerase chain reaction assay that has the objective of determining the number of Rhinovirus in an lung specimen.
multiplex qPCR threshold cycle for Rhinovirus in lung
A virus in lung datum that specifies whether Adenoviridae were detected by multiplex real time polymerase chain reaction assay.
presence of Adenoviridae in lung by multiplex real time polymerase chain reaction assay
A virus in lung datum that specifies whether a virus was detected by multiplex real time polymerase chain reaction assay.
presence of virus in lung by multiplex real time polymerase chain reaction assay
A virus in lung datum that specifies whether Human coronavirus 229E was detected by multiplex real time polymerase chain reaction assay.
presence of Human coronavirus 229E in lung by multiplex real time polymerase chain reaction assay
A virus in lung datum that specifies whether Human coronavirus OC43 was detected by multiplex real time polymerase chain reaction assay.
presence of Human coronavirus OC43 in lung by multiplex real time polymerase chain reaction assay
A virus in lung datum that specifies whether Human coronavirus NL63 was detected by multiplex real time polymerase chain reaction assay.
presence of Human coronavirus NL63 in lung by multiplex real time polymerase chain reaction assay
A virus in lung datum that specifies whether Human coronavirus HKU1 was detected by multiplex real time polymerase chain reaction assay.
presence of Human coronavirus HKU1 in lung by multiplex real time polymerase chain reaction assay
A virus in lung datum that specifies whether Cytomegalovirus was detected by multiplex real time polymerase chain reaction assay.
presence of Cytomegalovirus in lung by multiplex real time polymerase chain reaction assay
A virus in lung datum that specifies whether Human bocavirus was detected by multiplex real time polymerase chain reaction assay.
presence of Human bocavirus in lung by multiplex real time polymerase chain reaction assay
Human metapneumonoviruses A/B, by multiplexed qPCR
A virus in lung datum that specifies whether Human metapneumovirus was detected by multiplex real time polymerase chain reaction assay.
presence of Human metapneumovirus in lung by multiplex real time polymerase chain reaction assay
A virus in lung datum that specifies whether Human orthopneumovirus was detected by multiplex real time polymerase chain reaction assay.
presence of Human orthopneumovirus in lung by multiplex real time polymerase chain reaction assay
A virus in lung datum that specifies whether Influenza A virus was detected by multiplex real time polymerase chain reaction assay.
presence of Influenza A virus in lung by multiplex real time polymerase chain reaction assay
A virus in lung datum that specifies whether Influenza B virus was detected by multiplex real time polymerase chain reaction assay.
presence of Influenza B virus in lung by multiplex real time polymerase chain reaction assay
A virus in lung datum that specifies whether Influenza C virus was detected by multiplex real time polymerase chain reaction assay.
presence of Influenza C virus in lung by multiplex real time polymerase chain reaction assay
A virus in lung datum that specifies whether Human respirovirus 1 was detected by multiplex real time polymerase chain reaction assay.
presence of Human respirovirus 1 in lung by multiplex real time polymerase chain reaction assay
A virus in lung datum that specifies whether Human orthorubulavirus 2 was detected by multiplex real time polymerase chain reaction assay.
presence of Human orthorubulavirus 2 in lung by multiplex real time polymerase chain reaction assay
A virus in lung datum that specifies whether Human respirovirus 3 was detected by multiplex real time polymerase chain reaction assay.
presence of Human respirovirus 3 in lung by multiplex real time polymerase chain reaction assay
A virus in lung datum that specifies whether Human orthorubulavirus 4 was detected by multiplex real time polymerase chain reaction assay.
presence of Human orthorubulavirus 4 in lung by multiplex real time polymerase chain reaction assay
A virus in lung datum that specifies whether Picornaviridae was detected by multiplex real time polymerase chain reaction assay.
presence of Picornaviridae in lung by multiplex real time polymerase chain reaction assay
A virus in lung datum that specifies whether Rhinovirus was detected by multiplex real time polymerase chain reaction assay.
presence of Rhinovirus in lung by multiplex real time polymerase chain reaction assay
A bacteria in nasopharyngeal or oropharyngeal swab datum that specifies whether Bordetella pertussis was detected by multiplex real time polymerase chain reaction assay.
presence of Bordetella pertussis in nasopharynx or oropharynx by multiplex real time polymerase chain reaction assay
A bacteria in nasopharyngeal or oropharyngeal swab datum that specifies whether Chlamydia pneumoniae was detected by multiplex real time polymerase chain reaction assay.
presence of Chlamydia pneumoniae in nasopharynx or oropharynx by multiplex real time polymerase chain reaction assay
A bacteria in nasopharyngeal or oropharyngeal swab datum that specifies whether Haemophilus influenzae was detected by multiplex real time polymerase chain reaction assay.
presence of Haemophilus influenzae in nasopharynx or oropharynx by multiplex real time polymerase chain reaction assay
A bacteria in nasopharyngeal or oropharyngeal swab datum that specifies whether Legionella was detected by multiplex real time polymerase chain reaction assay.
presence of Legionella in nasopharynx or oropharynx by multiplex real time polymerase chain reaction assay
A bacteria in nasopharyngeal or oropharyngeal swab datum that specifies whether Moraxella catarrhalis was detected by multiplex real time polymerase chain reaction assay.
presence of Moraxella catarrhalis in nasopharynx or oropharynx by multiplex real time polymerase chain reaction assay
A bacteria in nasopharyngeal or oropharyngeal swab datum that specifies whether Mycoplasmoides pneumoniae was detected by multiplex real time polymerase chain reaction assay.
presence of Mycoplasmoides pneumoniae in nasopharynx or oropharynx by multiplex real time polymerase chain reaction assay
A bacteria in nasopharyngeal or oropharyngeal swab datum that specifies whether Salmonella was detected by multiplex real time polymerase chain reaction assay.
presence of Salmonella in nasopharynx or oropharynx by multiplex real time polymerase chain reaction assay
A bacteria in nasopharyngeal or oropharyngeal swab datum that specifies whether Staphylococcus aureus was detected by multiplex real time polymerase chain reaction assay.
presence of Staphylococcus aureus in nasopharynx or oropharynx by multiplex real time polymerase chain reaction assay
A bacteria in nasopharyngeal or oropharyngeal swab datum that is used to determine the presence of Streptococcus pneumoniae serotype 2 in the specimen.
Streptococcus pneumoniae serotype 2 in nasopharyngeal or oropharyngeal swab datum
Streptococcus pneumoniae serotype 3, by bacteriology result
A bacteria in nasopharyngeal or oropharyngeal swab datum that is used to determine the presence of Streptococcus pneumoniae serotype 3 in the specimen.
Streptococcus pneumoniae serotype 3 in nasopharyngeal or oropharyngeal swab datum
Streptococcus pneumoniae serotype 4, by bacteriology result
A bacteria in nasopharyngeal or oropharyngeal swab datum that is used to determine the presence of Streptococcus pneumoniae serotype 4 in the specimen.
Streptococcus pneumoniae serotype 4 in nasopharyngeal or oropharyngeal swab datum
A bacteria in nasopharyngeal or oropharyngeal swab datum that specifies whether Streptococcus pneumoniae was detected by multiplex real time polymerase chain reaction assay.
presence of Streptococcus pneumoniae in nasopharynx or oropharynx by multiplex real time polymerase chain reaction assay
A eukaryota in nasopharyngeal or oropharyngeal swab datum that specifies whether Pneumocystis jirovecii was detected by multiplex real time polymerase chain reaction assay.
presence of Pneumocystis jirovecii in nasopharynx or oropharynx by multiplex real time polymerase chain reaction assay
The threshold cycle that is the specified output of a multiplex real time polymerase chain reaction assay that has the objective of determining the number of Bordetella pertussis in a nasopharyngeal or oropharyngeal swab specimen.
multiplex qPCR threshold cycle for Bordetella pertussis in nasopharynx or oropharynx
The threshold cycle that is the specified output of a multiplex real time polymerase chain reaction assay that has the objective of determining the number of Chlamydia pneumoniae in a nasopharyngeal or oropharyngeal swab specimen.
multiplex qPCR threshold cycle for Chlamydia pneumoniae in nasopharynx or oropharynx
The threshold cycle that is the specified output of a multiplex real time polymerase chain reaction assay that has the objective of determining the number of Haemophilus influenzae in a nasopharynx specimen or oropharynx specimen.
multiplex qPCR threshold cycle for Haemophilus influenzae in nasopharynx or oropharynx
The threshold cycle that is the specified output of a multiplex real time polymerase chain reaction assay that has the objective of determining the number of Legionella in a nasopharyngeal or oropharyngeal swab specimen.
multiplex qPCR threshold cycle for Legionella in nasopharynx or oropharynx
The threshold cycle that is the specified output of a multiplex real time polymerase chain reaction assay that has the objective of determining the number of Moraxella catarrhalis in a nasopharyngeal or oropharyngeal swab specimen.
multiplex qPCR threshold cycle for Moraxella catarrhalis in nasopharynx or oropharynx
The threshold cycle that is the specified output of a multiplex real time polymerase chain reaction assay that has the objective of determining the number of Mycoplasmoides pneumoniae in a nasopharyngeal or oropharyngeal swab specimen.
multiplex qPCR threshold cycle for Mycoplasmoides pneumoniae in nasopharynx or oropharynx
The threshold cycle that is the specified output of a multiplex real time polymerase chain reaction assay that has the objective of determining the number of Salmonella in a nasopharyngeal or oropharyngeal swab specimen.
multiplex qPCR threshold cycle for Salmonella in nasopharynx or oropharynx
The threshold cycle that is the specified output of a multiplex real time polymerase chain reaction assay that has the objective of determining the number of Staphylococcus aureus in a nasopharyngeal or oropharyngeal swab specimen.
multiplex qPCR threshold cycle for Staphylococcus aureus in nasopharynx or oropharynx
The threshold cycle that is the specified output of a multiplex real time polymerase chain reaction assay that has the objective of determining the number of Streptococcus pneumoniae in a nasopharyngeal or oropharyngeal swab specimen.
multiplex qPCR threshold cycle for Streptococcus pneumoniae in nasopharynx or oropharynx
The threshold cycle that is the specified output of a multiplex real time polymerase chain reaction assay that has the objective of determining the number of Pneumocystis jirovecii in a nasopharyngeal or oropharyngeal swab specimen.
multiplex qPCR threshold cycle for Pneumocystis jirovecii in nasopharynx or oropharynx
The threshold cycle that is the specified output of a multiplex real time polymerase chain reaction assay that has the objective of determining the number of Adenoviridae in a nasopharyngeal or oropharyngeal swab specimen.
multiplex qPCR threshold cycle for Adenoviridae in nasopharynx or oropharynx
The threshold cycle that is the specified output of a multiplex real time polymerase chain reaction assay that has the objective of determining the number of Human coronavirus 229E in a nasopharyngeal or oropharyngeal swab specimen.
multiplex qPCR threshold cycle for Human coronavirus 229E in nasopharynx or oropharynx
The threshold cycle that is the specified output of a multiplex real time polymerase chain reaction assay that has the objective of determining the number of Human coronavirus OC43 in a nasopharyngeal or oropharyngeal swab specimen.
multiplex qPCR threshold cycle for Human coronavirus OC43 in nasopharynx or oropharynx
The threshold cycle that is the specified output of a multiplex real time polymerase chain reaction assay that has the objective of determining the number of Human coronavirus NL63 in a nasopharyngeal or oropharyngeal swab specimen.
multiplex qPCR threshold cycle for Human coronavirus NL63 in nasopharynx or oropharynx
The threshold cycle that is the specified output of a multiplex real time polymerase chain reaction assay that has the objective of determining the number of Human coronavirus HKU1 in a nasopharyngeal or oropharyngeal swab specimen.
multiplex qPCR threshold cycle for Human coronavirus HKU1 in nasopharynx or oropharynx
The threshold cycle that is the specified output of a multiplex real time polymerase chain reaction assay that has the objective of determining the number of Cytomegalovirus in a nasopharyngeal or oropharyngeal swab specimen.
multiplex qPCR threshold cycle for Cytomegalovirus in nasopharynx or oropharynx
The threshold cycle that is the specified output of a multiplex real time polymerase chain reaction assay that has the objective of determining the number of Human bocavirus in a nasopharyngeal or oropharyngeal swab specimen.
multiplex qPCR threshold cycle for Human bocavirus in nasopharynx or oropharynx
The threshold cycle that is the specified output of a multiplex real time polymerase chain reaction assay that has the objective of determining the number of Human metapneumovirus in a nasopharyngeal or oropharyngeal swab specimen.
multiplex qPCR threshold cycle for Human metapneumovirus in nasopharynx or oropharynx
The threshold cycle that is the specified output of a multiplex real time polymerase chain reaction assay that has the objective of determining the number of Human orthopneumovirus in a nasopharyngeal or oropharyngeal swab specimen.
multiplex qPCR threshold cycle for Human orthopneumovirus in nasopharynx or oropharynx
The threshold cycle that is the specified output of a multiplex real time polymerase chain reaction assay that has the objective of determining the number of Influenza A virus in a nasopharyngeal or oropharyngeal swab specimen.
multiplex qPCR threshold cycle for Influenza A virus in nasopharynx or oropharynx
The threshold cycle that is the specified output of a multiplex real time polymerase chain reaction assay that has the objective of determining the number of Influenza B virus in a nasopharyngeal or oropharyngeal swab specimen.
multiplex qPCR threshold cycle for Influenza B virus in nasopharynx or oropharynx
The threshold cycle that is the specified output of a multiplex real time polymerase chain reaction assay that has the objective of determining the number of Influenza C virus in a nasopharyngeal or oropharyngeal swab specimen.
multiplex qPCR threshold cycle for Influenza C virus in nasopharynx or oropharynx
The threshold cycle that is the specified output of a multiplex real time polymerase chain reaction assay that has the objective of determining the number of Human respirovirus 1 in a nasopharyngeal or oropharyngeal swab specimen.
multiplex qPCR threshold cycle for Human respirovirus 1 in nasopharynx or oropharynx
The threshold cycle that is the specified output of a multiplex real time polymerase chain reaction assay that has the objective of determining the number of Human orthorubulavirus 2 in a nasopharyngeal or oropharyngeal swab specimen.
multiplex qPCR threshold cycle for Human orthorubulavirus 2 in nasopharynx or oropharynx
The threshold cycle that is the specified output of a multiplex real time polymerase chain reaction assay that has the objective of determining the number of Human respirovirus 3 in a nasopharyngeal or oropharyngeal swab specimen.
multiplex qPCR threshold cycle for Human respirovirus 3 in nasopharynx or oropharynx
The threshold cycle that is the specified output of a multiplex real time polymerase chain reaction assay that has the objective of determining the number of Human orthorubulavirus 4 in a nasopharyngeal or oropharyngeal swab specimen.
multiplex qPCR threshold cycle for Human orthorubulavirus 4 in nasopharynx or oropharynx
The threshold cycle that is the specified output of a multiplex real time polymerase chain reaction assay that has the objective of determining the number of Enterovirus or Parechovirus in a nasopharyngeal or oropharyngeal swab specimen.
multiplex qPCR threshold cycle for Enterovirus or Parechovirus in nasopharynx or oropharynx
The threshold cycle that is the specified output of a multiplex real time polymerase chain reaction assay that has the objective of determining the number of Rhinovirus in a nasopharyngeal or oropharyngeal swab specimen.
multiplex qPCR threshold cycle for Rhinovirus in nasopharynx or oropharynx
A virus in nasopharyngeal or oropharyngeal swab datum that specifies whether Adenoviridae were detected by multiplex real time polymerase chain reaction assay.
presence of Adenoviridae in nasopharynx or oropharynx by multiplex real time polymerase chain reaction assay
A virus in nasopharyngeal or oropharyngeal swab datum that specifies whether Human coronavirus 229E was detected by multiplex real time polymerase chain reaction assay.
presence of Human coronavirus 229E in nasopharynx or oropharynx by multiplex real time polymerase chain reaction assay
A virus in nasopharyngeal or oropharyngeal swab datum that specifies whether Human coronavirus OC43 was detected by multiplex real time polymerase chain reaction assay.
presence of Human coronavirus OC43 in nasopharynx or oropharynx by multiplex real time polymerase chain reaction assay
A virus in nasopharyngeal or oropharyngeal swab datum that specifies whether Human coronavirus NL63 was detected by multiplex real time polymerase chain reaction assay.
presence of Human coronavirus NL63 in nasopharynx or oropharynx by multiplex real time polymerase chain reaction assay
A virus in nasopharyngeal or oropharyngeal swab datum that specifies whether Human coronavirus HKU1 was detected by multiplex real time polymerase chain reaction assay.
presence of Human coronavirus HKU1 in nasopharynx or oropharynx by multiplex real time polymerase chain reaction assay
A virus in nasopharyngeal or oropharyngeal swab datum that specifies whether Cytomegalovirus was detected by multiplex real time polymerase chain reaction assay.
presence of Cytomegalovirus in nasopharynx or oropharynx by multiplex real time polymerase chain reaction assay
A virus in nasopharyngeal or oropharyngeal swab datum that specifies whether Human bocavirus was detected by multiplex real time polymerase chain reaction assay.
presence of Human bocavirus in nasopharynx or oropharynx by multiplex real time polymerase chain reaction assay
A virus in nasopharyngeal or oropharyngeal swab datum that specifies whether Human metapneumovirus was detected by multiplex real time polymerase chain reaction assay.
presence of Human metapneumovirus in nasopharynx or oropharynx by multiplex real time polymerase chain reaction assay
A virus in nasopharyngeal or oropharyngeal swab datum that specifies whether Human orthopneumovirus was detected by multiplex real time polymerase chain reaction assay.
presence of Human orthopneumovirus in nasopharynx or oropharynx by multiplex real time polymerase chain reaction assay
A virus in nasopharyngeal or oropharyngeal swab datum that specifies whether Influenza A virus was detected by multiplex real time polymerase chain reaction assay.
presence of Influenza A virus in nasopharynx or oropharynx by multiplex real time polymerase chain reaction assay
A virus in nasopharyngeal or oropharyngeal swab datum that specifies whether Influenza B virus was detected by multiplex real time polymerase chain reaction assay.
presence of Influenza B virus in nasopharynx or oropharynx by multiplex real time polymerase chain reaction assay
A virus in nasopharyngeal or oropharyngeal swab datum that specifies whether Influenza C virus was detected by multiplex real time polymerase chain reaction assay.
presence of Influenza C virus in nasopharynx or oropharynx by multiplex real time polymerase chain reaction assay
A virus in nasopharyngeal or oropharyngeal swab datum that specifies whether Human respirovirus 1 was detected by multiplex real time polymerase chain reaction assay.
presence of Human respirovirus 1 in nasopharynx or oropharynx by multiplex real time polymerase chain reaction assay
A virus in nasopharyngeal or oropharyngeal swab datum that specifies whether Human orthorubulavirus 2 was detected by multiplex real time polymerase chain reaction assay.
presence of Human orthorubulavirus 2 in nasopharynx or oropharynx by multiplex real time polymerase chain reaction assay
A virus in nasopharyngeal or oropharyngeal swab datum that specifies whether Human respirovirus 3 was detected by multiplex real time polymerase chain reaction assay.
presence of Human respirovirus 3 in nasopharynx or oropharynx by multiplex real time polymerase chain reaction assay
A virus in nasopharyngeal or oropharyngeal swab datum that specifies whether Human orthorubulavirus 4 was detected by multiplex real time polymerase chain reaction assay.
presence of Human orthorubulavirus 4 in nasopharynx or oropharynx by multiplex real time polymerase chain reaction assay
A virus in nasopharyngeal or oropharyngeal swab datum that specifies whether Picornaviridae was detected by multiplex real time polymerase chain reaction assay.
presence of Picornaviridae in nasopharynx or oropharynx by multiplex real time polymerase chain reaction assay
A virus in nasopharyngeal or oropharyngeal swab datum that specifies whether Rhinovirus was detected by multiplex real time polymerase chain reaction assay.
presence of Rhinovirus in nasopharynx or oropharynx by multiplex real time polymerase chain reaction assay
A bacteria in nasopharyngeal or oropharyngeal swab datum that specifies whether bacteria were detected by multiplex real time polymerase chain reaction assay.
presence of bacteria in nasopharynx or oropharynx by multiplex real time polymerase chain reaction assay
A bacteria in nasopharyngeal or oropharyngeal swab datum that specifies whether Haemophilus parahaemolyticus was detected by multiplex real time polymerase chain reaction assay.
presence of Haemophilus parahaemolyticus in nasopharynx or oropharynx by multiplex real time polymerase chain reaction assay
A bacteria in nasopharyngeal or oropharyngeal swab datum that specifies whether Streptococcus pneumoniae was detected.
presence of Streptococcus pneumoniae in nasopharynx or oropharynx
A virus in nasopharyngeal or oropharyngeal swab datum that specifies whether a virus was detected by multiplex real time polymerase chain reaction assay.
presence of virus in nasopharynx or oropharynx by multiplex real time polymerase chain reaction assay
A virus in nasopharyngeal or oropharyngeal swab datum that specifies whether Measles morbillivirus was detected by polymerase chain reaction assay.
presence of Measles morbillivirus in nasopharynx or oropharynx by polymerase chain reaction assay
A bacteria in pleural fluid datum that specifies whether bacteria were detected by multiplex real time polymerase chain reaction assay.
presence of bacteria in pleural fluid by multiplex real time polymerase chain reaction assay
A bacteria in pleural fluid datum that specifies whether Bordetella pertussis was detected by multiplex real time polymerase chain reaction assay.
presence of Bordetella pertussis in pleural fluid by multiplex real time polymerase chain reaction assay
A bacteria in pleural fluid datum that specifies whether Escherichia coli was detected.
presence of Escherichia coli in pleural fluid
A bacteria in pleural fluid datum that specifies whether Haemophilus influenzae was detected.
presence of Haemophilus influenzae in pleural fluid
A bacteria in pleural fluid datum that specifies whether Haemophilus influenzae was detected by multiplex real time polymerase chain reaction assay.
presence of Haemophilus influenzae in pleural fluid by multiplex real time polymerase chain reaction assay
A bacteria in pleural fluid datum that specifies whether Haemophilus parahaemolyticus was detected by multiplex real time polymerase chain reaction assay.
presence of Haemophilus parahaemolyticus in pleural fluid by multiplex real time polymerase chain reaction assay
A bacteria in pleural fluid datum that specifies whether Legionella was detected by multiplex real time polymerase chain reaction assay.
presence of Legionella in pleural fluid by multiplex real time polymerase chain reaction assay
A bacteria in pleural fluid datum that specifies whether Moraxella catarrhalis was detected.
presence of Moraxella catarrhalis in pleural fluid
A bacteria in pleural fluid datum that specifies whether Moraxella catarrhalis was detected by multiplex real time polymerase chain reaction assay.
presence of Moraxella catarrhalis in pleural fluid by multiplex real time polymerase chain reaction assay
A bacteria in pleural fluid datum that specifies whether Mycoplasmoides pneumoniae was detected by multiplex real time polymerase chain reaction assay.
presence of Mycoplasmoides pneumoniae in pleural fluid by multiplex real time polymerase chain reaction assay
A bacteria in pleural fluid datum that specifies whether Salmonella was detected by multiplex real time polymerase chain reaction assay.
presence of Salmonella in pleural fluid by multiplex real time polymerase chain reaction assay
A bacteria in pleural fluid datum that specifies whether Staphylococcus aureus was detected.
presence of Staphylococcus aureus in pleural fluid
A bacteria in pleural fluid datum that specifies whether Staphylococcus aureus was detected by multiplex real time polymerase chain reaction assay.
presence of Staphylococcus aureus in pleural fluid by multiplex real time polymerase chain reaction assay
A bacteria in pleural fluid datum that specifies whether Beta Streptococcus Group F was detected.
presence of Beta Streptococcus Group F in pleural fluid
A bacteria in pleural fluid datum that specifies whether Streptococcus pneumoniae was detected.
presence of Streptococcus pneumoniae in pleural fluid
A bacteria in pleural fluid datum that specifies whether Streptococcus pneumoniae was detected by multiplex real time polymerase chain reaction assay.
presence of Streptococcus pneumoniae in pleural fluid by multiplex real time polymerase chain reaction assay
A eukaryota in pleural fluid datum that specifies whether Pneumocystis jirovecii was detected by multiplex real time polymerase chain reaction assay.
presence of Pneumocystis jirovecii in pleural fluid by multiplex real time polymerase chain reaction assay
The threshold cycle that is the specified output of a multiplex real time polymerase chain reaction assay that has the objective of determining the number of Bordetella pertussis in a pleural fluid specimen.
multiplex qPCR threshold cycle for Bordetella pertussis in pleural fluid
The threshold cycle that is the specified output of a multiplex real time polymerase chain reaction assay that has the objective of determining the number of Chlamydia pneumoniae in a pleural fluid specimen.
multiplex qPCR threshold cycle for Chlamydia pneumoniae in pleural fluid
The threshold cycle that is the specified output of a multiplex real time polymerase chain reaction assay that has the objective of determining the number of Haemophilus influenzae in a pleural fluid specimen.
multiplex qPCR threshold cycle for Haemophilus influenzae in pleural fluid
The threshold cycle that is the specified output of a multiplex real time polymerase chain reaction assay that has the objective of determining the number of Legionella in a pleural fluid specimen.
multiplex qPCR threshold cycle for Legionella in pleural fluid
The threshold cycle that is the specified output of a multiplex real time polymerase chain reaction assay that has the objective of determining the number of Moraxella catarrhalis in a pleural fluid specimen.
multiplex qPCR threshold cycle for Moraxella catarrhalis in pleural fluid
The threshold cycle that is the specified output of a multiplex real time polymerase chain reaction assay that has the objective of determining the number of Mycoplasmoides pneumoniae in a pleural fluid specimen.
multiplex qPCR threshold cycle for Mycoplasmoides pneumoniae in pleural fluid
The threshold cycle that is the specified output of a multiplex real time polymerase chain reaction assay that has the objective of determining the number of Salmonella in a pleural fluid specimen.
multiplex qPCR threshold cycle for Salmonella in pleural fluid
The threshold cycle that is the specified output of a multiplex real time polymerase chain reaction assay that has the objective of determining the number of Staphylococcus aureus in a pleural fluid specimen.
multiplex qPCR threshold cycle for Staphylococcus aureus in pleural fluid
The threshold cycle that is the specified output of a multiplex real time polymerase chain reaction assay that has the objective of determining the number of Streptococcus pneumoniae in a pleural fluid specimen.
multiplex qPCR threshold cycle for Streptococcus pneumoniae in pleural fluid
The threshold cycle that is the specified output of a multiplex real time polymerase chain reaction assay that has the objective of determining the number of Pneumocystis jirovecii in a pleural fluid specimen.
multiplex qPCR threshold cycle for Pneumocystis jirovecii in pleural fluid
The threshold cycle that is the specified output of a multiplex real time polymerase chain reaction assay that has the objective of determining the number of Adenoviridae in a pleural fluid specimen.
multiplex qPCR threshold cycle for Adenoviridae in pleural fluid
The threshold cycle that is the specified output of a multiplex real time polymerase chain reaction assay that has the objective of determining the number of Human coronavirus 229E in a pleural fluid specimen.
multiplex qPCR threshold cycle for Human coronavirus 229E in pleural fluid
The threshold cycle that is the specified output of a multiplex real time polymerase chain reaction assay that has the objective of determining the number of Human coronavirus OC43 in a pleural fluid specimen.
multiplex qPCR threshold cycle for Human coronavirus OC43 in pleural fluid
The threshold cycle that is the specified output of a multiplex real time polymerase chain reaction assay that has the objective of determining the number of Human coronavirus NL63 in a pleural fluid specimen.
multiplex qPCR threshold cycle for Human coronavirus NL63 in pleural fluid
The threshold cycle that is the specified output of a multiplex real time polymerase chain reaction assay that has the objective of determining the number of Human coronavirus HKU1 in a pleural fluid specimen.
multiplex qPCR threshold cycle for Human coronavirus HKU1 in pleural fluid
The threshold cycle that is the specified output of a multiplex real time polymerase chain reaction assay that has the objective of determining the number of Cytomegalovirus in a pleural fluid specimen.
multiplex qPCR threshold cycle for Cytomegalovirus in pleural fluid
The threshold cycle that is the specified output of a multiplex real time polymerase chain reaction assay that has the objective of determining the number of Human bocavirus in a pleural fluid specimen.
multiplex qPCR threshold cycle for Human bocavirus in pleural fluid
The threshold cycle that is the specified output of a multiplex real time polymerase chain reaction assay that has the objective of determining the number of Human metapneumovirus in a pleural fluid specimen.
multiplex qPCR threshold cycle for Human metapneumovirus in pleural fluid
The threshold cycle that is the specified output of a multiplex real time polymerase chain reaction assay that has the objective of determining the number of Human orthopneumovirus in a pleural fluid specimen.
multiplex qPCR threshold cycle for Human orthopneumovirus in pleural fluid
The threshold cycle that is the specified output of a multiplex real time polymerase chain reaction assay that has the objective of determining the number of Influenza A virus in a pleural fluid specimen.
multiplex qPCR threshold cycle for Influenza A virus in pleural fluid
The threshold cycle that is the specified output of a multiplex real time polymerase chain reaction assay that has the objective of determining the number of Influenza B virus in a pleural fluid specimen.
multiplex qPCR threshold cycle for Influenza B virus in pleural fluid
The threshold cycle that is the specified output of a multiplex real time polymerase chain reaction assay that has the objective of determining the number of Influenza C virus in a pleural fluid specimen.
multiplex qPCR threshold cycle for Influenza C virus in pleural fluid
The threshold cycle that is the specified output of a multiplex real time polymerase chain reaction assay that has the objective of determining the number of Human respirovirus 1 in a pleural fluid specimen.
multiplex qPCR threshold cycle for Human respirovirus 1 in pleural fluid
The threshold cycle that is the specified output of a multiplex real time polymerase chain reaction assay that has the objective of determining the number of Human orthorubulavirus 2 in a pleural fluid specimen.
multiplex qPCR threshold cycle for Human orthorubulavirus 2 in pleural fluid
The threshold cycle that is the specified output of a multiplex real time polymerase chain reaction assay that has the objective of determining the number of Human respirovirus 3 in a pleural fluid specimen.
multiplex qPCR threshold cycle for Human respirovirus 3 in pleural fluid
The threshold cycle that is the specified output of a multiplex real time polymerase chain reaction assay that has the objective of determining the number of Human orthorubulavirus 4 in a pleural fluid specimen.
multiplex qPCR threshold cycle for Human orthorubulavirus 4 in pleural fluid
The threshold cycle that is the specified output of a multiplex real time polymerase chain reaction assay that has the objective of determining the number of Picornaviridae in a pleural fluid specimen.
multiplex qPCR threshold cycle for Picornaviridae in pleural fluid
The threshold cycle that is the specified output of a multiplex real time polymerase chain reaction assay that has the objective of determining the number of Rhinovirus in a pleural fluid specimen.
multiplex qPCR threshold cycle for Rhinovirus in pleural fluid
A virus in pleural fluid datum that specifies whether Adenoviridae were detected by multiplex real time polymerase chain reaction assay.
presence of Adenoviridae in pleural fluid by multiplex real time polymerase chain reaction assay
A virus in pleural fluid datum that specifies whether a virus was detected by multiplex real time polymerase chain reaction assay.
presence of virus in pleural fluid by multiplex real time polymerase chain reaction assay
A virus in pleural fluid datum that specifies whether Chlamydia pneumoniae was detected by multiplex real time polymerase chain reaction assay.
presence of Chlamydia pneumoniae in pleural fluid by multiplex real time polymerase chain reaction assay
A virus in pleural fluid datum that specifies whether Human coronavirus 229E was detected by multiplex real time polymerase chain reaction assay.
presence of Human coronavirus 229E in pleural fluid by multiplex real time polymerase chain reaction assay
A virus in pleural fluid datum that specifies whether Human coronavirus OC43 was detected by multiplex real time polymerase chain reaction assay.
presence of Human coronavirus OC43 in pleural fluid by multiplex real time polymerase chain reaction assay
A virus in pleural fluid datum that specifies whether Human coronavirus NL63 was detected by multiplex real time polymerase chain reaction assay.
presence of Human coronavirus NL63 in pleural fluid by multiplex real time polymerase chain reaction assay
A virus in pleural fluid datum that specifies whether Human coronavirus HKU1 was detected by multiplex real time polymerase chain reaction assay.
presence of Human coronavirus HKU1 in pleural fluid by multiplex real time polymerase chain reaction assay
A virus in pleural fluid datum that specifies whether Cytomegalovirus was detected by multiplex real time polymerase chain reaction assay.
presence of Cytomegalovirus in pleural fluid by multiplex real time polymerase chain reaction assay
A virus in pleural fluid datum that specifies whether Human bocavirus was detected by multiplex real time polymerase chain reaction assay.
presence of Human bocavirus in pleural fluid by multiplex real time polymerase chain reaction assay
A virus in pleural fluid datum that specifies whether Human metapneumovirus was detected by multiplex real time polymerase chain reaction assay.
presence of Human metapneumovirus in pleural fluid by multiplex real time polymerase chain reaction assay
A virus in pleural fluid datum that specifies whether Human orthopneumovirus was detected by multiplex real time polymerase chain reaction assay.
presence of Human orthopneumovirus in pleural fluid by multiplex real time polymerase chain reaction assay
A virus in pleural fluid datum that specifies whether Influenza A virus was detected by multiplex real time polymerase chain reaction assay.
presence of Influenza A virus in pleural fluid by multiplex real time polymerase chain reaction assay
A virus in pleural fluid datum that specifies whether Influenza B virus was detected by multiplex real time polymerase chain reaction assay.
presence of Influenza B virus in pleural fluid by multiplex real time polymerase chain reaction assay
A virus in pleural fluid datum that specifies whether Influenza C virus was detected by multiplex real time polymerase chain reaction assay.
presence of Influenza C virus in pleural fluid by multiplex real time polymerase chain reaction assay
A virus in pleural fluid datum that specifies whether Human respirovirus 1 was detected by multiplex real time polymerase chain reaction assay.
presence of Human respirovirus 1 in pleural fluid by multiplex real time polymerase chain reaction assay
A virus in pleural fluid datum that specifies whether Human orthorubulavirus 2 was detected by multiplex real time polymerase chain reaction assay.
presence of Human orthorubulavirus 2 in pleural fluid by multiplex real time polymerase chain reaction assay
A virus in pleural fluid datum that specifies whether Human respirovirus 3 was detected by multiplex real time polymerase chain reaction assay.
presence of Human respirovirus 3 in pleural fluid by multiplex real time polymerase chain reaction assay
A virus in pleural fluid datum that specifies whether Human orthorubulavirus 4 was detected by multiplex real time polymerase chain reaction assay.
presence of Human orthorubulavirus 4 in pleural fluid by multiplex real time polymerase chain reaction assay
A virus in pleural fluid datum that specifies whether Picornaviridae was detected by multiplex real time polymerase chain reaction assay.
presence of Picornaviridae in pleural fluid by multiplex real time polymerase chain reaction assay
A virus in pleural fluid datum that specifies whether Rhinovirus was detected by multiplex real time polymerase chain reaction assay.
presence of Rhinovirus in pleural fluid by multiplex real time polymerase chain reaction assay
Mycobacterium tuberculosis in any sample, by bacteriology
An organism in specimen datum that specifies whether Mycobacterium tuberculosis was detected.
presence of Mycobacterium tuberculosis in specimen
Any pathogen except Legionella or K. pneumoniae, by multiplexed qPCR
A lung microbiology datum that specifies whether a pathogen excluding Legionella or Klebsiella pneumoniae was detected by multiplex real time polymerase chain reaction assay.
presence of any pathogen except Legionella or K. pneumoniae in lung by multiplex real time polymerase chain reaction assay
A pleural fluid microbiology datum that specifies whether pathogen and not Legionella or Klebsiella pneumoniae was detected by multiplex real time polymerase chain reaction assay.
presence of any pathogen except Legionella or K. pneumoniae in pleural fluid by multiplex real time polymerase chain reaction assay
A nasopharyngeal or oropharyngeal swab microbiology datum that specifies whether a pathogen was detected by multiplex real time polymerase chain reaction assay.
presence of pathogen in nasopharynx or oropharynx by multiplex real time polymerase chain reaction assay
A blood assay datum of the concentration of C-reactive protein.
blood C-reactive protein concentration
A bacteria in blood datum that specifies whether bacteria were detected.
presence of bacteria in blood
A bacteria in blood datum that specifies whether Acinetobacter was detected.
presence of Acinetobacter in blood
A eukaryota in blood datum that specifies whether Candida was detected.
presence of Candida in blood
A bacteria in blood datum that specifies whether Enterobacter was detected.
presence of Enterobacter in blood
A bacteria in blood datum that specifies whether Enterococcus was detected.
presence of Enterococcus in blood
A bacteria in blood datum that specifies whether Escherichia was detected.
presence of Escherichia in blood
A bacteria in blood datum that specifies whether Klebsiella was detected.
presence of Klebsiella in blood
A bacteria in blood datum that specifies whether Moraxella was detected.
presence of Moraxella in blood
A bacteria in blood datum that specifies whether Neisseria was detected.
presence of Neisseria in blood
A bacteria in blood datum that specifies whether Staphylococcus was detected.
presence of Staphylococcus in blood
A bacteria in blood datum that specifies whether Haemophilus was detected.
presence of Haemophilus in blood
A bacteria in blood datum that specifies whether Salmonella was detected.
presence of Salmonella in blood
A bacteria in blood datum that specifies whether Streptococcus was detected.
presence of Streptococcus in blood
A bacteria in blood datum that specifies whether Pseudomonas was detected.
presence of Pseudomonas in blood
A eukaryota in blood datum that specifies whether a eukaryote was detected.
presence of eukaryote in blood
A eukaryota in blood datum that specifies whether Plasmodium was detected.
presence of Plasmodium in blood
A bacteria in lung datum that specifies whether Salmonella was detected.
presence of Salmonella in lung
A bacteria in lung datum that specifies whether Mycoplasmoides was detected.
presence of Mycoplasmoides in lung
A bacteria in lung datum that specifies whether Chlamydia was detected.
presence of Chlamydia in lung
A bacteria in lung datum that specifies whether Bordetella was detected.
presence of Bordetella in lung
A bacteria in lung datum that specifies whether Legionella was detected.
presence of Legionella in lung
A eukaryota in lung datum that specifies whether Pneumocystis was detected.
presence of Pneumocystis in lung
A virus in lung datum that specifies whether Alphainfluenzavirus was detected.
presence of Alphainfluenzavirus in lung
A virus in lung datum that specifies whether Betainfluenzavirus was detected.
presence of Betainfluenzavirus in lung
A virus in lung datum that specifies whether Bocaparvovirus was detected.
presence of Bocaparvovirus in lung
A virus in lung datum that specifies whether Cytomegalovirus was detected.
presence of Cytomegalovirus in lung
A virus in lung datum that specifies whether Enterovirus was detected.
presence of Enterovirus in lung
A virus in lung datum that specifies whether Gammainfluenzavirus was detected.
presence of Gammainfluenzavirus in lung
A virus in lung datum that specifies whether Metapneumovirus was detected.
presence of Metapneumovirus in lung
A virus in lung datum that specifies whether Orthopneumovirus was detected.
presence of Orthopneumovirus in lung
A virus in lung datum that specifies whether Respirovirus was detected.
presence of Respirovirus in lung
A virus in lung datum that specifies whether Alphacoronavirus was detected.
presence of Alphacoronavirus in lung
A virus in lung datum that specifies whether Betacoronavirus was detected.
presence of Betacoronavirus in lung
A diagnosis at patient discharge that is an assertion that a patient has pneumonia.
diagnosis of pneumonia at patient discharge
A diagnosis at patient discharge that is an assertion that a patient has bronchiolitis.
diagnosis of bronchiolitis at patient discharge
A diagnosis at patient discharge that is an assertion that a patient has lower respiratory tract disease.
diagnosis of lower respiratory tract disease at patient discharge
A diagnosis at patient discharge that is an assertion that a patient has seizure.
diagnosis of seizure at patient discharge
A diagnosis at patient discharge that is an assertion that a patient has chronic mucocutaneous candidiasis.
diagnosis of chronic mucocutaneous candidiasis at patient discharge
A diagnosis at patient discharge that is an assertion that a patient has anemia.
diagnosis of anemia at patient discharge
A diagnosis at patient discharge that is an assertion that a patient has neonatal sepsis.
diagnosis of neonatal sepsis at patient discharge
A diagnosis at patient discharge that is an assertion that a patient has anemia and heart failure.
diagnosis of anemic heart failure at patient discharge
A diagnosis at patient discharge that is an assertion that a patient has osteomyelitis.
diagnosis of osteomyelitis at patient discharge
A diagnosis at patient discharge that is an assertion that a patient has asthma.
diagnosis of asthma at patient discharge
A diagnosis at patient discharge that is an assertion that a patient has otitis media.
diagnosis of otitis media at patient discharge
A diagnosis at patient discharge that is an assertion that a patient has neonatal asphyxia.
diagnosis of neonatal asphyxia at patient discharge
A diagnosis at patient discharge that is an assertion that a patient has pneumocystosis.
diagnosis of pneumocystosis at patient discharge
A diagnosis at patient discharge that is an assertion that a patient has cellulitis.
diagnosis of cellulitis at patient discharge
A diagnosis at patient discharge that is an assertion that a patient has pneumothorax.
diagnosis of pneumothorax at patient discharge
A diagnosis at patient discharge that is an assertion that a patient has cerebral palsy.
diagnosis of cerebral palsy at patient discharge
A diagnosis at patient discharge that is an assertion that a patient has congenital heart disease.
diagnosis of congenital heart disease at patient discharge
A diagnosis at patient discharge that is an assertion that a patient has physical disorder.
diagnosis of physical disorder at patient discharge
A diagnosis at patient discharge that is an assertion that a patient has protein-energy malnutrition.
diagnosis of protein-energy malnutrition at patient discharge
A diagnosis at patient discharge that is an assertion that a patient has pleural empyema.
diagnosis of pleural empyema at patient discharge
A diagnosis at patient discharge that is an assertion that a patient has pulmonary tuberculosis.
diagnosis of pulmonary tuberculosis at patient discharge
A diagnosis at patient discharge that is an assertion that a patient has epilepsy.
diagnosis of epilepsy at patient discharge
A diagnosis at patient discharge that is an assertion that a patient has septic arthritis.
diagnosis of septic arthritis at patient discharge
A diagnosis at patient discharge that is an assertion that a patient has bacterial sepsis.
diagnosis of bacterial sepsis at patient discharge
A diagnosis at patient discharge that is an assertion that a patient has fever-induced seizures.
diagnosis of seizure precipitated by febrile infection at patient discharge
A diagnosis at patient discharge that is an assertion that a patient has sickle cell anemia.
diagnosis of sickle cell anemia at patient discharge
A diagnosis at patient discharge that is an assertion that a patient has gastroenteritis.
diagnosis of gastroenteritis at patient discharge
A diagnosis at patient discharge that is an assertion that a patient has parasitic helminthiasis infectious disease.
diagnosis of parasitic helminthiasis infectious disease at patient discharge
A diagnosis at patient discharge that is an assertion that a patient has human immunodeficiency virus infectious disease.
diagnosis of human immunodeficiency virus infectious disease at patient discharge
A diagnosis at patient discharge that is an assertion that a patient has urinary system disease.
diagnosis of urinary system disease at patient discharge
A diagnosis at patient discharge that is an assertion that a patient has immunosuppression.
diagnosis of immunosuppression at patient discharge
A diagnosis at patient discharge that is an assertion that a patient has upper respiratory tract disease.
diagnosis of upper respiratory tract disease at patient discharge
A diagnosis at hospital admission that is an assertion that a patient has pulmonary tuberculosis.
diagnosis of pulmonary tuberculosis at hospital admission
A diagnosis at hospital admission that is an assertion that a patient has extrapulmonary tuberculosis.
diagnosis of extrapulmonary tuberculosis at hospital admission
A diagnosis at hospital admission that is an assertion that a patient has severe anemia.
diagnosis of severe anemia at hospital admission
Bronchiolitis or respiratory syncytial virus
A diagnosis at hospital admission that is an assertion that a patient has bronchiolitis or respiratory syncytial virus infectious disease at hospital admission.
diagnosis of bronchiolitis or respiratory syncytial virus infectious disease at hospital admission
A diagnosis at hospital admission that is an assertion that a patient has asthma.
diagnosis of asthma at hospital admission
A diagnosis at hospital admission that is an assertion that a patient has measles.
diagnosis of measles at hospital admission
A diagnosis at hospital admission that is an assertion that a patient has bronchitis.
diagnosis of bronchitis at hospital admission
A diagnosis at hospital admission that is an assertion that a patient has malaria.
diagnosis of malaria at hospital admission
A diagnosis at hospital admission that is an assertion that a patient has global developmental delay or cerebral palsy .
diagnosis of global developmental delay or cerebral palsy at hospital admission
A diagnosis that is an assertion that a patient has meningitis.
diagnosis of meningitis at hospital admission
A fourth-order administrative region of Bangladesh.
union council of Bangladesh
An information content entity about the multiple households that share a location and a common trait such as infrastructure.
community information
Bayley scales of infant and toddler development
A protocol published by psychologist Nancy Bayley to evaluate the developmental maturation of human beings within 1-42 months of age.
Bayley scale of infant and toddler development
A blood specimen collected from a maternal participant under investigation.
maternal blood specimen
A milk specimen collected from a maternal participant under investigation.
maternal milk specimen
A milk assay that has a maternal milk specimen as evaluant.
maternal milk assay
A blood assay that has a maternal blood specimen as evaluant.
maternal blood assay
A collecting specimen from organism that has the objective to obtain a saliva specimen.
saliva specimen collection process
A virus in blood datum that specifies whether Cytomegalovirus was detected.
presence of Cytomegalovirus in blood
A virus in blood datum that specifies whether a virus was detected.
A count of macrophages in a feces specimen.
number of macrophages in feces
A count of dead polymorphonuclear leukocytes in pus in a feces specimen.
number of pus cells in feces
A count of erythrocytes in a feces specimen.
number of erythrocytes in feces
A eukaryota in feces datum that specifies whether Ascaris was detected by microscopy assay.
presence of Ascaris in feces by microscopy assay
A eukaryota in feces datum that specifies whether Blastocystis hominis was detected by microscopy assay.
presence of Blastocystis hominis in feces by microscopy assay
Entamoeba histolytica or dispar, by microscopy
A eukaryota in feces datum that specifies whether Entamoeba histolytica or Entamoeba dispar was detected by microscopy assay.
presence of Entamoeba histolytica or Entamoeba dispar in feces by microscopy assay
A Escherichia coli in feces datum that specifies whether Escherichia coli was detected by microscopy assay.
presence of Escherichia coli in feces by microscopy assay
A eukaryota in feces datum that specifies whether Giardia was detected by microscopy assay.
presence of Giardia in feces by microscopy assay
A eukaryota in feces datum that specifies whether Pentatrichomonas hominis was detected by microscopy assay.
presence of Pentatrichomonas hominis in feces by microscopy assay
A feces microbiology datum that specifies whether a pathogen was detected by microscopy assay.
presence of pathogen in feces by microscopy assay
The site of a human subject enrollment.
location of human subject enrollment
A blood assay datum of the concentration of activin A.
blood activin A concentration
A milk assay datum of the concentration of icosanoic acid.
milk arachidic acid concentration
A milk assay datum of the concentration of arachidonic acid.
milk arachidonic acid concentration
A milk assay datum of the concentration of docosanoic acid.
milk docosanoic acid concentration
A milk assay datum of the concentration of decanoic acid.
milk decanoic acid concentration
A milk assay datum of the concentration of all-cis-icosa-8,11,14-trienoic acid.
milk all-cis-icosa-8,11,14-trienoic acid concentration
A milk assay datum of the concentration of docosahexaenoic acid.
milk docosahexaenoic acid concentration
A milk assay datum of the concentration of (7Z,10Z,13Z,16Z,19Z)-docosapentaenoic acid.
milk (7Z,10Z,13Z,16Z,19Z)-docosapentaenoic acid concentration
A milk assay datum of the concentration of (4Z,7Z,10Z,13Z,16Z)-docosa-4,7,10,13,16-pentaenoic acid.
milk (4Z,7Z,10Z,13Z,16Z)-docosa-4,7,10,13,16-pentaenoic acid concentration
A milk assay datum of the concentration of docosatetraenoic acid.
milk docosatetraenoic acid concentration
A milk assay datum of the concentration of icosadienoic acid.
milk icosadienoic acid concentration
A milk assay datum of the concentration of icosapentaenoic acid.
milk icosapentaenoic acid concentration
A milk assay datum of the concentration of icosenoic acid.
milk icosenoic acid concentration
A milk assay datum of the concentration of elaidic acid.
milk elaidic acid concentration
A milk assay datum of the concentration of gamma-linolenic acid.
milk gamma-linolenic acid concentration
A milk assay datum of the concentration of dodecanoic acid.
milk dodecanoic acid concentration
A milk assay datum of the concentration of tetracosanoic acid.
milk tetracosanoic acid concentration
A milk assay datum of the concentration of linoelaidic acid.
milk linoelaidic acid concentration
A milk assay datum of the concentration of linoleic acid.
milk linoleic acid concentration
A milk assay datum of the concentration of tetradecanoic acid.
milk myristic acid concentration
A milk assay datum of the concentration of (15Z)-tetracosenoic acid.
milk nervonic acid concentration
A milk assay datum of the concentration of oleic acid.
milk oleic acid concentration
A milk assay datum of the concentration of palmitelaidic acid.
milk palmitelaidic acid concentration
A milk assay datum of the concentration of hexadecanoic acid.
milk hexadecanoic acid concentration
A milk assay datum of the concentration of palmitoleic acid.
milk palmitoleic acid concentration
A milk assay datum of the concentration of octadecanoic acid.
milk octadecanoic acid concentration
A virus in blood datum that specifies whether Cytomegalovirus was detected by enzyme-linked immunosorbent assay.
presence of Cytomegalovirus in blood by enzyme-linked immunosorbent assay
The threshold cycle that is the specified output of a real time reverse-transcription polymerase chain reaction assay that has the objective of determining the number of Cytomegalovirus in a feces specimen.
qRT-PCR threshold cycle for Cytomegalovirus in feces
A blood assay datum of the concentration of interferon gamma.
blood interferon gamma concentration
A blood assay datum of the concentration of interleukin-10.
blood interleukin-10 concentration
A blood assay datum of the concentration of interleukin-1 beta.
blood interleukin-1 beta concentration
A blood assay datum of the concentration of interleukin-4.
blood interleukin-4 concentration
A blood assay datum of the concentration of interleukin-5.
blood interleukin-5 concentration
A blood assay datum of the concentration of interleukin-6.
blood interleukin-6 concentration
A blood assay datum of the concentration of interleukin-7.
blood interleukin-7 concentration
A blood assay datum of the concentration of interleukin-8.
blood interleukin-8 concentration
A blood assay datum of the concentration of tumor necrosis factor.
blood tumor necrosis factor concentration
A milk assay datum of the concentration of eotaxin.
milk eotaxin concentration
A milk assay datum of the concentration of granulocyte colony-stimulating factor.
milk granulocyte colony-stimulating factor concentration
Granulocyte-macrophage colony stimulating factor
A milk assay datum of the concentration of granulocyte-macrophage colony-stimulating factor.
milk granulocyte-macrophage colony-stimulating factor concentration
A milk assay datum of the concentration of interleukin-12 complex.
milk interleukin-12 complex concentration
A milk assay datum of the concentration of interleukin-13.
milk interleukin-13 concentration
A milk assay datum of the concentration of interleukin-15.
milk interleukin-15 concentration
A milk assay datum of the concentration of interleukin-17A.
milk interleukin-17A concentration
A milk assay datum of the concentration of interleukin-1 receptor antagonist protein.
milk interleukin-1 receptor antagonist protein concentration
A milk assay datum of the concentration of interleukin-2.
milk interleukin-2 concentration
A milk assay datum of the concentration of interleukin-9.
milk interleukin-9 concentration
A milk assay datum of the concentration of chemokine ligand 10.
milk chemokine ligand 10 concentration
A milk assay datum of the concentration of C-C motif chemokine 2.
milk C-C motif chemokine 2 concentration
A milk assay datum of the concentration of C-C motif chemokine 3.
milk C-C motif chemokine 3 concentration
A milk assay datum of the concentration of platelet-derived growth factor complex.
milk platelet-derived growth factor complex concentration
A milk assay datum of the concentration of C-C motif chemokine 5.
milk C-C motif chemokine 5 concentration
A milk assay datum of the concentration of pro-epidermal growth factor.
milk pro-epidermal growth factor concentration
A blood assay datum of the concentration of endotoxin.
blood endotoxin concentration
A milk assay datum of the concentration of lactadherin.
milk lactadherin concentration
A virus in feces datum that specifies whether Astrovirus was detected by real time polymerase chain reaction assay.
presence of Astrovirus in feces by real time polymerase chain reaction assay
A virus in feces datum that specifies whether Norovirus was detected by multiplex real time reverse-transcription polymerase chain reaction assay.
presence of Norovirus in feces by multiplex real time reverse-transcription polymerase chain reaction assay
A virus in feces datum that specifies whether Rotavirus was detected by real time polymerase chain reaction assay.
presence of Rotavirus in feces by real time polymerase chain reaction assay
A virus in feces datum that specifies whether Sapovirus was detected by real time polymerase chain reaction assay.
presence of Sapovirus in feces by real time polymerase chain reaction assay
The threshold cycle that is the specified output of a real time polymerase chain reaction assay that has the objective of determining the number of Astroviridae in a feces specimen.
qPCR threshold cycle for Astroviridae in feces
The threshold cycle that is the specified output of a real time polymerase chain reaction assay that has the objective of determining the number of Rotavirus in a feces specimen.
qPCR threshold cycle for Rotavirus in feces
The threshold cycle that is the specified output of a real time polymerase chain reaction assay that has the objective of determining the number of Sapovirus in a feces specimen.
qPCR threshold cycle for Sapovirus in feces
A eukaryota in feces datum that specifies whether Cryptosporidium was detected by real time polymerase chain reaction assay.
presence of Cryptosporidium in feces by real time polymerase chain reaction assay
A eukaryota in feces datum that specifies whether Entamoeba histolytica was detected by real time polymerase chain reaction assay.
presence of Entamoeba histolytica in feces by real time polymerase chain reaction assay
A eukaryota in feces datum that specifies whether Giardia was detected by real time polymerase chain reaction assay.
presence of Giardia in feces by real time polymerase chain reaction assay
The threshold cycle that is the specified output of a real time polymerase chain reaction assay that has the objective of determining the number of Entamoeba histolytica in a feces specimen.
qPCR threshold cycle for Entamoeba histolytica in feces
The threshold cycle that is the specified output of a real time polymerase chain reaction assay that has the objective of determining the number of Giardia in a feces specimen.
qPCR threshold cycle for Giardia in feces
Poliovirus serotype Sabin 1, by multiplexed qRT-PCR
A virus in feces datum that specifies whether Human poliovirus 1 strain Sabin was detected by multiplex real time reverse-transcription polymerase chain reaction assay.
presence of human Poliovirus 1 strain Sabin in feces by multiplex real time reverse-transcription polymerase chain reaction assay
Poliovirus serotype Sabin 2, by multiplexed qRT-PCR
A virus in feces datum that specifies whether Human poliovirus 2 strain Sabin was detected by multiplex real time reverse-transcription polymerase chain reaction assay.
presence of human Poliovirus 2 Sabin in feces by multiplex real time reverse-transcription polymerase chain reaction assay
Poliovirus serotype Sabin 3, by multiplexed qRT-PCR
A virus in feces datum that specifies whether Human poliovirus 3 strain Sabin was detected by multiplex real time reverse-transcription polymerase chain reaction assay.
presence of human Poliovirus 3 Sabin in feces by multiplex real time reverse-transcription polymerase chain reaction assay
Poliovirus serotype 1, by multiplexed qRT-PCR result
The threshold cycle that is the specified output of a multiplex real time reverse-transcription polymerase chain reaction assay that has the objective of determining the number of Poliovirus 1 in a feces specimen.
multiplex qRT-PCR threshold cycle for Poliovirus 1 in feces
Poliovirus serotype 2, by multiplexed qRT-PCR result
The threshold cycle that is the specified output of a multiplex real time reverse-transcription polymerase chain reaction assay that has the objective of determining the number of Poliovirus 2 in a feces specimen.
multiplex qRT-PCR threshold cycle for Poliovirus 2 in feces
Poliovirus serotype 3, by multiplexed qRT-PCR result
The threshold cycle that is the specified output of a multiplex real time reverse-transcription polymerase chain reaction assay that has the objective of determining the number of Poliovirus 3 in a feces specimen.
multiplex qRT-PCR threshold cycle for Poliovirus 3 in feces
A feces assay datum of the concentration of REG1B.
feces REG1B concentration
The threshold cycle that is the specified output of a fluorogenic PCR assay that has the objective of determining the number of Escherichia phage MS2 in a feces specimen.
TaqMan threshold cycle for Escherichia phage MS2 in feces
The threshold cycle that is the specified output of a fluorogenic PCR assay that has the objective of determining the number of Enterovirus in a feces specimen.
TaqMan threshold cycle for Enterovirus in feces
A blood assay datum of the concentration of vitamin D.
blood vitamin D concentration
A blood assay datum of the concentration of granulocyte colony-stimulating factor.
blood granulocyte colony-stimulating factor concentration
A milk assay datum of the concentration of interferon gamma.
milk interferon gamma concentration
A milk assay datum of the concentration of interleukin-10.
milk interleukin-10 concentration
A blood assay datum of the concentration of interleukin-17A.
blood interleukin-17A concentration
A milk assay datum of the concentration of interleukin-1 beta.
milk interleukin-1 beta concentration
A milk assay datum of the concentration of interleukin-4.
milk interleukin-4 concentration
A milk assay datum of the concentration of interleukin-5.
milk interleukin-5 concentration
A milk assay datum of the concentration of interleukin-6.
milk interleukin-6 concentration
A milk assay datum of the concentration of interleukin-7.
milk interleukin-7 concentration
A milk assay datum of the concentration of interleukin-8.
milk interleukin-8 concentration
A milk assay datum of the concentration of C-C motif chemokine 4.
milk C-C motif chemokine 4 concentration
A milk assay datum of the concentration of tumor necrosis factor.
milk tumor necrosis factor concentration
A milk assay datum of the concentration of alpha-linolenic acid.
milk alpha-linolenic acid concentration
The threshold cycle that is the specified output of a real time polymerase chain reaction assay that has the objective of determining the number of Cryptosporidium in a feces specimen.
qPCR threshold cycle for Crytptosporidium in feces
A blood assay datum of the concentration of interleukin-2.
blood interleukin-2 concentration
A laboratory test that has a feces specimen as specified input.
A count of dogs that live with a household.
number of dogs with household
An organism detection assay that detects microorganisms in a maternal urine specimen.
maternal urine microbiology assay
A bacteria in blood datum that specifies whether Treponema was detected by venereal disease research laboratory test.
presence of Treponema in blood by venereal disease research laboratory test
Assay that subjects a cerebrospinal fluid specimen to a test for microorganisms.
obsolete cerebrospinal fluid microbiology assay
A laboratory test that has a cerebrospinal fluid specimen as specified input.
An organism microbiology assay that detects microorganisms in a maternal blood specimen.
maternal blood microbiology assay
A second-order administrative region of Ethiopia.
zone of Ethiopia
A fourth-order administrative region of Ethiopia.
kebele of Ethiopia
A third-order administrative region of Ethiopia.
woreda of Ethiopia
An information content entity that specifies whether a blood smear has been performed.
indicator of whether blood smear performed
A eukaryota in placental blood datum that specifies whether a eukaryote was detected.
presence of eukaryote in placental blood
A collecting specimen from organism that has the objective to obtain a placental specimen.
placenta specimen collection process
A eukaryota in placental blood datum that specifies whether Plasmodium was detected.
presence of Plasmodium in placental blood
A eukaryota in placental blood datum that specifies whether Plasmodium was detected by loop-mediated thermal amplification.
presence of Plasmodium in placental blood by loop-mediated thermal amplification
A Plasmodium in placental blood by microscopy assay datum that specifies whether Plasmodium was detected.
presence of Plasmodium in placental blood by microscopy assay
A bacteria in blood datum that specifies whether Treponema was detected.
presence of Treponema in blood
A blood assay that has a offspring blood specimen as evaluant.
offspring blood assay
A blood specimen collected from an offspring participant under investigation.
offspring blood specimen
A blood microbiology assay that has a offspring blood specimen as evaluant.
offspring blood microbiology assay
A eukaryota in umbilical cord blood datum that specifies whether Plasmodium was detected by microscopy assay.
presence of Plasmodium in umbilical cord blood by microscopy assay
A eukaryota in umbilical cord blood datum that specifies whether a eukaryote was detected.
presence of eukaryote in umbilical cord blood
A eukaryota in umbilical cord blood datum that specifies whether Plasmodium was detected.
presence of Plasmodium in umbilical cord blood
A eukaryota in umbilical cord blood datum that is the output of a microscopy assay and is used to determine the presence of Plasmodium in the specimen.
Plasmodium in umbilical cord blood by microscopy assay datum
A eukaryota in placental blood datum that is the output of a microscopy assay and is used to determine the presence of Plasmodium in the specimen.
Plasmodium in placental blood by microscopy assay datum
A role of a material entity realized in drawing an arthropod in the direction of the material.
An infusion material extracted from alfalfa.
alfalfa infusion
A device manufactured by BioGents that is designed for operation with the BG-Sentinel trap and releases an attractant that mimics the scent of human skin.
An infusion material extracted from hay.
hay infusion
An information content entity that specifies that no attractant was used in an anthropod trap
information specifying no arthropod attractor used
A light trap that is designed to use motorized suction to trap arthropods in a collection bag once they approach the light attractant.
Cire. N. J. agrie. Exp. Stn. 1942 No.421 pp.8
An arthropod trap that is designed to collect gravid female arthropods or their eggs.
A light trap that uses carbon dioxide as attractant. The trap consists of a container of dry ice with holes in the bottom to allow the carbon dioxide to flow downward into a separate container, in which a motorized fan creates suction to collect arthropods.
obsolete encephalitis virus surveillance trap
A device manufactured by BioGents that is designed to count mosquitoes passing through the device, differentiating the mosquitoes from other arthropods.
A light trap that is designed to use motorized suction to trap arthropods in a collection bag once they approach the light attractant. This trap is also designed to be lightweight and operate in environments in which electricity may be scarce.
obsolete Centers for Disease Control and Prevention light trap
An arthropod trap that is manufactured by Biogents and is designed to attract arthropods through the use of a motorized fan to mimic convection currents produced by a human. The current also pulls arthropods into the trap, where a layer of gauze prevents the arthropods from escaping along with the air current.
An arthropod trap consisting of a static physical barrier designed to funnel arthropods in flight into a container.
A light trap that is designed to use motorized suction to trap arthropods in a collection bag once they approach the attractant. The light is supplied by an 8 watt tube, and the fan providing the suction has an 11-centimeter diameter.
obsolete Onderstepoort Veterinary Institute light-suction trap
An arthropod trap that consists of a box that is open on one end. The placement of the box and modifications to it are done in such a way that it becomes attractive to an arthropod as a place to rest during a period of inactivity.
Proceedings of the Eighty-Second Annual Meeting of the New Jersey Mosquito Control Association, Inc. 1989, pp 53-57.
An arthropod trap that is made of cloth and netting and is designed to be suspended from above (e.g. from a tree). It is also designed so that the arthropod enters the trap from beneath, being attracted to some bait, and is prevented from escaping upward by the suspended cloth, which allows them to be collected from the upper interior of the trap.
The American Journal of Tropical Medicine and Hygiene, Volume s1-19, Issue 2, 1 Mar 1939, p. 131 - 140
An arthropod trap that is designed to capture arthropods resting on a surface by coating the surface with adhesive.
An arthropod trap, consisting of a pit dug under the shelter of a plant, designed to provide a space for arthropods to rest and be collected.
An arthropod trap that consists of a bucket, which is lined with fabric and placed on its side, and a wet cloth inside the bucket. The placement of the box and modifications to it are done in such a way that it becomes attractive to an arthropod as a place to rest during a period of inactivity.
Kreppel et al. Parasites & Vectors (2015) 8:462
An arthropod trap that is powered by propane and is designed to emit a combination of carbon dioxide, heat, water, and oct-1-en-3-ol attractants while simultaneously using suction to trap arthropods.
An arthropod specimen collection process that involves exposing arthropods to pesticide, then collecting them once they become dead or immobilized.
38th Report East Malling Research Station 1949-50 , 1951, p.148
obsolete knockdown arthropod specimen collection process
A gravid trap consisting of an arthropod attractant and adhesive surface.
An arthropod trap that consists of a bucket, which is lined with adhesive and placed on its side, and a wet cloth inside the bucket. The placement of the box and modifications to it are done in such a way that it becomes attractive to an arthropod as a place to rest during a period of inactivity. The trap is designed for arthropods to become caught in the adhesive so that they can be collected.
A light trap designed to be placed inside a building.
A knockdown arthropod specimen collection process in which the pesticide is pyrethrum.
obsolete knockdown arthropod specimen collection by pyrethrum spray
An arthropod trap that uses light as an attractant.
An arthropod specimen collection process meant to collect live specimens.
obsolete live arthropod specimen collection process
An arthropod specimen collection process in which the arthropods are in the larval stage.
obsolete larval specimen collection process
An arthropod specimen collection by aspiration that occurs in the daytime.
obsolete daytime arthropod specimen collection by aspiration
An arthropod specimen collection by aspiration that occurs while the arthropod is biting a human.
obsolete human-biting arthropod specimen collection by aspiration
An arthropod trap that consists of a container holding a mesh layer above water and is designed to trap arthropods hatched from eggs dropped over the water by gravid females.
An arthropod specimen collection by aspiration that occurs while the arthropod is biting a human inside a building.
obsolete human-biting indoor arthropod specimen collection by aspiration
An arthropod specimen collection by aspiration designed to catch specimens that are in the process of biting a human outside a building.
obsolete human-biting outdoor arthropod specimen collection by aspiration
A live arthropod specimen collection process that involves the use of an aspirator, a device which is brought to an arthropod and causes the arthropod to be drawn by suction into a container.
obsolete arthropod specimen collection by aspiration
An arthropod specimen collection by aspiration that catches specimens resting inside an animal house.
obsolete arthropod resting in animal house specimen collection by aspiration
An animal-biting arthropod specimen collection by aspiration that occurs while the arthropod is resting outside a building during a period of inactivity.
obsolete arthropod resting outdoors specimen collection by aspiration
An arthropod trap that is positioned adjacent to a window of a building and is designed to collect arthropods flying out of the building.
Bull World Health Organ. 1948; 1(2): 253–296.
A live arthropod specimen collection process in which the arthropods are in the adult stage.
obsolete adult arthropod specimen collection process
An arthropod specimen collection by aspiration that occurs while the arthropod is biting an animal.
obsolete animal-biting arthropod specimen collection by aspiration
An arthropod resting outdoors specimen collection by aspiration that occurs while the arthropod rests on a processed material such as a wall or furniture.
obsolete arthropod resting outdoors on artificial support specimen collection by aspiration
A light trap designed to be placed outside a building.
A specimen collection process that has the objective of collecting arthropods as specimens.
obsolete arthropod specimen collection process
An animal-biting arthropod specimen collection by aspiration that occurs outside a building.
obsolete animal-biting outdoor arthropod specimen collection by aspiration
An arthropod resting outdoors specimen collection by aspiration that occurs while the arthropod rests on an unprocessed material such as a plant.
obsolete arthropod resting outdoors on natural support specimen collection by aspiration
An arthropod specimen collection process that has the objective of collecting mosquitoes from an aquatic environment.
obsolete aquatic arthropod specimen collection process
A count of the traps deployed in a study design execution.
number of traps
An arthropod specimen collection process that occurs while the arthropods land on a surface.
For example, while they are landing on a human bait.
obsolete landing arthropod specimen collection process
A device that consists of a network of mesh and is designed to capture adult arthropods.
Can be successfully used to catch resting or flying adult arthropods. The net typically is mounted on a frame that is attached to a handle to increase the reach. [ISBN:9781402066658]
An arthropod trap that is designed to trap an arthropod as it emerges from water at the beginning of its adult stage.
American Midland Naturalist, Vol. 97, No. 2 (Apr., 1977), pp. 381-389
obsolete trap for emerging adult arthropods
The original trap CDC gravid trap (or gravid trap of Reiter) consists of a 3 inch diameter PVC inlet tube housing a 6 V motor, as used in CDC traps, on which is mounted a four-bladed 3 inch counter-clockwise fan. The inlet tube is clamped between two vertical wooden boards that fit over a black plastic box (18.5 x 14.0 x 6.5 inches). A plastic 12 inch long PVC chimney slots into the upper end of the inlet tube. The top half consists of three struts that fit into and support a netting collecting bag. For this the middle of the collecting bag is reinforced with a circular patch of denim cloth. The oviposition attractant is made by adding 1 lb of hay and 1 oz each of dried brewer's yeast and lactalbumen powder to 30 gallons of tap water. This infusion is allowed to mature for 5 days. This original gravid mosquito trap of Reiter suffers from certain limitations, namely up to 10% of the catch of adults is damaged by passing through the fan blades, and adults tend to die of desiccation. [ISBN:9781402066658]
A gravid trap that consists of a pan holding a hay infusion, motorized fan, and collection bag. This trap is designed to attract gravid female arthropods to the infused material, which would serve as an oviposition medium, and then draw them into the bag with the current generated by the fan.
J Am Mosq Control Assoc. 1988 Dec;4(4):536-8.
obsolete Centers for Disease Control and Prevention gravid trap
An arthropod trap that uses as attractant an animal that is not human and is the size of a chicken or smaller.
trap containing small non-human animal bait
Small non-human animals used as bait include chickens and other birds, rabbits, rodents, and dogs.
obsolete arthropod trap containing small non-human animal bait
A device that is designed for the collection of arthropod larvae or pupae from water and has the shape of a ladle or a pan.
A dipper is a commonly used tool for collecting larvae and pupae from their aquatic development sites. Dippers vary in size, shape and the material they are constructed from. A variety of utensils have been used as dippers, e.g. soup ladles, rectangular enamel pie dishes, photographic trays, frying pans, plastic or enamel bowls, household metal strainers and spoons. Volumes of water collected by the dipper can vary from 100 ml to more than 1 liter depending on the specific dipper used. Dippers can be equipped with plastic or metal screen bottoms, or customized with long handles to increase their reach. [ISBN:9781402066658]"
An arthropod specimen collection process that occurs while an arthropod that is capable of flight is resting outdoors during a period of inactivity.
collection of resting insects capable of flight
obsolete resting flight-capable arthropod specimen collection process
An arthropod trap that consists of a transparent window placed in a box that holds a liquid solution deadly to arthropods. This trap is designed to stop an arthropod in flight, causing it to fall into the liquid and die.
For example, Jonsson developed a free-standing window trap consisting of a 16 x 20-cm perspex box, 16 cm high and divided in the middle by a 20 x 36-cm sheet of perspex (window). The two compartments of the box are filled to a depth of about 12 cm with 4-6% formalin containing a few drops of detergent; in winter ethylene glycol can be added to prevent freezing. One or two holes drilled in one side of the box at 12 cm and covered with fine netting prevent the trap overflowing after heavy rain. Traps are mounted on aluminium poles. Flying insects on hitting the transparent vertical plastic window fall into the formalin. The window trap may catch vectors that are seeking a host or moving for other purposes." [ISBN:9781402066658]
A device that is designed to provide a solid surface that is attractive to an arthropod as a place to rest during a period of inactivity.
trap or shelter for resting adult arthropods
Most commonly used to collect mosquitoes.
obsolete device for resting of adult arthropods for collection
A material entity that has an arthropod attractor role.
arthropod attractor
An arthropod specimen collection by aspiration that catches specimens resting inside a human house.
obsolete arthropod resting in human house specimen collection by aspiration
An arthropod trap designed to work with an animal (which could be human) inside a netted structure. This structure is designed so that an arthropod, attracted by the animal, can fly into the netted structure but can neither escape nor reach the animal.
A processed material that results from the suspension of plant material in a solvent for enough time to allow compounds to be extracted from the plant material into the solvent.
This label distinguishes the infused material from the infusion process that produces it. -JJ
infused material
An arthropod specimen collection process in which the arthropods are in the pupal stage.
obsolete pupal specimen collection process
An arthropod trap that is designed to be attractive to an arthropod as a place to rest during a period of inactivity.
A time measurement datum that measures a temporal interval of insecticide exposure.
duration of insecticide exposure
A light source that provides UV light for use in a distant area using a delivery system.
A light source that provides visible light for use in a distant area using a delivery system.
This species is not in NCBITaxon so is assigned a EUPATH ID.
Psorophora johnstonii
Psorophora mathesoni
Psorophora mexicana
This subspecies is not in NCBITaxon so is assigned a EUPATH ID.
Toxorhynchites rutilus rutilus
This taxonomic label is not in NCBITaxon, so this term is assigned a EUPATH ID.
Aedes atlanticus-tormentor morphological group
Aedes fijiensis
Aedes hodgkini
Aedes hokkaidensis
Aedes idahoensis
Aedes mathesoni
Aedes mathesoni complex
Aedes subdentatus
Aedes tricholabis
Aedes vexans arabiensis
Aedes vexans sensu lato
Aedes vexans vexans
Aedes washinoi
Anopheles culicifacies AD subgroup
Anopheles distinctus
Anopheles flavicosta
Anopheles georgianus
Anopheles listeri
Anopheles natalensis
Anopheles perplexens
Anopheles sinensis sensu lato
Anopheles umbrosus
Culex chorleyi
Culex cinerellus
Culex cuyanus
Culex lineata
Culex peringueyi
Culex salisburiensis
Culex trifoliatus
Sergentomyia theodori
Uranotaenia hopkinsi
Wyeomyia haynei
A data item that is about resistance to an insecticide.
A scalar measurement datum of the concentration of an insecticide.
insecticide concentration datum
An insecticide concentration datum expressed as a percent.
insecticide concentration in percent
An insecticide concentration datum that has a parts per notation unit.
insecticide concentration in parts per notation unit
An insecticide concentration datum that has an area density unit.
insecticide concentration in area density unit
An insecticide concentration datum that has a mass density unit.
insecticide concentration in mass density unit
An insecticide concentration datum that has a unit of mass unit per standard assay bottle, which is 250 ml.
insecticide concentration in mass per standard assay bottle
A data item that is about the concentration of an insecticide that kills 50% of a population of insects.
lethal insecticide concentration 50
A lethal insecticide concentration 50, expressed as a percent.
lethal insecticide concentration 50 in percent
A lethal insecticide concentration 50 that has a parts per notation unit.
lethal insecticide concentration 50 in parts per notation unit
A lethal insecticide concentration 50 that has an area density unit.
lethal insecticide concentration 50 in area density unit
A lethal insecticide concentration 50 that has a mass density unit.
lethal insecticide concentration 50 in mass density unit
A lethal insecticide concentration 50 that has a unit of mass unit per standard assay bottle, which is 250 ml.
lethal insecticide concentration 50 in mass per standard assay bottle
A data item that is about the concentration of an insecticide that kills 95% of a population of insects.
lethal insecticide concentration 95
A lethal insecticide concentration 95, expressed as a percent.
lethal insecticide concentration 95 in percent
A lethal insecticide concentration 95 that has a parts per notation unit.
lethal insecticide concentration 95 in parts per notation unit
A lethal insecticide concentration 95 that has an area density unit.
lethal insecticide concentration 95 in area density unit
A lethal insecticide concentration 95 that has a mass density unit.
lethal insecticide concentration 95 in mass density unit
A lethal insecticide concentration 95 that has a unit of mass unit per standard assay bottle, which is 250 ml.
lethal insecticide concentration 95 in mass per standard assay bottle
A data item that is about the concentration of an insecticide that kills 99% of a population of insects.
lethal insecticide concentration 99
A lethal insecticide concentration 99, expressed as a percent.
lethal insecticide concentration 99 in percent
A lethal insecticide concentration 99 that has a parts per notation unit.
lethal insecticide concentration 99 in parts per notation unit
A lethal insecticide concentration 99 that has an area density unit.
lethal insecticide concentration 99 in area density unit
A lethal insecticide concentration 99 that has a mass density unit.
lethal insecticide concentration 99 in mass density unit
A lethal insecticide concentration 99 that has a unit of mass unit per standard assay bottle, which is 250 ml.
lethal insecticide concentration 99 in mass per standard assay bottle
A data item that is about the concentration of an insecticide that kills 90% of a population of insects.
lethal insecticide concentration 90
A lethal insecticide concentration 90, expressed as a percent.
lethal insecticide concentration 90 in percent
A time measurement datum that is about the duration of exposure to an insecticide that results in the death of 90% of a population of insects.
lethal insecticide time 90
A time measurement datum that is about the duration of exposure to an insecticide that results in the death of 95% of a population of insects.
lethal insecticide time 95
A time measurement datum specifying the time at which half of a population of insects has died as a result of exposure to insecticide.
median knockdown time
A lethal insecticide concentration 90 that has a parts per notation unit.
lethal insecticide concentration 90 in parts per notation unit
A lethal insecticide concentration 90 that has an area density unit.
lethal insecticide concentration 90 in area density unit
A lethal insecticide concentration 90 that has a mass density unit.
lethal insecticide concentration 90 in mass density unit
A lethal insecticide concentration 90 that has a unit of mass unit per standard assay bottle, which is 250 ml.
lethal insecticide concentration 90 in mass per standard assay bottle
A data item that specifies the proportionality of the mean enzymatic activity of a field-collected population of specimens compared to that of a reference population.
ratio of specimen population mean enzymatic activity to that of reference specimen population
A data item that specifies the proportionality of the median enzymatic activity of a field-collected population of specimens compared to that of a reference population.
ratio of specimen population median enzymatic activity to that of reference specimen population
A data item that specifies the fraction of a population exhibiting higher enzymatic activity than the 99th percentile of a reference population.
population fraction with greater enzymatic activity than 99th percentile of reference population
A count of the specimens involved in an assay.
number of input specimens to assay
A data item that is the output of an assay to quantify the frequency of genetic variation resulting in Kdr L1014F.
A data item that is the output of an assay to quantify the frequency of genetic variation resulting in Kdr S989P.
A data item that is the output of an assay to quantify the frequency of genetic variation resulting in Kdr I1011M.
A data item that is the output of an assay to quantify the frequency of genetic variation resulting in Kdr I1011V.
A data item that is the output of an assay to quantify the frequency of genetic variation resulting in Kdr L1014S.
A data item that is the output of an assay to quantify the frequency of genetic variation resulting in Kdr L1014C.
A data item that is the output of an assay to quantify the frequency of genetic variation resulting in Kdr V1016G.
A data item that is the output of an assay to quantify the frequency of genetic variation resulting in Kdr V1016I.
A data item that is the output of an assay to quantify the frequency of genetic variation resulting in Kdr I1532T.
A data item that is the output of an assay to quantify the frequency of genetic variation resulting in Kdr F1534C.
A data item that is the output of an assay to quantify the frequency of genetic variation resulting in Kdr F1534L.
A data item that is the output of an assay to quantify the frequency of genetic variation resulting in Kdr F1534S.
A data item that is the output of an assay to quantify the frequency of genetic variation resulting in Kdr N1575Y.
A data item that is the output of an assay to quantify the frequency of genetic variation resulting in Kdr D1763Y.
A data item that is the output of an assay to quantify the frequency of genetic variation resulting in AChE1 G119S.
A data item that is the output of an assay to quantify the frequency of genetic variation resulting in Gste2 L119F.
A data item that is the output of an assay to quantify the frequency of genetic variation resulting in Rdl A296G.
A data item that is the output of an assay to quantify the frequency of genetic variation resulting in Rdl A296S.
Number of mosquito collections in a survey dataset.
A count of collections of specimens that have only arthropods as their members.
number of entomology collections
A data item that is the output of an assay to quantify the frequency of the reference sequence amino acid at Kdr L1014 or is calculated from data items of the frequency of a variant at that position.
A data item that is the output of an assay to quantify the frequency of the reference sequence amino acid at Kdr S989 or is calculated from data items of the frequency of a variant at that position.
A data item that is the output of an assay to quantify the frequency of the reference sequence amino acid at Kdr I1011 or is calculated from data items of the frequency of a variant at that position.
A data item that is the output of an assay to quantify the frequency of the reference sequence amino acid at Kdr V1016 or is calculated from data items of the frequency of a variant at that position.
A data item that is the output of an assay to quantify the frequency of the reference sequence amino acid at Kdr I1532 or is calculated from data items of the frequency of a variant at that position.
A data item that is the output of an assay to quantify the frequency of the reference sequence amino acid at Kdr F1534 or is calculated from data items of the frequency of a variant at that position.
A data item that is the output of an assay to quantify the frequency of the reference sequence amino acid at Kdr N1575 or is calculated from data items of the frequency of a variant at that position.
A data item that is the output of an assay to quantify the frequency of the reference sequence amino acid at Kdr D1763 or is calculated from data items of the frequency of a variant at that position.
A data item that is the output of an assay to quantify the frequency of the reference sequence amino acid at AChE1 G119 or is calculated from data items of the frequency of a variant at that position.
A data item that is the output of an assay to quantify the frequency of the reference sequence amino acid at AChE1 F290 or is calculated from data items of the frequency of a variant at that position.
A data item that is the output of an assay to quantify the frequency of the reference sequence amino acid at AChE1 F331 or is calculated from data items of the frequency of a variant at that position.
A data item that is the output of an assay to quantify the frequency of the reference sequence amino acid at Gste2 I114 or is calculated from data items of the frequency of a variant at that position.
A data item that is the output of an assay to quantify the frequency of the reference sequence amino acid at Gste2 L119 or is calculated from data items of the frequency of a variant at that position.
A data item that is the output of an assay to quantify the frequency of the reference sequence amino acid at Rdl A296 or is calculated from data items of the frequency of a variant at that position.
An arthropod specimen collection process in which the arthropods are in the embryo stage.
obsolete egg specimen collection process
An arthropod specimen collection process in which the arthropods are in the larval stage and a trap is used to collect the specimens.
larval specimen collection process from traps
A data item that is the specified output of an organism identification assay.
A data item that is about the concentration of an insecticide that kills 100% of a population of insects.
lethal insecticide concentration 100
A lethal insecticide concentration 100, expressed as a percent.
lethal insecticide concentration 100 in percent
A device that is designed for the collection of arthropod larvae or pupae from water and consists of a conical net.
obsolete well net for arthropod immatures
An arthropod specimen collection process that has the objective of collecting gravid female arthropods.
obsolete gravid female arthropod specimen collection process
An arthropod specimen collection process that involves a device that produces data specifying the types of arthropod collected.
obsolete arthropod collection process with automated identification
An adult arthropod specimen collection process that has the objective of collecting arthropods capable of flight, through the use of a barrier trap.
obsolete flying adult arthropod collection process by passive interception
A chemical substance manufactured by BioGents that is designed to attract mosquitoes by mimicking the scent of human skin.
BG-Lure
An identifier that encodes a geographic location into a short string of letters and digits.
geohash code
A geohash code encoding of geospatial location using 1 character.
geohash 1
A geohash code encoding of geospatial location using 2 characters.
geohash 2
A geohash code encoding of geospatial location using 3 characters.
geohash 3
A geohash code encoding of geospatial location using 4 characters.
geohash 4
A geohash code encoding of geospatial location using 5 characters.
geohash 5
A geohash code encoding of geospatial location using 6 characters.
geohash 6
A geohash code encoding of geospatial location using 7 characters.
geohash 7
A geohash code encoding of geospatial location using 32 characters.
geohash 32
An information content entity that either specifies the process by which latitude and longitude data were obtained, or specifies that it is missing knowledge.
geolocation provenance information
An objective specification to obtain geolocation data whose value has a particular degree of precision.
geolocation precision objective specification
A geolocation precision objective specification of zero decimal places.
geolocation precision objective of zero decimal places
A geolocation precision objective specification of one decimal place.
geolocation precision objective of one decimal place
A geolocation precision objective specification of two decimal places.
geolocation precision objective of two decimal places
A geolocation precision objective specification of three decimal places.
geolocation precision objective of three decimal places
A geolocation precision objective specification of four decimal places.
geolocation precision objective of four decimal places
A manufactured product that is a 3rd generation Indoor Residual Spraying (3GIRS) micro-encapsulated formulation of an existing organophosphate insecticide, Pirimiphos-methyl, co-developed through a partnership between Syngenta and IVCC.
Actellic-300cs insecticide
A count of the number of copies of the interspecific chromosomal inversion (2La) in Anopheles gambiae complex.
2La is located on chromosome arm 2L:20524058-42165532 (approximate location in the AgamP3 assembly; GenBank: GCF_000005575.2) as described in: Sharakhov, I.V., White, B.J., Sharakhova, M.V., Kayondo, J., Lobo, N.F., Santolamazza, F., Della Torre, A., Simard, F., Collins, F.H. and Besansky, N.J., 2006. Breakpoint structure reveals the unique origin of an interspecific chromosomal inversion (2La) in the Anopheles gambiae complex. Proceedings of the National Academy of Sciences, 103(16), pp.6258-6262. PMID: 16606844
number of copies of the 2La Anopheles gambiae complex chromosomal inversion
A measurement datum of the number of copies of the chromosomal inversion 2Rb in Anopheles gambiae.
2Rb is located on chromosome arm 2R:19023925-26758676 (location in the AgamP3 assembly; GenBank: GCF_000005575.2) as described in: Lobo, N.F., Sangaré, D.M., Regier, A.A., Reidenbach, K.R., Bretz, D.A., Sharakhova, M.V., Emrich, S.J., Traore, S.F., Costantini, C., Besansky, N.J. and Collins, F.H., 2010. Breakpoint structure of the Anopheles gambiae 2R b chromosomal inversion. Malaria journal, 9(1), pp.1-9. PMID:20974007
number of copies of the 2Rb Anopheles gambiae complex chromosomal inversion
A count of the number of copies of the trans-specific inversion 2Rc in Anopheles gambiae.
2Rc is located on chromosome arm 2R:26780000-31450000 (location in the AgamP3 assembly; GenBank: GCF_000005575.2) as described in: White, B.J., Cheng, C., Sangaré, D., Lobo, N.F., Collins, F.H. and Besansky, N.J., 2009. The population genomics of trans-specific inversion polymorphisms in Anopheles gambiae. Genetics, 183(1), pp.275-288. PMID:19581444
number of copies of the 2Rc Anopheles gambiae complex chromosomal inversion
A count of the number of copies of the chromosomal inversion 2Rd in Anopheles gambiae.
2Rd is located on chromosome arm 2R:31480000-42600000 (location in the AgamP3 assembly; GenBank: GCF_000005575.2) as described in: George, P., Sharakhova, M.V. and Sharakhov, I.V., 2010. High‐resolution cytogenetic map for the African malaria vector Anopheles gambiae. Insect molecular biology, 19(5), pp.675-682. PMID:20609021
number of copies of the 2Rd Anopheles gambiae complex chromosomal inversion
A measurement datum of the number of copies of the inversion 2Rj in Anopheles gambiae.
2Rj is located on chromosome arm 2R:3656857-14459087 (location in the AgamP3 assembly; GenBank: GCF_000005575.2) as described in: Coulibaly, M.B., Lobo, N.F., Fitzpatrick, M.C., Kern, M., Grushko, O., Thaner, D.V., Traoré, S.F., Collins, F.H. and Besansky, N.J., 2007. Segmental Duplication Implicated in the Genesis of Inversion 2 Rj of Anopheles gambiae. PLoS One, 2(9), p.e849. PMID:17786220
number of copies of the 2Rj Anopheles gambiae complex chromosomal inversion
A count of the number of copies of the chromosomal inversion 2Rk in Anopheles gambiae.
2Rk is described in: Mario Coluzzi, Adriana Sabatini, Alessandra della Torre, Maria Angela Di Deco, Vincenzo Petrarca. A polytene chromosome analysis of the Anopheles gambiae species complex. PMID: 12364623
number of copies of the 2Rk Anopheles gambiae complex chromosomal inversion
A count of the number of copies of the trans-specific inversion 2Ru in Anopheles gambiae.
2Ru is located on chromosome arm 2R:31480000-35500000 (location in the AgamP3 assembly; GenBank: GCF_000005575.2) as described in: White, B.J., Cheng, C., Sangaré, D., Lobo, N.F., Collins, F.H. and Besansky, N.J., 2009. The population genomics of trans-specific inversion polymorphisms in Anopheles gambiae. Genetics, 183(1), pp.275-288. PMID:19581444
number of copies of the 2Ru Anopheles gambiae complex chromosomal inversion
An information content entity that is about data collected at the community level (e.g., village) on multiple occasions.
community repeated measure
Information about a female insect regarding when and if it had a blood meal.
female insect feeding status
A female insect feeding status about a gravid female insect.
gravid female insect feeding status
A gravid female insect feeding status of having a visible blood meal.
fed gravid female insect status
A gravid female insect feeding status of not having a visible blood meal.
unfed gravid female insect status
A female insect feeding status of not having a visible blood meal.
unfed female insect status
A female insect feeding status of having a visible blood meal.
fed female insect status
A data item that is the output of an assay to quantify the frequency of the genetic variation resulting in cytochrome P450 CYP4J5 L43F associated with pyrethroid resistance and located in the 2La inversion of Anopheles gambiae.
An arthropod attractor that is manufactured by the American Biophysics Corporation and has (S)-lactic acid as its active ingredient in order to mimic the scent of human skin.
Lurex attractor
An arthropod specimen collection process in which tick specimens are collected by the general public i.e., citizen scientists.
tick specimen collection process by citizen scientists
Geolocation provenance information that specifies that data were provided directly from a source, rather than estimated or calculated.
geolocation provision information
Geolocation provenance information that specifies that the number of decimal places in the data were truncated.
geolocation obfuscation information
Geolocation provenance information that specifies that data were calculated by the curator or found using a geolocation lookup service.
geolocation estimation information from curator
Geolocation provenance information that specifies that data were estimated using information about an administrative region.
Usually this means an arbitrary or centroid location within that country, or the results of a geocoding service.
geolocation estimation from administrative region information
Geolocation provenance information that specifies that data were estimated from information about an administrative region of first order or higher.
geolocation data estimation information from first- or higher-order administrative region
Geolocation provenance information that specifies that data were estimated from from information about an administrative region of second order or higher.
geolocation estimation information from second- or higher-order administrative region
Geolocation provenance information that specifies that data were estimated from a street address or landmark.
Usually this will be the result of a geocoding service.
geolocation estimation information from street address or landmark
A conclusion based on data about a gene that is absolutely necessary or vital for the life of an organism, as inferred either from direct experimental evidence or from indirect evidence.
Achchuthan Shanmugasundram ORCID: 0000-0003-2349-6929
information on putatively essential gene
A data item that is the output of an assay to quantify the frequency of the reference sequence amino acid at Cyp4J5 L43 or is calculated from data items of the frequency of a variant at that position.
Anopheles nuneztovari sensu lato
Anaplasma phagocytophilum str. Ap-ha
Anaplasma phagocytophilum str. Ap-v1
A time measurement datum that specifies the date that starts a process that results in a collection of specimens.
date of start of process resulting in collection of specimens
A time measurement datum that specifies the date that ends a process that results in a collection of specimens.
date of end of process resulting in collection of specimens
An information content entity that specifies that, between the start and end dates of a process resulting in a collection of specimens, there was at least one date that no collection attempts were made.
indicator of specimen collection date discontinuity
An information content entity that is about a population of tick specimens.
information on collected tick population
A record of missing knowledge indicating a lack of information on collected tick population.
no record of collected tick population
An information on collected tick population that does not meet the criteria for established information on collected tick population, but indicates that at least one tick (or an unspecified number of ticks) of any life stage had been identified at any time in a second-order administrative region.
reported information on collected tick population
An information on collected tick population that indicates that at least six individual ticks or at least two of the three host-seeking life stages had been identified in a single collection period in a second-order administrative region.
established information on collected tick population
Anopheles pollicaris
Armigeres magnus
Armigeres traubi
Culex alis
Culex whitei
Anopheles culicifacies BCE subgroup
Aedes condolescens
Anopheles grabhamii
Anopheles hodgkini
Anopheles namibiensis
A collecting specimen from organism that has the objective to obtain an umbilical cord blood specimen.
umbilical cord blood specimen collection process
Hydroxychloroquine concentration (ug/mL)
A blood assay datum of the concentration of hydroxychloroquine.
blood hydroxychloroquine concentration
Severe acute respiratory syndrome coronavirus 2, by qRT-PCR
A virus in nasopharyngeal or oropharyngeal swab datum that specifies whether severe acute respiratory syndrome coronavirus 2 was detected by real time reverse-transcription polymerase chain reaction assay.
presence of Severe acute respiratory syndrome coronavirus 2 in nasopharynx or oropharynx by real time reverse-transcription polymerase chain reaction assay
A second-order administrative region of Uganda.
district of Uganda
A first-order administrative region of Uganda.
region of Uganda
A eukaryota in maternal urine datum that specifies whether Schistosoma mansoni was detected by microscopy assay.
presence of Schistosoma mansoni in maternal urine by microscopy assay
A urine assay that has a maternal urine specimen as evaluant.
maternal urine assay
A saliva assay that evaulates a specimen collected from the biological mother of an infant.
maternal saliva assay
A eukaryota in maternal urine datum that specifies whether Schistosoma was detected.
presence of Schistosoma in maternal urine
A eukaryota in maternal urine datum that specifies whether a eukaryote was detected.
presence of eukaryote in maternal urine
An information on suckling behavior that indicates whether, in the duration between health care encounters, an infant was only fed by suckling.
information on whether only fed by suckling
Information on disposal of human excreta material that specifies whether a latrine was observed by an investigation agent as being used for storage.
indicator of latrine used for storage
A household information that specifies whether the diversity of food consumed by the household meets the minimum standard set by the World Health Organization.
indicator of whether household met WHO diet minimum dietary diversity
A fourth-order administrative region of Tanzania.
ward of Tanzania
The first mention of an antibiotic that is administered as part of a treatment.
first antibiotic in treatment
A cerebrospinal fluid microbiology datum that specifies whether Mycobacterium tuberculosis was detected.
presence of Mycobacterium tuberculosis in cerebrospinal fluid by polymerase chain reaction assay
A eukaryota in urine datum that specifies whether Histoplasma capsulatum was detected by polymerase chain reaction assay.
presence of Histoplasma capsulatum in urine by polymerase chain reaction assay
A cerebrospinal fluid microbiology datum that specifies whether bacteria were detected.
presence of bacteria in cerebrospinal fluid
A urine microbiology datum that specifies whether bacteria were detected.
presence of bacteria in urine
A eukaryota in blood datum that specifies whether Cryptococcus was detected.
presence of Cryptococcus in blood
A cerebrospinal fluid microbiology datum that specifies whether Cryptococcus was detected.
presence of Cryptococcus in cerebrospinal fluid
A cerebrospinal fluid microbiology datum that specifies whether a eukaryote was detected.
presence of eukaryote in cerebrospinal fluid
A eukaryota in blood datum that specifies whether Histoplasma was detected.
presence of Histoplasma in blood
A cerebrospinal fluid microbiology datum that specifies whether Histoplasma was detected.
presence of Histoplasma in cerebrospinal fluid
A eukaryota in urine datum that specifies whether Histoplasma was detected.
presence of Histoplasma in urine
A bacteria in blood datum that specifies whether Mycobacterium was detected.
presence of Mycobacterium in blood
A cerebrospinal fluid microbiology datum that specifies whether Mycobacterium was detected.
presence of Mycobacterium in cerebrospinal fluid
A urine microbiology datum that specifies whether Mycobacterium was detected.
presence of Mycobacterium in urine
Shigella flexneri not serotype 6, by TAC result
The threshold cycle that is the specified output of a fluorogenic PCR assay that has the objective of detemining the number of Shigella flexneri excluding serotype 6 in a feces specimen.
The label and definition for this term have been changed from the previous release, mainly to correct a mistaken reference to serotype 7 rather than serotype 6.
TaqMan threshold cycle for Shigella flexneri in feces excluding serotype 6
A body mass index (BMI) calculated from measurements of the biological mother of a child.
maternal body mass index
A treatment information that specifies the date of the last administration of a steroid in the treatment.
date of end of steroid treatment
Treatment information that specifies whether a caregiver of a participant under investigation reported administering zinc to the participant.
indicator of caregiver reporting zinc administered
The second mention of an antibiotic that is administered as part of a treatment.
second antibiotic in treatment
A treatment information that specifies the date of the last administration of the antibiotic that is mentioned first as part of the treatment.
date of end of first antibiotic treatment
A treatment information that specifies the date of the last administration of the antibiotic that is mentioned second as part of the treatment.
date of end of second antibiotic treatment
A treatment information that specifies the date of the last administration of albuterol in the treatment.
date of end of albuterol treatment
A treatment information that specifies the date of the last administration of ranitidine in the treatment.
date of end of ranitidine treatment
The second mention of a medication that is administered as part of a treatment.
second medication in treatment
The third mention of a medication that is administered as part of a treatment.
third medication in treatment
The fourth mention of a medication that is administered as part of a treatment.
fourth medication in treatment
Maternal stool intestinal inflammation test
A feces assay to detect inflammation, for which the specimen is collected from the biological mother of an infant.
maternal feces assay to detect inflammation
An age measurement datum of the age at which developmental maturation of a human being is evaluated according to the Bayley scale of infant and toddler development.
age of Bayley scale evaluation
An information content entity that specifies food products, including water, fed to a neonate within approximately an hour after its birth.
information on food fed to neonate at birth
Shigella flexneri serotype 6, by TAC result
The threshold cycle that is the specified output of a fluorogenic PCR assay that has the objective of determining the number of Shigella flexneri 6 in a feces specimen.
TaqMan threshold cycle for Shigella flexneri 6 in feces
A location of human subject enrollment in which the biological mother of a child becomes the bearer of a participant under investigation role that is secondary to that of her child.
location of maternal human subject enrollment
A time measurement datum of the duration of a treatment consisting of oral administrations of medication with a nebulizer.
duration of treatment with nebulizer
An information on suckling behavior that indicates whether it started within a hour after baby delivery.
indicator of suckling behavior within hour after baby delivery
An information content entity that specifies whether bag valve mask ventilation was performed during a baby delivery.
indicator of bag valve mask ventilation performed during baby delivery
Information that specifies the frequency at which a planned process, in which a birth attendant participates, is observed by an investigation agent.
information on frequency of observed birth attendant activity
Health care information that is about health care processes that occur during admission for baby delivery and involve the same patient.
information on health care during admission for baby delivery
Healthcare activities just before delivery
Health care information that is about health care processes that occur immediately before baby delivery and involve the same patient.
information on health care immediately preceding baby delivery
Health care information that is about health care processes that occur during baby delivery and involve the same patient.
information on health care during baby delivery
Healthcare activities <1 hour after delivery
Health care information that is about health care processes that occur in the hour after baby delivery and involve the same patient.
information on health care in hour after baby delivery
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.
Foodon product type
food product
A mushroom (or toadstool) is the fleshy, spore-bearing fruiting body of a fungus, typically produced above ground on soil or on its food source.
mushroom (whole organism)
infant formula
A chemical food component in liquid form.
liquid chemical food component
A solid product is a hard or soft product capable of retaining its own shape at room temperature (20 degrees C.). A soft product that is spreadable or formable is considered semisolid.
food (solid)
food cooking
One of the large, unbroken masses of land into which the Earth's surface is divided.
A reference to a place on the Earth, by its name or by its geographical location.
Coverage (read depth or depth) is the average number of reads representing a given nucleotide in the reconstructed sequence.
A subnational region is a type of subnational entity similar to a nation's state, province, or territory.
subnational region
Specific behavior of a newborn or infant mammal that results in the derivation of nourishment from the breast.
A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs.
Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
Catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1). Catalyzes RNA-template-directed extension of the 3'- end of a DNA strand by one deoxynucleotide at a time.
DNA nucleotidyltransferase (RNA-directed) activity
RNA-dependent deoxyribonucleate nucleotidyltransferase activity
RNA-directed DNA polymerase, group II intron encoded
RNA-directed DNA polymerase, transposon encoded
deoxynucleoside-triphosphate:DNA deoxynucleotidyltransferase (RNA-directed) activity
Catalysis of the reaction: acetylcholine + H2O = choline + acetate.
acetyl.beta-methylcholinesterase activity
Catalysis of the reaction: R-X + glutathione = H-X + R-S-glutathione. R may be an aliphatic, aromatic or heterocyclic group; X may be a sulfate, nitrile or halide group.
S-(hydroxyalkyl)glutathione lyase activity
glutathione S-alkyl transferase activity
glutathione S-aralkyltransferase activity
The reproductive process in which the parent is separated from its offspring either by giving birth to live young or by laying eggs.
The process of 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.
respiratory gaseous exchange by respiratory system
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.
The process in which a gene's sequence is converted into a mature gene product (protein or RNA). This includes the production of an RNA transcript and its processing, translation and maturation for protein-coding genes.
The covalent alteration of one or more amino acid residues within a histone protein.
Catalysis of the hydrolysis of any ester bond.
hydrolase activity, acting on ester bonds
A protein complex that in its canonical form is composed of two identical immunoglobulin heavy chains and two identical immunoglobulin light chains, held together by disulfide bonds and sometimes complexed with additional proteins. An immunoglobulin complex may be embedded in the plasma membrane or present in the extracellular space, in mucosal areas or other tissues, or circulating in the blood or lymph.
An immunoglobulin complex that is present in the plasma membrane of B cells and that in its canonical form is composed of two identical immunoglobulin heavy chains and two identical immunoglobulin light chains and a signaling subunit, a heterodimer of the Ig-alpha and Ig-beta proteins.
B cell receptor accessory molecule complex
A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which at least one component is a protein and the constituent parts function together.
Catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1); the synthesis of DNA from deoxyribonucleotide triphosphates in the presence of a nucleic acid template and a 3'hydroxyl group.
deoxyribonucleate nucleotidyltransferase activity
deoxyribonucleic acid polymerase activity
A protein complex that contains a disulfide-linked heterodimer of T cell receptor (TCR) chains, which are members of the immunoglobulin superfamily, and mediates antigen recognition, ultimately resulting in T cell activation. The TCR heterodimer is associated with the CD3 complex, which consists of the nonpolymorphic polypeptides gamma, delta, epsilon, zeta, and, in some cases, eta (an RNA splice variant of zeta) or Fc epsilon chains.
An immunoglobulin complex that is secreted into extracellular space and found in mucosal areas or other tissues or circulating in the blood or lymph. In its canonical form, a circulating immunoglobulin complex is composed of two identical heavy chains and two identical light chains, held together by disulfide bonds. Some forms of are polymers of the basic structure and contain additional components such as J-chain and the secretory component.
A protein complex that possesses DNA polymerase activity and is involved in template directed synthesis of DNA.
A nonsteroidal regulator, composed of two covalently linked inhibin beta-A subunits (sometimes known as activin beta-A or activin/inhibin beta-A).
A protein complex that is composed of an interleukin-12 alpha (p35, product of the IL12A gene) and an interleukin-12 beta subunit (p40, product of the IL12B gene) and is secreted into the extracellular space.
Catalysis of the hydrolysis of a carboxylic ester bond.
hydrolase activity acting on ester bonds
A protein complex that binds iron and acts as a major iron storage system. Intracellular and extracellular ferritin complexes have different ratios of two types of ferritin monomer, the L (light) chain and H (heavy) chain.
A protein complex composed of two identical immunoglobulin heavy chains of the IgM isotype and two identical immunoglobulin light chains, held together by disulfide bonds, and in its circulating form complexed with J chain in polymeric forms. An IgM immunoglobulin complex may be embedded in the plasma membrane or present in the extracellular space, in mucosal areas or other tissues, or circulating in the blood or lymph.
The inhibition of an antigen's biological effects by antibody binding to it. An example is neutralization of diphtheria toxin by preventing its entry into human cells via the binding of antibody specific for diphtheria toxin.
A protein complex consisting of two chains of platelet-derived growth factor (PDGF) subunits. PDGF dimers bind to PDGF receptors in the plasma membrane and induce receptor dimerisation and activation. PDGFs are involved in a wide variety of signalling processes. PDGFs are found in all vertebrates where at least 2 different chains (A and B) exist. In human (and other mammals), four types of PDGF chains (A, B, C, and D) are known which form five different dimers (AA, AB, BB, CC and DD).
A small, often T-shaped contraceptive device that is inserted into a person's uterus to prevent pregnancy.
contraceptive coil
intra-uterine contraceptive device
intra-uterine device
plastic intrauterine device
intrauterine contraceptive device
Any of various rates involving number of births in a population; usually used as shorthand for crude birth rate.
birthrate
birth rate
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.
The presence of any abnormality of the genitourinary system.
Abnormality of the oral cavity, i.e., the opening or hollow part of the mouth.
Hydrocephalus is an active distension of the ventricular system of the brain resulting from inadequate passage of CSF from its point of production within the cerebral ventricles to its point of absorption into the systemic circulation.
Too much cerebrospinal fluid in the brain
Epistaxis, or nosebleed, refers to a hemorrhage localized in the nose.
Any abnormality of the eye, including location, spacing, and intraocular abnormalities.
An eye that is more deeply recessed into the plane of the face than is typical.
Abnormal alignment, positioning, or spacing of the teeth, i.e., misaligned teeth.
A state of unease characterized by diffuse motor activity or motion, subject to limited control, nonproductive, or disorganized behavior.
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).
Yellow pigmentation of the skin due to bilirubin, which in turn is the result of increased bilirubin concentration in the bloodstream.
An abnormal accumulation of fluid beneath the skin, or in one or more cavities of the body.
Abnormal excessive perspiration (sweating) despite the lack of appropriate stimuli like hot and humid weather.
Pruritus is an itch or a sensation that makes a person want to scratch. This term refers to an abnormally increased disposition to experience pruritus.
An abnormality of the fetus or the birth of the fetus, excluding structural abnormalities.
Abnormality of prenatal development or birth
A state of disinterestedness, listlessness, and indifference, resulting in difficulty performing simple tasks or concentrating.
Complete absence of wakefulness and content of conscience, which manifests itself as a lack of response to any kind of external stimuli.
A delay in the achievement of motor or mental milestones in the domains of development of a child, including motor skills, speech and language, cognitive skills, and social and emotional skills. This term should only be used to describe children younger than five years of age.
Failure to thrive (FTT) refers to a child whose physical growth is substantially below the norm.
Smaller than normal size according to sex and gestational age related norms, defined as a weight below the 10th percentile for the gestational age.
An abnormality of the integument, which consists of the skin and the superficial fascia.
A noncongenital process of hair loss, which may progress to partial or complete baldness.
The birth of a baby of less than 37 weeks of gestational age.
Any abnormality of the cardiovascular system.
Abnormality of the cardiovascular 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.
Necrosis of the myocardium caused by an obstruction of the blood supply to the heart and often associated with chest pain, shortness of breath, palpitations, and anxiety as well as characteristic EKG findings and elevation of serum markers including creatine kinase-MB fraction and troponin.
An abnormality of the hematopoietic system.
Abnormality of blood and blood-forming tissues
Abnormality of the haematopoietic system
An abnormal decreased number of leukocytes in the blood.
An abnormal susceptibility to bleeding, often referred to as a bleeding diathesis. A bleeding diathesis may be related to vascular, platelet and coagulation defects.
A kind of anemia in which the volume of the red blood cells is normal.
Sudden loss of renal function, as manifested by decreased urine production, and a rise in serum creatinine or blood urea nitrogen concentration (azotemia).
Abnormal acid accumulation or depletion of base.
Metabolic acidosis (MA) is characterized by a fall in blood pH due to a reduction of serum bicarbonate concentration. This can occur as a result of either the accumulation of acids (high anion gap MA) or the loss of bicarbonate from the gastrointestinal tract or the kidney (hyperchloremic MA). By definition, MA is not due to a respirary cause.
Body temperature elevated above the normal range.
Excessive thirst manifested by excessive fluid intake.
An abnormal increase in the number of leukocytes in the blood.
An abnormality of the viscera of the abdomen.
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.
Reduced body temperature due to failed thermoregulation.
An abnormality of the respiratory system, which include the airways, lungs, and the respiratory muscles.
Difficult or labored breathing. Dyspnea is a subjective feeling only the patient can rate, e.g., on a Borg scale.
Respiratory distress is objectively observable as the physical or emotional consequences from the experience of dyspnea. The physical presentation of respiratory distress is generally referred to as labored breathing, while the sensation of respiratory distress is called shortness of breath or dyspnea.
Lack of breathing with no movement of the respiratory muscles and no exchange of air in the lungs. This term refers to a disposition to have recurrent episodes of apnea rather than to a single event.
Abnormally increased level of blood lactate (2-hydroxypropanoic acid). Lactate is produced from pyruvate by lactate dehydrogenase during normal metabolism. The terms lactate and lactic acid are often used interchangeably but lactate (the component measured in blood) is strictly a weak base whereas lactic acid is the corresponding acid. Lactic acidosis is often used clinically to describe elevated lactate but should be reserved for cases where there is a corresponding acidosis (pH below 7.35).
Higher than normal levels of lactate in blood
Cephalgia, or pain sensed in various parts of the head, not confined to the area of distribution of any nerve.
Increased respiratory rate or depth of breathing
An anomaly of the rhythm or depth of breathing.
An increased amount of bilirubin in the blood.
An abnormality of the composition of urine or the levels of its components.
Abnormality of the homeostasis (concentration) of a monoatomic ion.
Abnormal increased size of the viscera of the abdomen.
An unpleasant sensation characterized by physical discomfort (such as pricking, throbbing, or aching) localized to the back.
An unpleasant sensation characterized by physical discomfort (such as pricking, throbbing, or aching) localized to the lower back.
The presence of free hemoglobin in the urine.
Death of the fetus in utero after at least 22 weeks of gestation.
An abnormality of temperature homeostasis.
A deficiency in the intake of energy and nutrients.
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 tumor (abnormal growth of tissue) of the skin.
Stridor is a high pitched sound resulting from turbulent air flow in the upper airway.
An abnormal accumulation of excess fluid in the lower extremity resulting in swelling of the feet and extending upward to the lower leg.
Redness of the skin, caused by hyperemia of the capillaries in the lower layers of the skin.
A functional abnormality of the immune system.
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.
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
Vascular abnormalities restricted to skin
Abnormality of the urinary system physiology
An abnormality of the skin that is not localized to any one particular region.
Cognitive, psychiatric or memory anomaly.
A subjective manifestation of disease localized to the abdomen.
A type of abdominal pain that comes and goes in waves, most often starting and ending suddenly and being of severe intensity.
Number of leukocytes per volume of blood beyond normal limits.
Impaired ability to eat related to problems gathering food and getting ready to suck, chew, or swallow it.
An abnormal functionality of the kidney.
An anomaly in the processes involved in the maintenance of an internal equilibrium.
An unpleasant sensory and emotional experience associated with actual or potential tissue damage, or described in terms of such damage.
A functional anomaly of the nervous system.
Abnormality of nervous system physiology
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.
Abnormality of the digestive system
A functional anomaly of the digestive system.
Abnormality of digestive system physiology
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.
Constitutional symptom
Pain in the ear can be a consequence of otologic disease (primary or otogenic otalgia), or can arise from pathologic processes and structures other than the ear (secondary or referred otalgia).
A high-pitched whistling sound associated with labored breathing.
An anomalous (adventitious) sound produced by the breathing process.
Widening of the nostrils upon inhalation as a manifestation of respiratory distress.
A pulling inward of the soft tissues between the ribs upon inhalation. This is a sign of increased use of the chest muscles for breathing and is a manifestation of respiratory distress.
The state in which profound and widespread reduction of effective tissue perfusion leads first to reversible, and then if prolonged, to irreversible cellular injury.
Increased discharge of mucus from the nose.
A dermatosis characterized by generalized shiny, enamel-like, hyperpigmented scales in an irregular pattern. The scales may peel or desquamate, rather like old, sun-baked blistered paint, often with areas of underlying hypopigmentation. This has led to the terms peeling paint or flaky paint dermatosis (See the Figure in PMID:24285001).
An abnormal level of an analyte measured in the blood.
Abnormal circulating metabolite concentration
Health status of a family member with respect to the disease being investigated in a proband.
Any form of seizure occurring at the time of a fever (temperature at or above 38.0 degrees Celcius) without infection of the central nervous system, and without an alternative cause such as severe metabolic derangement, occurring at any age.
Seizure precipitated by febrile infection
A palpable swelling in both feet and ankles caused by palpable swelling caused by an increase in interstitial fluid volume (excess fulid).
A cough with a characteristic sound that has been compared to a seal's bark.
Relative coldness of a body part to palpitation, often acccompanied by feelings of coldness.
Systemic inflammatory response to infection in newborn babies.
Pulmonary hemorrhage is a bleeding within the lungs. Older children and adults may spit blood or bloody sputum. Neonates, infants and young children usually do not spit up blood. Anemia, pulmonary infiltrates, increasingling bloody return on BAL and the presence of hemosiderin-laden macrophages in broncho-alveolar lavage (BAL) fluid or lung biopsy can diagnose lung bleeding. Alveolar macrophages contain phagocytosed red blood cells and stain positive for hemosiderin, a product of hemoglobin degradation, after about 48-72 hours following pulmonary hemorraghe. Previous or recurrent bleeding can thus be distinguished from fresh events. A differentiation into local or diffuse is of importance. Also differentiate if pulmonary hemorrhage is due to a primary lung disorder or a manifestation of a systemic disease.
Pregnancy-induced hypertension in association with significant amounts of protein in the urine.
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.
An acute hypersensitivity reaction due to exposure to a previously encountered antigen.
An unpleasant sensation characterized by physical discomfort (such as pricking, throbbing, or aching) localized to the eye.
A small elevation of the skin containing cloudy or purulent material usually consisting of necrotic inflammatory cells.
Warts, benign growths on the skin or mucous membranes that cause cosmetic problems as well as pain and discomfort. Warts most often occur on the hands, feet, and genital areas.
Reduced ability to control, or a failure to resist a temptation, urge, or impulse.
measurement unit label
Examples of measurement unit labels are liters, inches, weight per volume.
A measurement unit label is as a label that is part of a scalar measurement datum and denotes a unit of measure.
2009-03-16: provenance: a term measurement unit was proposed for OBI (OBI_0000176) , edited by Chris Stoeckert and Cristian Cocos, and subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definition of this, different, term.
2009-03-16: review of this term done during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI.
PERSON: Melanie Courtot
objective specification
In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction.
A directive information entity that describes an intended process endpoint. When part of a plan specification the concretization is realized in a planned process in which the bearer tries to effect the world so that the process endpoint is achieved.
2009-03-16: original definition when imported from OBI read: "objective is an non realizable information entity which can serve as that proper part of a plan towards which the realization of the plan is directed."
2014-03-31: In the example of usage ("In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction") there is a protocol which is the ChIP assay protocol. In addition to being concretized on paper, the protocol can be concretized as a realizable entity, such as a plan that inheres in a person. The objective specification is the part that says that some protein and DNA interactions are identified. This is a specification of a process endpoint: the boundary in the process before which they are not identified and after which they are. During the realization of the plan, the goal is to get to the point of having the interactions, and participants in the realization of the plan try to do that.
Answers the question, why did you do this experiment?
PERSON: Barry Smith
PERSON: Bjoern Peters
PERSON: Jennifer Fostel
goal specification
OBI Plan and Planned Process/Roles Branch
Pour the contents of flask 1 into flask 2
A directive information entity that describes an action the bearer will take.
OBI Plan and Planned Process branch
action specification
datum label
A label is a symbol that is part of some other datum and is used to either partially define the denotation of that datum or to provide a means for identifying the datum as a member of the set of data with the same label
GROUP: IAO
9/22/11 BP: changed the rdfs:label for this class from 'label' to 'datum label' to convey that this class is not intended to cover all kinds of labels (stickers, radiolabels, etc.), and not even all kind of textual labels, but rather the kind of labels occuring in a datum.
data item
Data items include counts of things, analyte concentrations, and statistical summaries.
An information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements.
2/2/2009 Alan and Bjoern discussing FACS run output data. This is a data item because it is about the cell population. Each element records an event and is typically further composed a set of measurment data items that record the fluorescent intensity stimulated by one of the lasers.
2009-03-16: data item deliberatly ambiguous: we merged data set and datum to be one entity, not knowing how to define singular versus plural. So data item is more general than datum.
2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym.
2014-03-31: See discussion at http://odontomachus.wordpress.com/2014/03/30/aboutness-objects-propositions/
JAR: datum -- well, this will be very tricky to define, but maybe some information-like stuff that might be put into a computer and that is meant, by someone, to denote and/or to be interpreted by some process... I would include lists, tables, sentences... I think I might defer to Barry, or to Brian Cantwell Smith JAR: A data item is an approximately justified approximately true approximate belief
PERSON: Chris Stoeckert
PERSON: Jonathan Rees
data
symbol
a serial number such as "12324X"
a stop sign
a written proper name such as "OBI"
An information content entity that is a mark(s) or character(s) used as a conventional representation of another entity.
20091104, MC: this needs work and will most probably change
2014-03-31: We would like to have a deeper analysis of 'mark' and 'sign' in the future (see https://github.com/information-artifact-ontology/IAO/issues/154).
PERSON: James A. Overton
based on Oxford English Dictionary
information content entity
Examples of information content entites include journal articles, data, graphical layouts, and graphs.
A generically dependent continuant that is about some thing.
2014-03-10: The use of "thing" is intended to be general enough to include universals and configurations (see https://groups.google.com/d/msg/information-ontology/GBxvYZCk1oc/-L6B5fSBBTQJ).
information_content_entity 'is_encoded_in' some digital_entity in obi before split (040907). information_content_entity 'is_encoded_in' some physical_document in obi before split (040907). Previous. An information content entity is a non-realizable information entity that 'is encoded in' some digital or physical entity.
10 feet. 3 ml.
A scalar measurement datum is a measurement datum that is composed of two parts, numerals and a unit label.
2009-03-16: we decided to keep datum singular in scalar measurement datum, as in this case we explicitly refer to the singular form
Would write this as: has_part some 'measurement unit label' and has_part some numeral and has_part exactly 2, except for the fact that this won't let us take advantage of OWL reasoning over the numbers. Instead use has measurment value property to represent the same. Use has measurement unit label (subproperty of has_part) so we can easily say that there is only one of them.
scalar measurement datum
An information content entity whose concretizations indicate to their bearer how to realize them in a process.
2009-03-16: provenance: a term realizable information entity was proposed for OBI (OBI_0000337) , edited by the PlanAndPlannedProcess branch. Original definition was "is the specification of a process that can be concretized and realized by an actor" with alternative term "instruction".It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term.
2013-05-30 Alan Ruttenberg: What differentiates a directive information entity from an information concretization is that it can have concretizations that are either qualities or realizable entities. The concretizations that are realizable entities are created when an individual chooses to take up the direction, i.e. has the intention to (try to) realize it.
8/6/2009 Alan Ruttenberg: Changed label from "information entity about a realizable" after discussions at ICBO
Werner pushed back on calling it realizable information entity as it isn't realizable. However this name isn't right either. An example would be a recipe. The realizable entity would be a plan, but the information entity isn't about the plan, it, once concretized, *is* the plan. -Alan
directive information entity
algorithm
PMID: 18378114.Genomics. 2008 Mar 28. LINKGEN: A new algorithm to process data in genetic linkage studies.
A plan specification which describes the inputs and output of mathematical functions as well as workflow of execution for achieving an predefined objective. Algorithms are realized usually by means of implementation as computer programs for execution by automata.
Philippe Rocca-Serra
PlanAndPlannedProcess Branch
adapted from discussion on OBI list (Matthew Pocock, Christian Cocos, Alan Ruttenberg)
curation status specification
The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value.
Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting)
data set
Intensity values in a CEL file or from multiple CEL files comprise a data set (as opposed to the CEL files themselves).
A data item that is an aggregate of other data items of the same type that have something in common. Averages and distributions can be determined for data sets.
2009/10/23 Alan Ruttenberg. The intention is that this term represent collections of like data. So this isn't for, e.g. the whole contents of a cel file, which includes parameters, metadata etc. This is more like java arrays of a certain rather specific type
2014-05-05: Data sets are aggregates and thus must include two or more data items. We have chosen not to add logical axioms to make this restriction.
person:Allyson Lister
person:Chris Stoeckert
image
An image is an affine projection to a two dimensional surface, of measurements of some quality of an entity or entities repeated at regular intervals across a spatial range, where the measurements are represented as color and luminosity on the projected on surface.
data about an ontology part
Data about an ontology part is a data item about a part of an ontology, for example a term
plan specification
PMID: 18323827.Nat Med. 2008 Mar;14(3):226.New plan proposed to help resolve conflicting medical advice.
A directive information entity with action specifications and objective specifications as parts, and that may be concretized as a realizable entity that, if realized, is realized in a process in which the bearer tries to achieve the objectives by taking the actions specified.
2009-03-16: provenance: a term a plan was proposed for OBI (OBI_0000344) , edited by the PlanAndPlannedProcess branch. Original definition was " a plan is a specification of a process that is realized by an actor to achieve the objective specified as part of the plan". It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term.
2014-03-31: A plan specification can have other parts, such as conditional specifications.
2022-01-16 Updated definition to that proposed by Clint Dowloand, IAO Issue 231.
Alternative previous definition: a plan is a set of instructions that specify how an objective should be achieved
Clint Dowland
2/3/2009 Comment from OBI review. Action specification not well enough specified. Conditional specification not well enough specified. Question whether all plan specifications have objective specifications. Request that IAO either clarify these or change definitions not to use them
measurement datum
Examples of measurement data are the recoding of the weight of a mouse as {40,mass,"grams"}, the recording of an observation of the behavior of the mouse {,process,"agitated"}, the recording of the expression level of a gene as measured through the process of microarray experiment {3.4,luminosity,}.
A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device.
2/2/2009 is_specified_output of some assay?
obsolescence reason specification
The reason for which a term has been deprecated. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value.
The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology.
textual entity
Words, sentences, paragraphs, and the written (non-figure) parts of publications are all textual entities
A textual entity is a part of a manifestation (FRBR sense), a generically dependent continuant whose concretizations are patterns of glyphs intended to be interpreted as words, formulas, etc.
AR, (IAO call 2009-09-01): a document as a whole is not typically a textual entity, because it has pictures in it - rather there are parts of it that are textual entities. Examples: The title, paragraph 2 sentence 7, etc.
MC, 2009-09-14 (following IAO call 2009-09-01): textual entities live at the FRBR (http://en.wikipedia.org/wiki/Functional_Requirements_for_Bibliographic_Records) manifestation level. Everything is significant: line break, pdf and html versions of same document are different textual entities.
PERSON: Lawrence Hunter
text
document
A journal article, patent application, laboratory notebook, or a book
A collection of information content entities intended to be understood together as a whole
publication
journal article, newspaper story, book, etc.
A document that is the output of a publishing process.
PERSON: Jie Zheng
published document
Revisit the term in Octorber 2020. Improve the defintion.
A cartesian spatial coordinate datum is a representation of a point in a spatial region, in which equal changes in the magnitude of a coordinate value denote length qualities with the same magnitude
2009-08-18 Alan Ruttenberg - question to BFO list about whether the BFO sense of the lower dimensional regions is that they are always part of actual space (the three dimensional sort) http://groups.google.com/group/bfo-discuss/browse_thread/thread/9d04e717e39fb617
AR notes: We need to discuss whether it should include site.
cartesian spatial coordinate datum
A cartesion spatial coordinate datum that uses one value to specify a position along a one dimensional spatial region
one dimensional cartesian spatial coordinate datum
A scalar measurement datum that is the result of measurement of length quality
length measurement datum
denotator type
The Basic Formal Ontology ontology makes a distinction between Universals and defined classes, where the formal are "natural kinds" and the latter arbitrary collections of entities.
A denotator type indicates how a term should be interpreted from an ontological perspective.
Barry Smith, Werner Ceusters
A scalar measurement datum that is the result of measurement of mass quality
mass measurement datum
A scalar measurement datum that is the result of measuring a temporal interval
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 planned process of making information, such as literature, music, and software etc., available to the public for sale or for free.
Person: Jie Zheng
VEuPathDB
publishing process
A document that is in preparation for submission to be published.
EFO_0001795 in preparation
document in preparation for publication
Recording the current temperature in a laboratory notebook. Writing a journal article. Updating a patient record in a database.
A planned process in which a document is created or added to by including the specified input in it.
6/11/9: Edited at OBI workshop. We need to be able identify a child form of information artifact which corresponds to something enduring (not brain like). This used to be restricted to physical document or digital entity as the output, but that excludes e.g. an audio cassette tape
Bjoern Peters
wikipedia http://en.wikipedia.org/wiki/Documenting
documenting
A new pubmed ID being created for a journal article, and the associated pubmed record containing information to the journal article. A license plate number registered at the DMV to be belonging to a specific vehicle and owner. Placing a barcode on a product and entering information in a database that this barcode is assigned.
A planned process in which a new CRID is created, associated with an entity, and stored in the CRID registry thereby registering it as being associated with some entity
2014-05-05: It is the CRID registry that assigns CRIDs, not the users of the registry.
Person:Bjoern Peters
Person:Melanie Courtot
assigning a centrally registered identifier
The sentence "The article has Pubmed ID 12345." contains a CRID that has two parts: one part is the CRID symbol, which is '12345'; the other part denotes the CRID registry, which is Pubmed.
A symbol that is part of a CRID and that is sufficient to look up a record from the CRID's registry.
PERSON: Bill Hogan
Original proposal from Bjoern, discussions at IAO calls
centrally registered identifier symbol
An information content entity that consists of a CRID symbol and additional information about the CRID registry to which it belongs.
2014-05-05: In defining this term we take no position on what the CRID denotes. In particular do not assume it denotes a *record* in the CRID registry (since the registry might not have 'records').
Alan, IAO call 20101124: potentially the CRID denotes the instance it was associated with during creation.
Note, IAO call 20101124: URIs are not always CRID, as not centrally registered. We acknowledge that CRID is a subset of a larger identifier class, but this subset fulfills our current needs. OBI PURLs are CRID as they are registered with OCLC. UPCs (Universal Product Codes from AC Nielsen)are not CRID as they are not centrally registered.
centrally registered identifier
PubMed is a CRID registry. It has a code set of PubMed identifiers associated with journal articles.
A code set of CRID records, each consisting of a CRID symbol and additional information which was recorded in the code set through an assigning a centrally registered identifier process.
Justin Whorton
centrally registered identifier registry
identifier
An information content entity that is the outcome of a dubbing process and is used to refer to one instance of entity shared by a group of people to refer to that individual entity.
Mathias Brochhausen
proper name
Sep 29, 2016: The current definition has been amended from the previous version: "A proper name is an information content entity that is the outcome of a dubbing process and is used to refer to one instance of entity shared by a group of people to refer to that individual entity." to more accuratly reflect the necessary and sufficient condition on the class. (MB)
A planned process that provides a reference to an individual entity shared by a group of subscribers to refer to that individual entity.
dubbing process
naming
identifier creating process
An information content entity that is a collection of other information content entities that has been created to identify or annotate things in a specified domain, and where the intention of its creators is that the collection has a one-to-one correspondence with those things.
code map
code system
codeset
coding system
controlled vocabulary
Code sets might include non-entities/things (e.g. missing thumbs).
Does not imply absence vs. presence of any taxonomy.
Does not imply that aggregated entities denote particulars, universals, or defined classes (a.k.a. attributive collections) or even that they denote only one of these three types of entities.
Each aggregated entity is often (but not necessarily) associated with a text string—variously called a “description,” “name,” “title,” or “label”—that helps humans reach the target of denotation. When there is no such string, it is almost always because the entities take the form of human language words. For example, a “sex” or “gender” code set could contain “MALE” and “FEMALE,” or even “M” and “F” (by convention, we understand what these mean).
For National Drug Codes (NDCs) and similar code sets, there doesn’t even have to be a single, fully-concretized copy somewhere (for example, for NDCs there is no centralized database or repository where they all live as one instance of concretization of code set). The code set can be “distributively” concretized. This seems like an unusual exception, but it also likely applies to Universal Product Codes (UPCs) and their follow on Global Trade Item Numbers (GTINs).
For each given domain, there can potentially exist multiple code sets. The multiplicity of code sets is partially due to the different specific purposes of those code sets.
Many code sets are created for a specific purpose in addition to merely identifying or annotating core ideas of a specified domain.
The information content entities do not denote each other.
code set
ontology module
I have placed this under 'data about an ontology part', but this can be discussed. I think this is OK if 'part' is interpreted reflexively, as an ontology module is the whole ontology rather than part of it.
ontology file
This class and it's subclasses are applied to OWL ontologies. Using an rdf:type triple will result in problems with OWL-DL. I propose that dcterms:type is instead used to connect an ontology URI with a class from this hierarchy. The class hierarchy is not disjoint, so multiple assertions can be made about a single ontology.
base ontology module
An ontology module that comprises only of asserted axioms local to the ontology, excludes import directives, and excludes axioms or declarations from external ontologies.
editors ontology module
An ontology module that is intended to be directly edited, typically managed in source control, and typically not intended for direct consumption by end-users.
source ontology module
main release ontology module
An ontology module that is intended to be the primary release product and the one consumed by the majority of tools.
TODO: Add logical axioms that state that a main release ontology module is derived from (directly or indirectly) an editors module
bridge ontology module
An ontology module that consists entirely of axioms that connect or bridge two distinct ontology modules. For example, the Uberon-to-ZFA bridge module.
import ontology module
A subset ontology module that is intended to be imported from another ontology.
TODO: add axioms that indicate this is the output of a module extraction process.
import file
subset ontology module
An ontology module that is extracted from a main ontology module and includes only a subset of entities or axioms.
ontology slim
subset ontology
curation subset ontology module
A subset ontology that is intended as a whitelist for curators using the ontology. Such a subset will exclude classes that curators should not use for curation.
analysis ontology module
An ontology module that is intended for usage in analysis or discovery applications.
analysis subset ontology module
single layer ontology module
A subset ontology that is largely comprised of a single layer or strata in an ontology class hierarchy. The purpose is typically for rolling up for visualization. The classes in the layer need not be disjoint.
ribbon subset
single layer subset ontology module
exclusion subset ontology module
A subset of an ontology that is intended to be excluded for some purpose. For example, a blacklist of classes.
antislim
external import ontology module
An imported ontology module that is derived from an external ontology. Derivation methods include the OWLAPI SLME approach.
external import
species subset ontology module
A subset ontology that is crafted to either include or exclude a taxonomic grouping of species.
taxon subset
reasoned ontology module
An ontology module that contains axioms generated by a reasoner. The generated axioms are typically direct SubClassOf axioms, but other possibilities are available.
generated ontology module
An ontology module that is automatically generated, for example via a SPARQL query or via template and a CSV.
TODO: Add axioms (using PROV-O?) that indicate this is the output-of some reasoning process
template generated ontology module
An ontology module that is automatically generated from a template specification and fillers for slots in that template.
taxonomic bridge ontology module
ontology module subsetted by expressivity
obo basic subset ontology module
A subset ontology that is designed for basic applications to continue to make certain simplifying assumptions; many of these simplifying assumptions were based on the initial version of the Gene Ontology, and have become enshrined in many popular and useful tools such as term enrichment tools. Examples of such assumptions include: traversing the ontology graph ignoring relationship types using a naive algorithm will not lead to cycles (i.e. the ontology is a DAG); every referenced term is declared in the ontology (i.e. there are no dangling clauses). An ontology is OBO Basic if and only if it has the following characteristics: DAG Unidirectional No Dangling Clauses Fully Asserted Fully Labeled No equivalence axioms Singly labeled edges No qualifier lists No disjointness axioms No owl-axioms header No imports
ontology module subsetted by OWL profile
EL++ ontology module
A role borne by pathogen in virtue of the fact that it or one of its products is sufficiently close to an organism towards which it has the pathogenic disposition to allow realization of the pathogenic disposition.
pathogen role
A quality that inheres in an organism population and is the number of organisms in the population infected with an infectious agent at a specified time.
infection prevalence
A material entity with a pathogenic disposition.
pathogen
A molecular entity with a toxin disposition and that is a structural component of a pathogen and is released from the pathogen only upon cytolysis.
endotoxin
A material entity bearing an antibacterial disposition.
antibacterial
An infection bearing the primary infection role.
primary infection
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.
infection
A process that attenuates an immune response.
immunosuppression
The surgical removal (cutting out) of part or all of uterus.
A protein modification that effectively either removes neutral hydrogen atoms (proton and electron), or adds oxygen atoms to a residue with or without the removal of hydrogen atoms.
A protein modification that by reaction of iodoacetamide effectively replaces a residue alpha-amino- or alpha-imino-hydrogen with a carboxamidomethyl group.
iodoacetamide derivatized amino-terminal residue
eastern equine encephalomyelitis virus EEEV
post-transfusion hepatitis non A non B virus
negative-sense genome single-stranded RNA viruses
Cell-associated subacute sclerosing panencephalitis
Subacute sclerosing panencephalitis virus
subacute sclerosing panencephalitis virus, SSPEV
human immunodeficiency virus type 1 HIV 1
human immunodeficiency virus type 1 HIV-1
human immunodeficiency virus type 1 HIV1
human immunodeficiency virus type 1, HIV-1
human immunodeficiency virus type I HIV-1
human immunodeficiency virus type-1 HIV-1
"Alphaproteobacteriota" Whitman et al. 2018
purple photosynthetic bacteria and relatives
"Firmicutes" corrig. Gibbons and Murray 1978 (Approved Lists 1980)
Bacillota corrig. Gibbons and Murray 2021
Coquillettidia (Coquillettidia) richiardii
Bacillus thuringiensis Berliner 1915 (Approved Lists 1980)
Bacillus thuringiensis (SUBSP. ISRAELENSIS)
Bacillus thuringiensis subsp. israelensis
Bacillus thuringiensis serovar israelensis
ducks, geese, chickens, fowl, quail, currasows and allies
Anopheles maculipennis sensu lato BTLHVDV-2014
Mycobacterium Lehmann and Neumann 1896 (Approved Lists 1980)
Mycobacterium tuberculosis typus humanus
Mycobacterium tuberculosis variant tuberculosis
Filterable agent of primary atypical pneumonia
Chryseobacterium indologenes (Yabuuchi et al. 1983) Vandamme et al. 1994
Severe acute respiratory syndrome coronavirus 2
"Chlorobacterium" Guillebeau 1890, nom. rejic. Opin. 6 (not "Chlorobacterium" Lauterborn 1916)
probable synonym or variety: "Pseudomonas polycolor" Clara 1930
Pseudomonas perfectomarina (ex ZoBell and Upham 1944) Baumann et al. 1983
Pseudomonas stutzeri (Lehmann and Neumann 1896) Sijderius 1946 (Approved Lists 1980)
"Mycobacterium abcessus" Moore and Frerichs 1953
"Mycobacterium chelonei" (sic) Bergey et al. 1923
Human rotavirus (serotype G / strain 116E)
Moraxella (subgen. Moraxella Lwoff 1939) nonliquefaciens (Scarlett 1916) Bovre 1984
Moraxella (subgen. Branhamella Catlin 1970) catarrhalis (Frosch and Kolle 1896) Bovre 1984
Diplokokkus intracellularis meningitidis
Micrococcus meningitidis cerebrospinalis
Ajellomyces capsulatus (Kwon-Chung) McGinnis & Katz, 1979
"Salmonella paratyphi-A" (Brion and Kaiser 1902) Castellani and Chalmers 1919
Salmonella choleraesuis choleraesuis (serotype paratyphi A)
Salmonella choleraesuis subsp. choleraesuis serovar Paratyphi A
Salmonella enterica subsp. enterica serovar Paratyphi A
'Klebsiella aerogenes' (Kruse) Taylor et al. 1956
Anopheles barbirostris subgroup clade III
Haemamoeba vivax Grassi and Feletti, 1890
Salmonella cholerae-suis subsp. cholerae-suis
Salmonella choleraesuis subsp. choleraesuis
Aeromonas hydrophila (Chester 1901) Stanier 1943 (Approved Lists 1980)
Ochlerotatus (Ochlerotatus) camptorhynchus
Plesiomonas shigelloides corrig. (Bader 1954) Habs and Schubert 1962 (Approved Lists 1980)
Burkholderia/Oxalobacter/Ralstonia group
Corynebacteriales Goodfellow and Jones 2015
Mycobacteriales Janke 1924 (Approved Lists 1980)
Achromobacter xylosoxidans subsp. xylosoxidans
Alcaligenes denitrificans subsp. xylosoxydans
Alcaligenes xylosoxidans subsp. xylosoxidans
Salmonella enterica subsp. enterica serovar Typhi
Acinetobacter calcoaceticus/baumannii complex
Bacillus/Lactobacillus/Streptococcus group
Enterobacteriaceae and related endosymbionts
whales, hippos, ruminants, pigs, camels etc.
Ehrlichia phagocytophila (Foggie 1949) Philip 1962 (Approved Lists 1980)
agent of human granulocytic ehrlichiosis
Cytophaga-Flexibacter-Bacteroides phylum
A condition of the newborn characterized by the destruction of red blood cells initiated by the transmission of anti-A or anti-B antibodies from a mother to the child via the placenta against A or B antigens of the newborn's blood.
Hemolytic Disease due to ABO Isoimmunization
The presence of more than one fungal and/or bacterial organism in a culture.
A measurement of the total number of induced abortions experienced by a female subject.
A measurement of the total number of spontaneous abortions (in which the fetus is less than 20 weeks gestational age) experienced by a female subject.
Any rod-shaped, Gram-negative, non-spore forming, motile or non-motile bacteria which can ferment lactose with the production of acid and gas.
The gestational age of the subject at birth.
A 10-item, self-rating questionnaire designed to screen postpartum women for indications of depression.
Edinburgh Postnatal Depression Scale (EPDS)
A measurement of the distance between the pubic symphysis and the top of the palpable uterus.
Any method that uses a visual display of structural or functional patterns of organs or tissues for diagnostic evaluation.
Severe Acute Respiratory Infection (SARI)
A respiratory infectious disorder that leads to an acute illness that requires medical attention.
A note acknowledging a source of information or quoting a passage.
A sterile liquid preparation infused into a vein. IV fluid is prescribed as a replacement of fluid, electrolytes, calories, vitamins, and other nutritional substances. In addition, IV fluids are used to administer blood products and medications such as chemotherapy. Examples of IV fluids include Normal Saline, Ringers Solution, and Lactated Ringers Solution. (NCI)
A variation from processes or procedures defined in a protocol. Deviations usually do not preclude the overall evaluability of subject data for either efficacy or safety, and are often acknowledged and accepted in advance by the sponsor. (CDISC Glossary)
A subtype of Staphylococcus characterized by an inability to produce free plasma coagulase.
A period of three months; especially one of the three three-month periods into which human pregnancy is divided.
A genus of single-stranded positive sense RNA viruses containing a single RNA molecule. The viral particles are not enveloped and are icosahedral in structure.
The development of a problematic medical situation that occurs concurrently with the birth of a neonate.
A blood smear technique used to make a thick blood smear on a microscope slide which is generally used to look for blood parasites such as those causing malaria.
A blood smear technique used to make a thin blood smear on a microscope slide which is generally used to look for blood parasites such as those causing malaria.
A bacterium that is assigned to the genus Streptococcus that is able to reduce the iron content in hemoglobin in red blood cells, thus producing green colored colonies on blood agar plates.
A bacterium that is assigned to the genus Streptococcus that is able to facilitate the complete rupturing of red blood cells, thus producing wide, clear, zones around colonies on blood agar plates.
A non-taxonomic grouping of beta hemolytic species within the Streptococcus genus that are assigned to the F group.
Findings observed at the end of a pregnancy.
A tightening of the involuntary smooth muscles of the uterus.
Hemorrhage from the vagina that may range from light spotting to heavy flow during pregnancy.
a pathological bodily process that occurs after a medical intervention. An adverse event is likely caused by the medical intervention; however, such a causal association is not required to be an adverse event.
A surgery where incisions are made through a woman's abdomen and uterus to deliver her baby.
A study design that starts with an exposure and moves forward to the outcome of interest, even if the data are collected retrospectively. As an example, a group of patients who have variable exposure to a risk factor of interest can be followed over time for an outcome.
WEB: http://www.uptodate.com/contents/glossary-of-common-biostatistical-and-epidemiological-terms
A study design in which patients are randomly assigned to two or more interventions.
A data transformation that add two or more numbers, magnitudes, quantities, or particulars as determined by or as if by the mathematical process of addition.
tracker: https://github.com/obcs/obcs/issues/7
summing data values
A data item that is produced as the output of a summing data transformation and represents the total value of the input data.
sum value
medication material
A processed specimen which is the output of a density gradient centrifugation of an anticoagulated blood specimen that contains most of the white blood cells and platelets.
buffy coat specimen
Volume of blood collected in milliliters
A scalar measurement datum that is the output of a volume measurement assay that has a blood specimen as evaluant.
need volume measurement assay from OBI first
Person: Chris Stoeckert, Helena Ellis, Jie Zheng
A count that is about the aggregate of individuals who have been recruited to participate in a study.
Alice Nzinga
count of current total human study participant
A study design in which all participants or a representative subset of participants are examined at only a single time for characteristics of a interest (e.g. a specific disease).
cross sectional study design
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.
'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)
biological feature identification objective
Biological_feature_identification_objective is an objective role carried out by the proposition defining the aim of a study designed to examine or characterize a particular biological feature.
Jennifer Fostel
Calibration standard, positive control substance, vehicle Good Laboratory Practices: Questions and Answers - Test Control and Reference Substance Characterization http://www.epa.gov/enforcement/monitoring/programs/fifra/glpqanda-character.html
a role inhering in a material entity that is realized when characteristics or responses elicited by the substance are used for comparison or reference.
Person:Jennifer Fostel
OBI
reference substance role
Chromatography column in chemistry is a tube and contents (typically glass) used to purify individual chemical compounds from mixtures of compounds. It is often used for preparative applications on scales from micrograms up to kilograms.
open tracker https://sourceforge.net/tracker/index.php?func=detail&aid=2881353&group_id=177891&atid=886178
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.
A device that facilitates the separation of mixtures. The function of a chromatography device involves passing a mixture dissolved in a "mobile phase" through a stationary phase, which separates the analyte to be measured from other molecules in the mixture and allows it to be isolated.
LCQ Fleet Ion Trap MSn manufactured by thermo fisher scientific
A mass spectrometer is an instrument which is used to measure the mass to charge ratio of ions. All mass spectrometers consist of three basic parts: an ion source, a mass analyzer, and a detector system. The stages within the mass spectrometer are: 1. Production of ions from the sample 2. Separation of ions with different masses 3. Detection of the number of ions of each mass produced 4.Collection of data to generate the mass spectrum
investigation
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).
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
evaluant role
When a specimen of blood is assayed for glucose concentration, the blood has the evaluant role. When measuring the mass of a mouse, the evaluant is the mouse. When measuring the time of DNA replication, the evaluant is the DNA. When measuring the intensity of light on a surface, the evaluant is the light source.
a role that inheres in a material entity that is realized in an assay in which data is generated about the bearer of the evaluant role
Role call - 17nov-08: JF and MC think an evaluant role is always specified input of a process. Even in the case where we have an assay taking blood as evaluant and outputting blood, the blood is not the specified output at the end of the assay (the concentration of glucose in the blood is)
examples of features that could be described in an evaluant: quality.... e.g. "contains 10 pg/ml IL2", or "no glucose detected")
Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term.
assay
Assay the wavelength of light emitted by excited Neon atoms. Count of geese flying over a house.
A planned process with the objective to produce information about the material entity that is the evaluant, by physically examining it or its proxies.
12/3/12: BP: the reference to the 'physical examination' is included to point out that a prediction is not an assay, as that does not require physical examiniation.
measuring
scientific observation
sample preparation for assay
A sample_preparation_for_assay is a protocol_application including material_enrollments and biomaterial_transformations. definition_source: OBI.
study
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
culture medium
Buffer, dye, a catalyst, a solvating agent.
A role inhering in a biological or chemical entity that is intended to be applied in a scientific technique to participate (or have molecular components that participate) in a chemical reaction that facilitates the generation of data about some entity distinct from the bearer, or the generation of some specified material output distinct from the bearer.
PERSON:Matthew Brush
Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term. May 28 2013. Updated definition taken from ReO based on discussions initiated in Philly 2011 workshop. Former defnition described a narrower view of reagents in chemistry that restricts bearers of the role to be chemical entities ("a role played by a molecular entity used to produce a chemical reaction to detect, measure, or produce other substances"). Updated definition allows for broader view of reagents in the domain of biomedical research to include larger materials that have parts that participate chemically in a molecular reaction or interaction.
(copied from ReO) Reagents are distinguished from instruments or devices that also participate 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, instruments 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 will realize only one of these roles in the execution of a given assay or technique. 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).
reagent role
A cell lysis, production of a cloning vector, creating a buffer.
A planned process which results in physical changes in a specified input material
material transformation
material processing
study subject role
Human subjects in a clinical trial, rats in a toxicogenomics study, tissue cutlures subjected to drug tests, fish observed in an ecotoxicology study. Parasite example: people are infected with a parasite which is then extracted; the particpant under investigation could be the parasite, the people, or a population of which the people are members, depending on the nature of the study. Lake example: a lake could realize this role in an investigation that assays pollution levels in samples of water taken from the lake.
A role that is realized through the execution of a study design in which the bearer of the role participates and in which data about that bearer is collected.
A participant can realize both "specimen role" and "participant under investigation role" at the same time. However "participant under investigation role" is distinct from "specimen role", since a specimen could somehow be involved in an investigation without being the thing that is under investigation.
GROUP: Role Branch
Following OBI call November 2012,26th: 1. it was decided there was no need for moving the children class and making them siblings of study subject role. 2. it also settles the disambiguation about 'study subject'. This is about the individual participating in the investigation/study, Not the 'topic' (as in 'toxicity study') of the investigation/study This note closes the issue and validates the class definition to be part of the OBI core editor = PRS
participant under investigation role
a responsible party role played by a person responsible for the overall conduct of a study
Person: Jennifer Fostel
CDISC definition: A person responsible for the conduct of the clinical trial at a trial site. If a trial is conducted by a team of individuals at a trial site, the investigator is the responsible leader of the team and may be called the principal investigator. 2. The individual principal investigator. 2. The individual under whose immediate direction the test article is administered or dispensed to, or used involving, a subject, or, in the event of an investigation conducted by a team of individuals, is See also sponsor-investigator.; Leiter der klinischen Prufung.Under the German Drug Law, the physician who is head of the clinical investigation (CDISC): coordinating investigator (CDISC) (also study coordinator, MUSC); sponsor-investigator. An individual who both initiates and conducts, alone or with others, a clinical trial, and under whose immediate direction the investigational product is administered to, dispensed to, or used by a subject.NOTE: The term does not include any person other than an individual, hence not a corporation, agency (CDISC)
principal investigator role
liver section; a portion of a culture of cells; a nemotode or other animal once no longer a subject (generally killed); portion of blood from a patient.
a role borne by a material entity that is gained during a specimen collection process and that can be realized by use of the specimen in an investigation
22Jun09. The definition includes whole organisms, and can include a human. The link between specimen role and study subject role has been removed. A specimen taken as part of a case study is not considered to be a population representative, while a specimen taken as representing a population, e.g. person taken from a cohort, blood specimen taken from an animal) would be considered a population representative and would also bear material sample role.
Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation.
blood taken from animal: animal continues in study, whereas blood has role specimen. something taken from study subject, leaves the study and becomes the specimen.
parasite example - when parasite in people we study people, people are subjects and parasites are specimen - when parasite extracted, they become subject in the following study specimen can later be subject.
specimen role
PMID: 18208636.Br J Nutr. 2008 Jan 22;:1-11.Effect of vitamin D supplementation on bone and vitamin D status among Pakistani immigrants in Denmark: a randomised double-blinded placebo-controlled intervention study.
An intervention design is a study design in which a controlled process applied to the subjects (the intervention) serves as the independent variable manipulated by the experimentalist. The treatment (perturbation or intervention) defined can be defined as a combination of values taken by independent variable manipulated by the experimentalists are applied to the recruited subjects assigned (possibly by applying specific methods) to treatment groups. The specificity of intervention design is the fact that independent variables are being manipulated and a response of the biological system is evaluated via response variables as monitored by possibly a series of assays.
A device manufacture with the intent to provide a porous unsized paper used for filtering.
The group of randomized participants that are assigned to a treatment arm of the trial
a study population role where the bearer is a population of material entities and the role is realized in the implementation of a study design wherein the entities bearing the study population role are observed or subjected to intervention according to the study design and are biological replicates, i.e. they receive the same treatment under the protocol
study group role
population
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
An assay that produces a picture of an entity.
chromatin immunoprecipitation
Yang et al, Int J Clin Exp Pathol. 2015; 8(3): 2746–275 PMID:26045780. Cells were lysed and sonicated to shear DNA to lengths between 200-1000 bp. The sample was then incubated with antibodies against Acety-H3 to immunoprecipitate protein-DNA complexes using protein A agarose beads. The isolated protein-DNA complexes were treated with proteinase K digestion to remove histones. QPCR was then performed using primers specific for TGF-β1, MMP-9 and PI3K promoters at 95°C for 5 min, followed by 40 cycles at 95 °C for 20 s, 58°C for 20 s, and 72°C for 20 s. Each QPCR reaction was repeated in triplicate. QPCR was followed by a melt curve analysis to determine the reaction specificity. The relative gene expression was calculated using 2-ΔΔCt method.
An immunoprecipitation in which chromatin (i.e. packaged DNA which can include protein and RNA complexes) is cut into short regions, reversibly cross linked, and antibodies or tags are used to select for pieces of chromatin with desired characteristics.
Bjoern Peters, Randi Vita, James A. Overton
ChIP
The person perform microarray experiments and submit microarray results (including raw data, processed data) with experiment description to ArrayExpress.
A role borne by an entity and that is realized in a process that is part of an investigation in which an objective is achieved. These processes include, among others: planning, overseeing, funding, reviewing.
Implementing a study means carrying out or performing the study and providing reagents or other materials used in the study and other tasks without which the study would not happen.
Philly2013: Historically, this role would have been borne only by humans or organizations. However, we now also want to enable representing investigations run by robot scientists such as ADAM (King et al, Science, 2009)
Philly2013: Historically, this role would have been borne only by humans or organizations. However, we now also want to enable investigations run by robot scientists such as ADAM (King et al, Science, 2009)
Saline treated rat; one of three identically-treated subjects
a reference subject role which inheres in an organism or entity of organismal origin so that the characteristics or responses of the participant playing the reference participant role are used for comparison or reference
reference subject role
enzymatic cleavage
Polymorphism R62W results in resistance of CD23 to enzymatic cleavage in cultured cells. Genes Immun. 2007 Apr;8(3):215-23. Epub 2007 Feb 15. PMID: 17301828
a material processing that digests the fraction of input material that is susceptible to that enzyme
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.
organism feature identification objective
Organism_feature_identification_objective is a biological_feature_identification_objective role describing a study designed to examine or characterize a biological feature monitored at the level of the organism, e.g. height, weight, stage of development, stage of life cycle.
protocol
PCR protocol, has objective specification, amplify DNA fragment of interest, and has action specification describes the amounts of experimental reagents used (e..g. buffers, dNTPS, enzyme), and the temperature and cycle time settings for running the PCR.
A plan specification which has sufficient level of detail and quantitative information to communicate it between investigation agents, so that different investigation agents will reliably be able to independently reproduce the process.
OBI branch derived + wikipedia (http://en.wikipedia.org/wiki/Protocol_%28natural_sciences%29)
Injecting a drug into a mouse. Adding IL-2 to a cell culture. Adding NaCl into water.
is a process with the objective to place a material entity bearing the 'material to be added role' into a material bearing the 'target of material addition role'.
Class was renamed from 'administering substance', as this is commonly used only for additions into organisms.
adding a material entity into a target
Glucose in blood (measured in an assay to determine the concentration of glucose).
A measurand role borne by a molecular entity or an atom and realized in an analyte assay which achieves the objective to measure the magnitude/concentration/amount of the analyte in the entity bearing evaluant role.
interestingly, an analyte is still an analyte even if it is not detected. for this reason it does not bear a specified input role
pH (technically the inverse log of [H+]) may be considered a quality; this remains to be tested.
qualities such as weight, color are not assayed but measured, so they do not fall into this category.
analyte role
eluate
Raman spectroscopic detection of haemoproteins in the eluate from high-performance liquid chromatography. J Chromatogr. 1983 Jan 7;254:285-8. PMID: 6298263
a eluate is a material entity which results from an elution, e.g. from a chromatography column. it has as part a material entity with role mobile phase
need to add restriction to indicate: has_part some (material entity has_role mobile phase) need to add mobile phase as role
eluted material
drug added to a buffer contained in a tube; substance injected into an animal;
A role of a material entity that is realized in an "adding a material entity into a target" process where the bearer of the role is added into another material entity (the target).
9 March 09 from discussion with PA branch
material to be added role
Concluding that a gene is upregulated in a tissue sample based on the band intensity in a western blot. Concluding that a patient has a infection based on measurement of an elevated body temperature and reported headache. Concluding that there were problems in an investigation because data from PCR and microarray are conflicting. Concluding that 'defects in gene XYZ cause cancer due to improper DNA repair' based on data from experiments in that study that gene XYZ is involved in DNA repair, and the conclusion of a previous study that cancer patients have an increased number of mutations in this gene.
A planned process in which data gathered in an investigation is evaluated in the context of existing knowledge with the objective to generate more general conclusions or to conclude that the data does not allow one to draw general conclusion
drawing a conclusion based on data
The process of a scientist thinking about and deciding what reagents to use as part of a protocol for an experiment. Note that the scientist could be human or a "robot scientist" executing software.
a process of creating or modifying a plan specification
7/18/2011 BP: planning used to itself be a planned process. Barry Smith pointed out that this would lead to an infinite regression, as there would have to be a plan to conduct a planning process, which in itself would be the result of planning etc. Therefore, the restrictions on 'planning' were loosened to allow for informal processes that result in an 'ad hoc plan '. This required changing from 'has_specified_output some plan specifiction' to 'has_participant some plan specification'.
planning
The mass analyzer of the Voyager-DE(tm) STR Biospectrometry Workstation
A Mass analyzer is a device that separates ions according to their mass-to-charge ratio. All mass spectrometers are based on dynamics of charged particles in electric and magnetic fields in vacuum where the two laws of Lorentz force law and Newton's second law of motion apply.
The ion source of a Voyager-DE??? STR Biospectrometry Workstation
An ion source is a device that is part of a mass spectrometer that ionizes the material under analysis. The ions are then transported by magnetic or electric fields to the mass analyzer. Techniques for ionization have been key to determining what types of samples can be analyzed by mass spectrometry. Electron ionization and chemical ionization are used for gases and vapors. In chemical ionization sources, the material is ionized by chemical ion-molecule reactions during collisions in the source. Two techniques often used with liquid and solid biological samples include electrospray ionization (due to John Fenn PMID 2675315.) and matrix-assisted laser desorption/ionization (MALDI, due to M. Karas and F. Hillenkamp (Measuring Mass: From Positive Rays to Proteins by Michael A. Grayson (Editor) (ISBN 0-941901-31-9))).
The ion detector of the Voyager-DE(tm) STR Biospectrometry Workstation
An ion detector is a device that measures and records the charge induced or current produced when an ion passes by or hits a surface. Example: In a scanning instrument the signal produced in the detector during the course of the scan versus where the instrument is in the scan (at what m/Q) will produce a mass spectrum, a record of ions as a function of m/Q.
light emission function
A light emission function is an excitation function to excite a material to a specific excitation state that it emits light.
magnify function
A magnify function is a function to increase the size of a transmitted object image through the precise arrangement of energy diffraction elements along an imaging path.
contain function
A contain function is a function to constrain a material entities location in space
heat function
A heat function is a function that increases the internal kinetic energy of a material
material separation function
A material separation function is a function that increases the resolution between two or more material entities. The to distinction between the entities is usually based on some associated physical quality.
synthesizing function
A synthesizing function is a function to assemble new output materials from distinct input materials. The output materials typically consist of chemically distinct monomeric objects or object aggregate polymers.
filter function
A filter function is a function to prevent the flow of certain entities based on a quality or qualities of the entity while allowing entities which have different qualities to pass through
electricity supply function
the function of supplying current during a neuroscience experiment.
An electricity supply function is an energy supply function to transfer electricity from one source to another, typically a consumer of the electricity or as a stimulus during a neuroscience experiment.
power supply
ionization function
An ionization function is a function to physically convert an atom or molecule into an ion by adding or removing charged particles such as electrons or other ions.
cool function
A cool function is a function to decrease the internal kinetic energy of a material below the initial kinetic energy of that type of material.
image acquisition function
An image acquisition function is a function to acquire an image of a material
Taped, glued, pinned, dried or molecularly bonded to a solid support
A solid support function is a function of a device on which an entity is kept in a defined position and prevented in its movement
solid support function
environment control function
An environmental control function is a function that regulates a contained environment within specified parameter ranges. For example the control of light exposure, humidity and temperature.
a complementary nucleotide probe role which inheres in nucleic acid molecular entity and is realized by the use of the entity bearing the role to initiate chain elongation.
(cell and molecular biology) A short strand of RNA that is synthesized along single-stranded DNA during replication, initiating DNA polymerase-catalyzed synthesis of the complementary strand. http://www.answers.com/topic/rna-primer
primer role
PCR product
PCR products are the results of amplifcation process. Detection of a PCR products is used to detect DNA and RNA.
is double stranded DNA that is the specified output of a polymerase chain reaction
We are using PCR and not the written out words, as this is the most common used.
a model or standard for making comparisons; wordnet.princeton.edu/perl/webwn 19 feb 2009
a reference substance role which inheres in nucleic acid material entity and is realized in the process of using the nucleic acid bearing the template role as a reference during synthesis of a reverse copy.
nucleic acid template role
Opisthorchis viverrini: Detection by polymerase chain reaction (PCR) in human stool samples. Exp Parasitol. 2008 Sep 9. PMID: 18805413
PCR is the process in which a DNA polymerase is used to amplify a piece of DNA by in vitro enzymatic replication. As PCR progresses, the DNA thus generated is itself used as a template for replication. This sets in motion a chain reaction in which the DNA template is exponentially amplified.
PCR
polymerase chain reaction
reverse transcriptase
enzyme and has_function some GO:0003964 (RNA-directed DNA polymerase activity)
extract
Up-regulation of inflammatory signalings by areca nut extract and role of cyclooxygenase-2 -1195G>a polymorphism reveal risk of oral cancer. Cancer Res. 2008 Oct 15;68(20):8489-98. PMID: 18922923
an extract is a material entity which results from an extraction process
extracted material
averaging objective
A mean calculation which has averaging objective is a descriptive statistics calculation in which the mean is calculated by taking the sum of all of the observations in a data set divided by the total number of observations. It gives a measure of the 'center of gravity' for the data set. It is also known as the first moment.
An averaging objective is a data transformation objective where the aim is to perform mean calculations on the input of the data transformation.
James Malone
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.
polyacrylamide gel
Assessing CMT cell line stability by two dimensional polyacrylamide gel electrophoresis and mass spectrometry based proteome analysis. J Proteomics. 2008 Jul 21;71(2):160-7. PMID: 18617143
a material entity resulting from the polymerization of acrylamide with TEMED in some buffer solution
creating a mouse infected with LCM virus
is the specification of an objective to add a material into a target material. The adding is asymmetric in the sense that the target material largely retains its identity
adding material objective
High-throughput genotyping of oncogenic human papilloma viruses with MALDI-TOF mass spectrometry. Clin Chem. 2008 Jan;54(1):86-92. Epub 2007 Nov 2.PMID: 17981923
An assay which generates data about a genotype from a specimen of genomic DNA. A variety of techniques and instruments can be used to produce information about sequence variation at particular genomic positions.
The objective to measure the concentration of glucose in a blood sample
an assay objective to determine the presence or concentration of an analyte in the evaluant
analyte measurement objective
agarose gel
Performance comparison of capillary and agarose gel electrophoresis for the identification and characterization of monoclonal immunoglobulins. Am J Clin Pathol. 2008 Mar;129(3):451-8. PMID: 18285269
a material entity resulting from the polymerization of agarose after heating agarose suspended in some buffer solution
example of usage: In lab test for blood glucose, the test is the assay, the blood bears evaluant_role and glucose bears the analyte role. The evaluant is considered an input to the assay and the information entity that records the measurement of glucose concentration the output
An assay with the objective to capture information about the presence, concentration, or amount of an analyte in an evaluant.
peritoneum of an animal receiving an interperitoneal injection; solution in a tube receiving additional material; location of absorbed material following a dermal application.
A role of a material entity that is realized in an "adding a material entity into a target" process where the bearer of the role (the target) receives the addition of another material entity.
From Branch discussion with BP, AR, MC -- there is a need for the recipient to interact with the administered material. for example, a tooth receiving a filling was not considered to be a target role.
target of material addition role
measure function
A glucometer measures blood glucose concentration, the glucometer has a measure function.
Measure function is a function that is borne by a processed material and realized in a process in which information about some entity is expressed relative to some reference.
The objective to create a mouse infected with LCM virus. The objective to create a defined solution of PBS.
an objective specifiction that creates an specific output object from input materials.
artifact creation objective
material transformation objective
Manufacturing is a process with the intent to produce a processed material which will have a function for future use. A person or organization (having manufacturer role) is a participant in this process
Manufacturing implies reproducibility and responsibility AR
This includes a single scientist making a processed material for personal use.
manufacturing
is the objective to manufacture a material of a certain function (device)
manufacturing objective
Identification of a proteins cut out from a 2D gel by cleaving it into peptides using trypsin digestion using electrospray ionizatino to ensure the peptides are charged, and accelerating them with an electro magnetic field in which the flight path is determined by the mass / charge ratio of the peptides. Comparing the mass/charge ratio of peptides in the proteins with databases of protein sequences allows to identify which protein gave rise to the peptides.
An assay that identifies the amount and type of material entities present in a sample by fragmenting the sample and measuring the mass-to-charge ratio of the resulting particles.
injecting a mouse with PBS solution, weighing it, and recording the weight according to a study design.
a planned process that carries out a study design
removed axiom has_part some (assay or 'data transformation') per discussion on protocol application mailing list to improve reasoner performance. The axiom is still desired.
6/11/9: edited at workshop. Used to be: study design execution is a process with the objective to generate data according to a concretized study design. The execution of a study design is part of an investigation, and minimally consists of an assay or data transformation.
reverse transcribed polymerase chain reaction
Harmonisation of multi-centre real-time reverse-transcribed PCR results of a candidate prognostic marker in breast cancer: an EU-FP6 supported study of members of the EORTC - PathoBiology Group. Span PN, Sieuwerts AM, Heuvel JJ, Spyratos F, Duffy MJ, Eppenberger-Castori S, Vacher S, O'Brien K, McKiernan E, Pierce A, Vuaroqueaux V, Foekens JA, Sweep FC, Martens JW. Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094
reverse transcribe pcr is a process which allow amplification of cDNA during a pcr reaction while the cDNA results from a retrotranscription of messenger RNA isolated from a material entity.
3/21/10, BP:Modified definition to clarify that this is not the assay, but the material transformation
reverse transcription polymerase chain reaction
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.
the sodium and chloride ions in a glass of salt water
a material entity that consists of all the molecules of a specific type that are located in some bounded region and which is part of a more massive material entity that has parts that are other such aggregates
Collective
Discussion in Karslruhe with, among others, Alan Rector, Stefan Schulz, Marijke Keet, Melanie Courtot, and Alan Ruttenberg. With inspiration from the paper Granularity, scale and collectivity: When size does and does not matter, Alan Recto, Jeremy Rogers, Thomas Bittner, Journal of Biomedical Informatics 39 (2006) 333-349
scattered molecular aggregate
A chromatography consumable is a consumable that is used in a chromatography experiment.
Illumina (Solexa) sequencing is an example of DNA sequencing
A sequencing assay which determines information on the sequence of a DNA molecule.
The objective to obtain multiple aliquots of an enzyme preparation. The objective to obtain cells contained in a sample of blood.
is an objective to transform a material entity into spatially separated components.
a portion of urine collected from an organism
4/10/2011BP: It seems to me that the editor notes refer to a previous version, and are no longer relevant.
This could be instead a kind of collection of secreted stuff. Among secreted stuff there is passive, and active. urine is secreted, passiv. lavage is secreted, active
are we happy calling collection of urine a material separation?
Mixing two fluids. Adding salt into water. Injecting a mouse with PBS.
is a material processing with the objective to combine two or more material entities as input into a single material entity as output.
created at workshop as parent class for 'adding material into target', which is asymmetric, while combination encompasses all addition processes.
blood drawn from a human for glucose assay
a material entity derived from a portion of blood collected from an organism
drawing blood from a patient for analysis, collecting a piece of a plant for depositing in a herbarium, buying meat from a butcher in order to measure its protein content in an investigation
A planned process with the objective of collecting a specimen.
Philly2013: A specimen collection can have as part a material entity acquisition, such as ordering from a bank. The distinction is that specimen collection necessarily involves the creation of a specimen role. However ordering cell lines cells from ATCC for use in an investigation is NOT a specimen collection, because the cell lines already have a specimen role.
Philly2013: The specimen_role for the specimen is created during the specimen collection process.
label changed to 'specimen collection process' on 10/27/2014, details see tracker: http://sourceforge.net/p/obi/obi-terms/716/
5/31/2012: This process is not necessarily an acquisition, as specimens may be collected from materials already in posession
1) Detection of IL-2 (analyte) in a cell supernatant (evaluant), using plate bound anti IL-2 antibodies, and a reporter enzyme-linked reporter antibody. 2) Measurement of IgG antibody (analyte) titer in a serum sample (evaluant) using plate bound antigen and a reporter anti-IgG antibody.
An analyte assay where binding of an enzyme linked antibody to a material entity that is immobilized on solid support is detected utilizing a chemiluminescent reaction. Depending on the setup, the enzyme-linked antibody could be binding directly to the analyte, or it serves as a secondary antibody detecting binding of the primary antibody to the analyte.
a material obtained from an organism in order to be a representative of the whole
we need to work on this: Is taking a urine sample a material separation process? If not, we will need to specify what 'taking a sample from organism' entails. We can argue that the objective to obtain a urine sample from a patient is enough to call it a material separation process, but it could dilute what material separation was supposed to be about.
A data item that is produced as the output of a center calculation data transformation and represents the center value of the input data.
center value
The objective to obtain multiple aliquots of an enzyme preparation.
A material separation objective aiming to separate material into multiple portions, each of which contains a similar composition of the input material.
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
putting a mouse in the blender. Not: putting a mouse on a scale
A material entity which is the output of a process in which one or more whole organisms are prepared in a way to make it easier to study them, and in which the great majority of organismal parts are maintained
does this include injecting a dye to a patient to be able to visualize parts of his brain? If not, we should state that the components of the organism are substantially re-arranged.
separation into different composition objective
The objective to obtain cells contained in a sample of blood.
A material separation objective aiming to separate a material entity that has parts of different types, and end with at least one output that is a material with parts of fewer types (modulo impurities).
We should be using has the grain relations or concentrations to distinguish the portioning and other sub-objectives
The objective to collect bits of excrement in the rainforest. The objective to obtain a blood sample from a patient.
A objective specification to obtain a material entity for potential use as an input during an investigation.
creating a mixture of molecules in solution
is a process with the objective to prepare a liquid solution of one or more chemicals at desired concentrations.
PMID: 19419533. Arabidopsis RNA immunoprecipitation. Terzi LC, Simpson GG. Plant J. 2009 Jul;59(1):163-8.
is a process which realizes a material separation objective by relying on antibodies to specifically binding to material entity
In biology, a host is an organism that harbors a virus or parasite, or a mutual or commensal symbiont, typically providing nourishment and shelter. http://en.wikipedia.org/wiki/Host_(biology) 30 March 09
host role is a role played by an organism and realized by providing nourishment, shelter or a means of reproduction to another organism within the organism playing the host role
30Mar09 virus reproducing inside a cell; bacteria causing a disease, host can be harmed or not. we want to avoid a cat sitting on my lap and an animal care technician; these are not examples or hosts; dental cares = on tooth, but part of outer layer of tooth, so covered by "within" in the definition
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.
In a study in which gene expression is measured in patients between 8 month to 4 years old that have mild or severe malaria and in which the hypothesis is that gene expression in that age group is a function of disease status, disease status is the independent variable.
a directive information entity that is part of a study design. Independent variables are entities whose values are selected to determine its relationship to an observed phenomenon (the dependent variable). In such an experiment, an attempt is made to find evidence that the values of the independent variable determine the values of the dependent variable (that which is being measured). The independent variable can be changed as required, and its values do not represent a problem requiring explanation in an analysis, but are taken simply as given. The dependent variable on the other hand, usually cannot be directly controlled
2/2/2009 Original definition - In the design of experiments, independent variables are those whose values are controlled or selected by the person experimenting (experimenter) to determine its relationship to an observed phenomenon (the dependent variable). In such an experiment, an attempt is made to find evidence that the values of the independent variable determine the values of the dependent variable (that which is being measured). The independent variable can be changed as required, and its values do not represent a problem requiring explanation in an analysis, but are taken simply as given. The dependent variable on the other hand, usually cannot be directly controlled.
In the Philly 2013 workshop the label was chosen to distinguish it from "dependent variable" as used in statistical modelling. See: http://en.wikipedia.org/wiki/Statistical_modeling
Web: http://en.wikipedia.org/wiki/Dependent_and_independent_variables
2009-03-16: work has been done on this term during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify thisdefinition please notify OBI.
study design independent variable
An objective specification maintains some or all of the qualities of a material over time.
DNA that has been produced in an enzymatic amplification process
A planned process in which a person or their legal representative is informed about key facts about potential risks and benefits of a process and makes a documented decision as to whether the person in question will participate.
09/28/2009 Alan Ruttenberg: This is made a subclass of the higher level processual entity in BFO because I don't want to take a stand on whether it is a process aggregate. Analogous to the situation with Material entity.
a quality of a DNA molecule that inheres in its bearer due to the order of its DNA nucleotide residues.
A ruler, a microarray scanner, a Geiger counter.
A device in which a measure function inheres.
A person or organization that has a manufacturer role
a process with that achieves the objective to maintain some or all of the characteristics of an input material over time
A statement in a journal article indicating that the age of a patient at the onset of disease is not known. A statement indicating that the weight of a mouse was not measured.
An information content entity created to indicate that information about something is not available to the person recording it.
This class should probably end up in IAO. It could be further breaken down to indicate different kinds of lack of knowledge, e.g. inability to determine something vs. no attempt made to determine something vs. no informatino available if it was even attempted to determine something. The design pattern should be generalizable. 'unknown sex' is the first example, and needed immediately.
A primer in a PCR reaction. A probe on an Affymetrix chip.
A role played by a nucleic acid molecule that is used in a planned process for its ability to bind a nucleic acid molecules with complementary nucleotide sequence
A database record indicating that the tissue sample in a microarray experiment came from an organism for which the biological sex is not known to the person who created the record.
a record indicating that the biological sex of an organism is not known.
I think the statement is still about the instance of the biological sex quality of an organism. It is also about information available to the person making the statement.
A serum neutralization of viral infectivity assay which is performed in a 96-well plate.
serum neutralization of viral infectivity assay
An analyte assay that measures virus-neutralizing abilities of different sera. Different dilutions of serum are mixed with virus and used to infect cells. At the lower dilutions, antibodies will block infection, but at higher dilutions, there will be too few antibodies to have an effect.The neutralization titer is expressed as the reciprocal of the highest dilution at which virus infection is blocked.
material obtained through a liver biopsy from a human patient
a specimen that was taken from a live organism
MO_705 premortem
an extract which is the output of an extraction process in which RNA molecules are isolated from a specimen.
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
real time reverse-transcription polymerase chain reaction assay
An assay that uses a reverse transcription step (an RNA strand is reverse transcribed into its DNA complement using the enzyme reverse transcriptase) before a PCR assay.
Using a Luminex machine to detect IFN-gamma and IL-10 in the supernatant of a cell culture.
An analyte assay in which a series of beads coated with antibodies, antigens, or other small molecules are used to detect an analyte of interest.
is a material entity bearing the disposition to infect an organism
IEDB
infectious agent
the part of the execution of an intervention design study which is varied between two or more subjects in the study
A device with a separation function realized in a planed process
A measurement datum that is reported on a categorical scale.
A biologist who uses a sequencing services fulfills the role of a service consumer
a role which inheres in a person who uses a service
Jackson Lab provides experimental animals, EBI provides training on databases, a core facility provides access to a DNA sequencer.
is a role which inheres in a person or organization and is realized in in a planned process which provides access to training, materials or execution of protocols for an organization or person
an intervention design in which the treatment is the administration of a compound
This is meant to include all kinds of material administrations, including vaccinations, chemical compounds etc.
A tissue sample that has been sliced and stained for a histology study. A blood specimen that has been centrifuged to obtain the white blood cells.
A specimen that has been intentionally physically modified.
A tissue sample that has been sliced and stained for a histology study.
A device that can be used to restrict the location of material entities over time
03/21/2010: Added to allow classification of children (similar to what we want to do for 'measurement device'. Lookint at what classifies here, we may want to reconsider a contain function assigned to a part of an entity is necessarily also a function of the whole (e.g. is a centrifuge a container because it has test tubes as parts?)
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
Staining cells in a tissue slice with a dye.
The directed combination of a material entity with a specimen.
Taking a polaroid picture of a patients skin lesion; Using a digital camera to take a picture of a gel
A planned process that captures an image of an object.
An extract that is the output of an extraction process in which nucleic acid molecules are isolated from a specimen.
The output of an extraction process in which DNA molecules are purified in order to exclude DNA from organellas.
A device that moves charged particles through a medium by using an electric field induced by electrodes.
An device that is used to determine the order of nucleotides in nucleic acid sequences.
An electrophoresis system in which an electric field is applied to a gel matrix
An device that is used to determine the order of amino acids in protein sequences.
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.
reverse transcription polymerase chain reaction assay
An assay that determines the concentration of RNA in a sample in which an RNA strand is first reverse transcribed into its DNA complement (complementary DNA, or cDNA) using the enzyme reverse transcriptase, and the resulting cDNA is amplified using traditional or real-time PCR.
The time it takes for 50% of a class of stochastic processes to occur.
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.
selective organism creation objective
an objective specification to generate a population or type of organism within species that have some uniform behavioral, morphological, physiological, or genetic characteristics with similarly bred organisms.
WEB: wikipedia http://en.wikipedia.org/wiki/Cultivar http://en.wikipedia.org/wiki/Ecotype http://en.wikipedia.org/wiki/Strain_%28biology%29
selectively maintained organism
An organism that is bred to have some uniform behavioral, morphological, physiological, or genetic characteristics with similarly bred organisms
Bjoern Peters, Helen Parkinson, Philippe Rocca-Serra, Jie Zheng, Chris Stoeckert
MO_9 StrainOrLine, MO_71 Ecotype, MO_124 Cultivar
A DNA microarray used to detect polymorphisms in DNA samples
A ChIP-ChIP assay in which immunoprecipitated chromatin is run on a SNP array to detect polymorphism specific DNA elements in the isolated chromatin
genetic population background information
genotype information 'C57BL/6J Hnf1a+/-' in this case, C57BL/6J is the genetic population background information
a genetic characteristics information which is a part of genotype information that identifies the population of organisms
proposed and discussed on San Diego OBI workshop, March 2011
Group: OBI group
epigenetic modification identification objective
A molecular feature identification objective that aims to detect epigenetic modifications, such as DNA methylation, histone modifications.
Chris Stoeckert, Jie Zheng
Person: Chris Stoeckert
genotyping by high throughput sequencing assay
A genotyping assay that uses a high througput sequencer
genotype information
Genotype information can be: Mus musculus wild type (in this case the genetic population background information is Mus musculus), C57BL/6J Hnf1a+/- (in this case, C57BL/6J is the genetic population background information and Hnf1a+/- is the allele information
a genetic characteristics information that is about the genetic material of an organism and minimally includes information about the genetic background and can in addition contain information about specific alleles, genetic modifications, etc.
discussed on San Diego OBI workshop, March 2011
A study design that assays differences between distinct species.
allele information
genotype information 'C57BL/6J Hnf1a+/-' in this case, Hnf1a+/- is the allele information
a genetic alteration information that about one of two or more alternative forms of a gene or marker sequence and differing from other alleles at one or more mutational sites based on sequence. Polymorphisms are included in this definition.
Person: Chris Stoeckert, Jie Zheng
wild type allele information
an allele information that is about the allele found most frequently in natural populations, or in standard laboratory stocks for a given organism.
MO_605 genotype
protein and DNA interaction identification objective
A sequence feature identification objective that aims to characterize the interactions between protein and DNA which includes identification of transcription factor binding sites.
MO_933 binding_site_identification_design
genetic characteristics information
a data item that is about genetic material including polymorphisms, disease alleles, and haplotypes.
MO_66 IndividualGeneticCharacteristics
MO definition: The genotype of the individual organism from which the biomaterial was derived. Individual genetic characteristics include polymorphisms, disease alleles, and haplotypes. examples in ArrayExpress wild_type MutaMouse (CD2F1 mice with lambda-gt10LacZ integration) AlfpCre; SNF5 flox/knockout p53 knock out C57Bl/6 gp130lox/lox MLC2vCRE/+ fer-15; fem-1 df/df pat1-114/pat1-114 ade6-M210/ade6-M216 h+/h+ (cells are diploid)
A study design that classifies an individual or group of individuals on the basis of alleles, haplotypes, SNPs.
A study design that assays differences between multiple strains, cultivars, serovars, isolates, lines from organisms of a single species.
cell specimen
A specimen primarily composed of a cell or cells collected from a multicellular organism or a cell culture.
Discussed on obi call Jan 23, 2017. To improve cell specimen that include single cell specimen. Details see tracker: https://sourceforge.net/p/obi/obi-terms/828/
PERSON: Chris Stoeckert, Jie Zheng, Alexander Diehl
specimen from organism
A specimen that derives from an anatomical part or substance arising from an organism. Examples of tissue specimen include tissue, organ, physiological system, blood, or body location (arm).
tissue specimen
linear amplification
An example is the use of the T7 promoter for amplification by transcribing many RNA copies.
An enzymatic amplification which amplifies nucleic acid sequence by making many copies off the same template.
Using a laser to stimulate a cell culture that was previously labeled with fluorescent antibodies to detect light emmission at a different wavelength in order to determine the presence of surface markers the antibodies are specific for.
An assay in which a material's fluorescence is determined.
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.
time point
MO_738 timepoint
sequence assembly algorithm
An algorithm used to assemble individual sequence reads into larger contiguous sequences (contigs). Assembly details include but are not limited to assembler type (overlap-layout-consensus, deBruijn), assembler version, and any relevant quality control information such as per cent known genes/ESTs captured.
NIAID GSCID-BRC metadata working group
A service performing DNA sequencing, a service preforming cell analysis. A service performing cell line immortalization
A service which has a material entity as specified input and/or specified output.
The rate of disassociation of a peptide from a complex with an MHC molecule measured by the ratio of bound and unbound peptide per unit of time.
A scalar measurement datum that represents the number of events occuring over a time interval
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.
The part of a FASTA file that contains the letters ACTGGGAA
A sequence data item that is about the primary structure of DNA
8/29/11 call: This is added after a request from Melanie and Yu. They should review it further. This should be a child of 'sequence data', and as of the current definition will infer there.
GenBank ID
A CRID symbol uniquely indentifies the submitted GeneBank sequence record.
investigation description
A textual entity that describes an investigation.
project description
specimen identifier
A CRID symbol denotes a specimen and used to distinguish one specimen from another in an investigation.
specimen ID
PubMed ID
A CRID symbol that is sufficient to look up a citation from the PubMed, a literature database of life sciences and biomedical information.
Edits was made on Aug 24, 2016 based on OBI dev call, details see tracker: https://sourceforge.net/p/obi/obi-terms/819/
PMID
PubMed Identifier
Website: http://en.wikipedia.org/wiki/Wikipedia:PMID
average depth of sequence coverage
An average value of the depth of sequence coverage based both on external (e.g. Cot-based size estimates) and internal (average coverage in the assembly) measures of genome size.
specimen collection time measurement datum
A time measurement datum that is the measure of the time when the specimens are collected.
collection date
latitude coordinate measurement datum
A measurement datum that is the measure of the latitude coordinate of a site.
latitude
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
organism identification objective
A biological feature identification objective to identify the organism species in a specimen.
Penn Group
organism species detection objective
An organism detection assay that identifies the organism species in a specimen.
sequence annotation algorithm
An algorithm used to identify sequence features (e.g. protein coding regions) in the assembled contig sequence. This may also include a description of any manual curation that may have generated or validated the annotation.
Bioinformatics Resource Center
An organization that is one of the Internet-based research centers established and funded by NIAID (the National Institute of Allergy and Infectious Diseases). The Bioinformatics Resource Centers (BRCs) were formed in response to the threats posed by emerging and re-emerging pathogens, particularly CDC Category A, B, and C pathogens, and their potential use in bioterrorism. The intention of NIAID in funding these bioinformatics centers is to assist researchers involved in the experimental characterization of such pathogens and the formation of drugs, vaccines, or diagnostic tools to combat them.
BRC
Website: http://en.wikipedia.org/wiki/Bioinformatics_Resource_Centers
country name
A textual entity that denotes a geographic location that is a site or part of a site that is identified as a country in the political geography.
Website: http://en.wikipedia.org/wiki/Country
investigation identifier
A CRID symbol used to identify an investigation.
Person: Chris Stoeckert, Jie Zhneg
project ID
grant identifier
A CRID symbol used to identify a grant.
grant ID
grant
A plan specification of organization A to give money to organization B so that B conducts investigations. Organization A has funder role and Organization B has research organization role.
Discussed on Feb 13, 2012 dev call. Details see the tracker: https://sourceforge.net/tracker/?func=detail&aid=3483338&group_id=177891&atid=886178
Group: OBI
AR: Grant isn't a plan specification, it has a part which is a plan specification. See tracker: https://sourceforge.net/tracker/?func=detail&aid=3483338&group_id=177891&atid=886178
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
specimen collector role
An Investigation agent role borne by a person or organization which is realized in a specimen collection process.
A device made to be used in an analyte assay for immobilization of substances that bind the analyte at regular spatial positions on a surface.
PERSON: Chris Stoeckert, Jie Zheng, Alan Ruttenberg
A material entity comprised of cultured cells and the media in which they are being propagated or stored.
OBI-CLO Alignment Working Group (Spring 2013)
A cell culture includes the cells in culture, as well as the media and all additives in which the cells are being grown or in which they are stored.
organization of specimen provider principal investigator
An organization that is the affiliation of the principal investigator providing the specimens for the investigation
organization of Bioinformatics Resource Center contact person
An organization that is the affiliation of the person who is contact representative of a Bioinformatics Resource Center
Bioinformatics Resource Center Contact's Institution
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.
Bioinformatics Resource Center contact person
A person who is the contact representative of a Bioinformatics Resource Center
Bioinformatics Resource Center Contact Name
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
email address of Bioinformatics Resource Center contact person
An email address of the person who is contact representative of a Bioinformatics Resource Center
Bioinformatics Resource Center Contact's email
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
email address of specimen collector
An email address of the person collecting the specimen
sequencing facility organization
An organization that provides sequence determination service
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
specimen collector
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
sample preparation for sequencing assay
A sample preparation for assay that preparation of nucleic acids for a sequencing assay
email address of specimen provider principal investigator
An email address of the principal investigator providing the specimens for the investigation
sequencing service
A service provides sequencing service which is the realization of some sequencing such as RNA and DNA sequencing in which the service provider role is realized.
The conclusion that a gene is upregulated in a tissue sample based on the band intensity in a western blot. The conclusion that a patient has a infection based on measurement of an elevated body temperature and reported headache. The conclusion that there were problems in an investigation because data from PCR and microarray are conflicting. The following are NOT conclusions based on data: data themselves; results from pure mathematics, e.g. "13 is prime".
An information content entity that is inferred from data.
In the Philly 2013 workshop, we recognized the limitations of "conclusion textual entity", and we introduced this as more general. The need for the 'textual entity' term going forward is up for future debate.
A processed material that serves as a liquid vehicle for freezing cells for long term quiescent stroage, which contains chemicls needed to sustain cell viability across freeze-thaw cycles.
cell freezing medium
A value specification that is specifies one category out of a fixed number of nominal categories
A value specification that consists of two parts: a numeral and a unit label
The value of 'positive' in a classification scheme of "positive or negative"; the value of '20g' on the quantitative scale of mass.
An information content entity that specifies a value within a classification scheme or on a quantitative scale.
This term is currently a descendant of 'information content entity', which requires that it 'is about' something. A value specification of '20g' for a measurement data item of the mass of a particular mouse 'is about' the mass of that mouse. However there are cases where a value specification is not clearly about any particular. In the future we may change 'value specification' to remove the 'is about' requirement.
grant agency
An organization that provides funding support for projects such as investigations.
'funding organization' http://vivoweb.org/ontology/core#FundingOrganization
sequence annotation
A planned process that identifies and reports sequence features (e.g. protein coding regions) in sequence data.
sequence annotation provider
A person or organization reporting the feature annotation results from the analysis of a macromolecular sequence.
sequence assembly name
A textual entity that is used to denote a sequence assembly.
sequence annotation reporting role
A reporting party role that is realized by a person or organization who reports the feature annotation results from the analysis of a macromolecular sequence.
taxonomic diversity assessment by targeted gene survey
An assay that dteremines taxonomic and community diversity information by sequencing specific genomic regions used as marker of identity or diversity.
biodiversity assessment objective
biodiversity assessment objective is an objective of a planned process aimed at producing data item whose interpretation should provide insight about variety of biological species found in a biological sample at macroscopic or microscopic level
PERSON:Philippe Rocca-Serra
PRS for OBI
Measuring if sera from an influenza A virus immunizedmouse binds to Hemagglutinin protein that is immobilized on a microarray.
An analyte assay where binding of the analyte to immobilized matrix is measured.
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
collection of specimens
Blood cells collected from multiple donors over the course of a study.
A material entity that has two or more specimens as its parts.
Details see tracker: https://sourceforge.net/p/obi/obi-terms/778/
A container with an environmental control function.
For details see tracker item: http://sourceforge.net/p/obi/obi-terms/793/
digital object identifier
The doi symbol: "10.1109/5.771073" resolves to ieee website: http://ieeexplore.ieee.org/xpl/articleDetails.jsp?reload=true&arnumber=771073
A centrally registered identifier symbol used to uniquely identify objects given by International DOI Foundation. The DOI system is particularly used for electronic documents such as journal articles.
Discussed on Aug 22, 2016 OBI dev call. Details see tracker: https://sourceforge.net/p/obi/obi-terms/818/
https://en.wikipedia.org/wiki/Digital_object_identifier https://www.doi.org/
Lung, liver, and spleen tissue samples were collected from female BALB/c mice and fixed in 100% formalin solution, embedded in paraffin, sectioned, and stained with hematoxylin and eosin. The stained samples were examined for signs of pathological changes under light microscopy.
An imaging assay that utilizes a microscope to magnify features of the visualized material of interest that are not visible to naked eye.
A value specification that specifies the temperature of some thing.
temperature value specification
An assay to determine the temperature of an evaluant.
Test performed using antibodies produced by human B-cells that bind with human immunodeficiency virus (HIV) antigens
An analyte assay that measures the presence or amount of antibodies to a specified antigen.
venereal disease research laboratory test
An analyte assay that is meant to detect general antibodies that react with substances that are produced by cellular damage caused by Treponema pallidum indicating a syphilis infection. VDRL tests require a microscope and can be done on cerebrospinal fluid as well as blood.
An analyte assay that is meant to detect hepatitis B virus (HBV) surface antigens.
measurand role
A role borne by a material entity and realized in an assay which achieves the objective to measure the magnitude/concentration/amount of the measurand in the entity bearing evaluant role.
inclusion based on age, sex, and living region (rural area or specified city).
An inclusion criterion that is based on fitting within the defined characteristics of a population based study design.
defined population inclusion criterion
An organism detection assay that uses a differential medium to achieve its objective.
EuPathDB, https://www.uwyo.edu/molb2210_lab/info/biochemical_tests.htm
A scalar value specification that specifies the point in time that a human participant under investigation self-administers a medication material
A scalar value specification that specifies the value of the quantity of a material entity administered to an organism as a treatment
case role in case-control study
A role that is borne by a case-control study design participant under investigation that is associated with the outcome mentioned in the study design.
John Judkins, Bjoern Peters
control role in case-control study
A role that is borne by a case-control study design participant under investigation that is not associated with the outcome mentioned in the study design.
A specimen that is derived from cerbrospinal fluid.
digestive system fluid or secretion specimen
A specimen that is derived from digestive system fluid or secretion.
A specimen that is derived from bone marrow.
A specimen that is derived from pleural fluid.
A specimen that is stored on a swab as the output of a collecting specimen with swab process.
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).
A specimen that is collected with a swab from the surface of a nasopharynx.
A specimen that is collected with a swab from the surface of a oropharynx.
A DNA sequencing assay that intends to provide information on the DNA sequences of multiple genomes (a metagenome) from different organisms present in the same input sample.
Whole metagenome sequencing has been used to explore the composition and metabolic capability of communities of microbes found in the environment (e.g. in soil, water, etc.) and in humans and other species (e.g. in the gut, oral cavity, etc.).
A study design that entails the creation of two types of roles, such that each participant under investigation bears one or the other. What distinguishes the two types of roles is an 'outcome', which is associated with participants that have the case role but not associated with participants that have the control role. A case-control study examines the hypothesis that the presence of the outcome in case participants is associated with an 'exposure' that is not associated with control participants.
Cytogenetics; the histopathological diagnosis of malaria and other parasites; differentiate nuclear and cytoplasmic morphology of the various blood cells like platelets, RBCs, WBCs
An assay that uses a Giemsa stain to characterize cells.
A specimen composed of an individual organism to be studied in an investigation.
An organism detection assay that detects microorganisms in a blood specimen.
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.
A bone marrow biopsy removes bone with the marrow inside to look at under a microscope
A biopsy where a small amount of bone and a small amount of fluid and bone marrow are collected.
A study design that samples only subjects who have experienced a particular event (outcome or exposure). Such a design, in contrast to a cohort study, does not permit calculation of absolute risk as non-case subjects are not included.
A container with a narrow neck that is made of glass.
A glass bottle that coated with material designed to control insects.
A polymerase chain reaction with modification intended to reduce non-specific binding in products due to the amplification of unexpected primer binding sites. The nested polymerase chain reaction (PCR) involves the use of two primer sets and two successive PCR reactions. The first set of primers are designed to anneal to sequences upstream from the second set of primers and are used in an initial PCR reaction.
An electrophoresis in which antigen and antibody move in opposite directions and form precipitates in the area between the cells where they meet in concentrations of optimal proportions.
A linear amplification that uses a thermostable ligase to amplify a piece of DNA. Because the enzyme retains activity after multiple thermal cycles, the ligations may be repeated to linearly increase product.
An enzymatic amplification in which a piece of DNA is amplified at a constant temperature of 60 - 65 degree C using either two or three sets of primers and a polymerase with high strand displacement activity in addition to a replication activity. This amplification does not need thermal cyclers and may be a low cost alternative to PCR.
detection of pathogenic organisms objective
An organism feature identification objective that aims to detect whether an organism contains pathogenic organisms.
insecticide resistance detection objective
An organism feature identification objective that aims to detect insecticide resistance of an insect.
A specimen used in a blood meal assay to determine what is the source of blood ingested by a mosquito.
A specimen of the blood ingested by an arthropod.
The mosquito feeds on a human for example, ingests the blood of the human, this blood is then taken from the tummy of a mosquito and a PCR may be run on this specimen to identify that the mosquito definitely fed on a human.
An assay that uses polymerase chain reaction technique to amplify DNA.
restriction fragment length polymorphism assay
An assay that uses digestion of DNA with specific restriction enzymes followed by gel electropheresis to detect differences in the sizes of the generated fragments that are due to genetic differences (polymorphisms) in homologous sequences.
restriction fragment length polymorphism
restriction fragment length polymorphism analysis
An assay to identify a specific individual organism from a DNA specimen by looking at unique patterns in their DNA.
An assay that aims to detect the presence and/or frequency of resistance to insecticides in an organism or organism population.
insecticide resistance by monitoring known mutations assay
An insecticide resistance assay that detects, in a population, presence and frequency of mutant alleles for previously characterized mutations with insecticide resistance phenotypes.
insecticide resistance by detecting enzyme activity assay
An insecticide resistance assay that is based on determination the catalytic activity of an enzyme associated with insecticide resistance phenotypes.
An insecticide resistance assay that is typically conducted to measure the effects of a substance on a living organism.
insecticide resistance by detecting alpha esterase activity assay
An insecticide resistance by detecting enzyme activity assay that measures activity of alpha esterase.
insecticide resistance by detecting beta esterase activity assay
An insecticide resistance by detecting enzyme activity assay that measures activity of beta esterase.
insecticide resistance by detecting acetylcholinesterase activity assay
An insecticide resistance by detecting enzyme activity assay that measures activity of acetylcholinesterase.
insecticide resistance by detecting glutathione S-transferase activity assay
An insecticide resistance by detecting enzyme activity assay that measures activity of glutathione S-transferase (GST).
insecticide resistance by detecting carboxylic ester hydrolase activity assay
An insecticide resistance by detecting enzyme activity assay that measures activity of carboxylic ester hydrolase using p-nitrophenyl acetate as a substrate.
insecticide resistance by detecting mixed-function oxidase assay
An insecticide resistance by detecting enzyme activity assay that measures whether mixed-function oxidase activity present.
An insecticide resistance bioassay without the use of any synergist.
topical application insecticide resistance bioassay
An insecticide resistance bioassay by adding insecticide directly to the thorax of the insect.
direct insecticide resistance diagnostic assay
A direct insecticide resistance assay that at preset insecticide dosage scoring mortality to determine resistance of a population.
insecticide resistance dose response assay
A direct insecticide resistance assay in which an insect population is exposed to a range of insecticide dosage scoring mortality to determine resistance.
insecticide resistance time response assay
A direct insecticide resistance assay to determine resistance as a consequence of the time of exposure to insecticide.
Centre for Disease Control and Prevention bottle bioassay
A direct insecticide resistance diagnostic assay performs in a glass bottle coated with insecticides for detecting resistance to insecticides in vector populations.
A direct insecticide resistance diagnostic assay uses WHO cone kit.
A direct insecticide resistance diagnostic assay uses WHO paper kit.
A direct insecticide resistance diagnostic assay tests survival of larvae in a medium supplemented with insecticide.
insecticide resistance dose response by bottle assay
An insecticide resistance dose response assay that performs in a glass bottle coated with insecticides.
insecticide resistance dose response by survival of larvae assay
An insecticide resistance dose response assay that tests survival of larvae in a medium supplemented with insecticide.
insecticide resistance dose response by WHO paper kit assay
An insecticide resistance dose response assay using WHO paper kit.
insecticide resistance time response by bottle assay
An insecticide resistance time response assay that is performed in a glass bottle coated with insecticides, with the presence of a synergist.
insecticide resistance time response by WHO paper kit assay
An insecticide resistance time response assay using WHO paper kit, with the presence of a synergist.
insecticide resistance by amplification refractory mutation system assay
An insecticide resistance by monitoring known mutations assay that detects any mutation involving single base changes or small deletions using amplification refractory mutation system (ARMS). The ARMS is based on the use of sequence-specific PCR primers that allow amplification of test DNA only when the target allele is contained within the sample. Following an ARMS reaction the presence or absence of a PCR product is diagnostic for the presence or absence of the target allele. It can be used to analyze human genomic DNA for one or more mutations.
Amplification Refractory Mutation System
insecticide resistance by primer introduced restriction analysis PCR assay
An insecticide resistance by monitoring known mutations assay that detects Single Nucleotide Polymorphisms (SNPs) using PCR technique and mismatched primers that is close to the mutation of interest and digested the PCR productions using restriction enzymes.
Primer Introduced Restriction Analysis PCR
polymerase chain reaction-primer-introduced restriction analysis
insecticide resistance by nested polymerase chain reaction assay
An insecticide resistance by monitoring known mutations assay that detects gene mutation based on nested polymerase chain reaction technique.
insecticide resistance by ligase detection reaction assay
An insecticide resistance assay that is based on monitoring known mutations using ligase detection reaction exquisitely discriminate between a mismatched and complementary DNA helix.
insecticide resistance by ligase detection reaction-fluorescent microsphere assay
An insecticide resistance by ligase detection reaction assay that uses fluorescently labeled conserved probes in ligase detection reaction.
ligase detection reaction-fluorescent microsphere assay
insecticide resistance by PCR amplification of specific alleles assay
An insecticide resistance assay that is based on monitoring known mutations by PCR amplification of specific alleles to detect polymorphic or mutant alleles.
allele-specific amplification and amplification refractory mutation system
insecticide resistance by fluorogenic PCR assay
An insecticide resistance assay that is based on monitoring known mutations by PCR technique that uses target specific probes labeled with fluorogenic chromophores to detect gene mutation.
insecticide resistance by PCR-RFLP assay
An insecticide resistance by monitoring known mutations assay based on restriction fragment length polymorphism assay.
insecticide resistance by short interspersed elements PCR assay
An insecticide resistance assay that is based on monitoring known mutations by PCR amplification of short interspersed elements (SINEs).
An organism detection assay that detects pathogens.
A pathogen detection assay that identifies the presence or absence of specific peptide epitopes of circumsporozoite (CS) protein of the most important Plasmodium falciparum and two strains (variants 210 and 247) of the more widespread Plasmodium vivax using a dipstick wicking test strip.
pathogen detection by Rapid Analyte Measurement Platform assay
A pathogen detection assay that is based on Rapid Analyte Measurement Platform (RAMP) technology to quantify immunologically active substances.
pathogen detection by loop-mediated isothermal amplification assay
A pathogen detection assay that is based on loop-mediated isothermal amplification.
An assay that analyzes the specimen taken from blood meal fed organism, such as insect.
blood meal by counter current immunoelectrophoresis assay
A blood meal assay that uses a counter current immunoelectrophoresis technique.
DNA based blood meal finger printing assay
A DNA fingerprinting assay that uses DNA extracted from blood meal fed organism, such as insect.
An organism detection assay that is based on the size of organism.
organism identification by cross mating assay
organism detection by cross mating assay
An organism detection assay that is based on genetic crossings between specimens collected in the field to determine whether fertile progeny is produced.
organism identification by cytological chromosome examination assay
organism detection by cytological chromosome examination assay
An organism detection assay that is based on analysis of polytene chromosomes through cytological examination of the banding pattern of the species.
organism identification by isoenzyme electrophoresis assay
organism detection by isoenzyme electrophoresis assay
An organism detection assay that is based on electrophoresis to determine the isozymes that are present in a specific population to determine the species.
organism identification by morphological examination assay
organism detection by morphological examination assay
An organism detection assay that is based on examination of morphology and the use of specific taxonomic keys to determine the species of the specimen.
An organism detection assay that is based on PCR.
organism identification by specific DNA hybridization assay
organism detection by specific DNA hybridization assay
An organism detection assay that is based on DNA hybrdization.
organism identification by salinity tolerance assay
organism detection by salinity tolerance assay
An organism detection assay of mosquito species that is on the basis of mosquito survival depending on the salt concentration in the water used to lay their eggs to differentiate between morphologically very similar species.
A sputum specimen that is collected from an organism following its inhalation of a nebulized salt solution.
passage process
A material processing that consists of first growing an organism in an environmental system and then removing the organism to be grown in another environmental system, a process which may be repeated with the objective of altering the organism or increasing its number.
passage history record
A data item that is about the sequence of environmental systems in each of which is grown an organism in a passage process.
John Judkins
An amplicon sequencing assay in which the amplicon is derived from universal primers used to amplify the 16S ribosomal RNA gene from isolate bacterial genomic DNA or metagenomic DNA from a microbioal community. Resulting sequences are compared to reference 16S sequence databases to identify or classify bacteria present within a given sample.
A sequencing assay in which a DNA or RNA input molecule is amplified by PCR and the product sequenced.
karyotype information
A genetic characteristics information that is about the number and appearance of chromosomes in the nucleus of an eukaryotic cell.
Jie Zheng
EFO_0004426 karyotype
partial karyotype information
A karyotype information that is about the structural variation of partial genome rather than whole genome.
full karyotype information
A karyotype information that is about the structural variation of the whole genome.
OBI group
single-value binding of antibody with reporter to antigen assay
Detection of SARS-CoV-2 IgG antibodies by an immunoassay method, such as enzyme-linked immunosorbent assay. This test is used in conjunction with SARS-CoV-2 IgA and IgM to aid in the diagnosis of COVID-19 and in the identification of individuals infected with SARS-CoV-2.
An assay that detects the linking of antigens and antibodies via special signaling mechanisms, such as EIA, ELISA, chemiluminescence, etc. that produces one measure (quantitative or qualitative) of the analyte of interest
LOINC indicates that this class would not include flow cytometry or any technique that can determine the localization of an analyte, such as peroxidase immune staining or indirect immunofluorescence (IFA)
Mark Andrew Miller, ORCID:0000-0001-9076-6066
LOINC User's Guide, Version 2.68, PUBLISHED JUNE 2020, page 47
A specimen that is collected with a suctioning tube from the trachea.
A specimen that is collected with a mid-turbinate nasal swab from the turbinate area of the nasal cavity.
A specimen that is collected with a suctioning tube from the nasal cavity.
nasal wash specimen|nasopharyngeal aspirate
lower respiratory tract aspirate specimen
A specimen that is collected with a suctioning tube from the lower respiratory tract.
A specimen that is derived from the upper respiratory tract
A specimen that is derived from the lower respiratory tract.
A specimen that is derived from the anterior nasal wall
aspiration specimen collection
Procedure using suction, usually with a thin needle and syringe, to remove bodily fluid or tissue.
An investigation in which some entity is monitored, and data concerning that entity collected, interpreted, and disseminated, for the purpose of managing, directing, or protecting that entity, or some other entity.
A cluster study group consisting of eight pregnant women who lived close enough to each other so that a community promoter could readily walk to each compound.
A study group role that is the result of the allocation of a cluster of study-defined groupings of people in a clinical trial to receive a specific intervention/treatment, or no intervention, according to the trial's protocol.
A compound study group consisting of geographically proximate households that share a common water source.
A study group role that is the result of the allocation of a compound of geographically-proximate households with a shared component in a clinical trial to receive a specific intervention/treatment, or no intervention, according to the trial's protocol.
A light source that provides ultraviolet (UV) light for use in a distant area using a delivery system.
adult arthropod specimen collection process
animal-biting arthropod specimen collection by aspiration
animal-biting outdoor arthropod specimen collection by aspiration
aquatic arthropod specimen collection process
arthropod resting in animal house specimen collection by aspiration
arthropod resting outdoors on artificial support specimen collection by aspiration
arthropod resting outdoors on natural support specimen collection by aspiration
arthropod resting outdoors specimen collection by aspiration
arthropod specimen collection by aspiration
A live arthropod specimen collection process that involves the use of an aspirator, a device which draws an arthropod by suction into a container.
human-biting arthropod specimen collection by aspiration
human-biting indoor arthropod specimen collection by aspiration
human-biting outdoor arthropod specimen collection by aspiration
knockdown arthropod specimen collection by pyrethrum spray
knockdown arthropod specimen collection process
live arthropod specimen collection process
An arthropod trap, consisting of a pit dug in the ground to provide a space for arthropods to rest and be collected.
Centers for Disease Control and Prevention light trap
A light trap that is designed similarly to the New Jersey trap—in that it uses motorized suction and light attractant—and is powered by a six-volt battery.
This trap is also designed to be lightweight and operate in environments in which electricity may be scarce.
Onderstepoort Veterinary Institute light-suction trap
An arthropod trap that consists of a bucket, which is lined with fabric and placed on its side, and a wet cloth inside the bucket. The placement of the box and modifications to it are done in such a way that it becomes attractive to an arthropod as a place to rest during a period of inactivity (not actively seeking a host).
A study design where the selection of the individuals that are included into the study are intended to be representative of all individuals in the a priori defined specific population and is done at the population level or among the population groups, generally to find the cause, incidence or spread of the disease or to see the response to the treatment, nutrition or environment.
https://link.springer.com/referenceworkentry/10.1007%2F978-1-4419-1005-9_45, EFO_0001430 population based design
A specimen that derives from a biofilm that forms on the inner surface of an endotracheal tube while the tube is in the trachea. The specimen is collected upon removal of the tube from the trachea.
A specimen that derives from a biofilm that forms on the inner surface of an endotracheal tube while the tube is in the trachea. The specimen is collected by suction without removing the tube.
A length measurement datum between a point at sea or ground level and some point above it.
Adapted from https://www.merriam-webster.com/dictionary/altitude
Specimen collection duration of 3 nights that a trap is set out for collection of mosquitoes. Urine collected over a 24 hour period of specimen collection duration.
A time measurement datum that is the count of collection cycles over which a specimen collection process occurs.
prevalence of Plasmodium falciparum in Mosquito samples assayed by PCR
A data item that is the frequency of detection of a specified pathogenic organism in collected specimens.
prevalence of blood meal specimens from a host organism
prevalence of blood meal host organism in specimens measured as % of blood meal specimens collected from mosquitoes that had human blood as a meal.
A data item that is the frequency of blood whose source is from a specified host organism in collected blood meal specimens.
presence of blood from host organism in blood meal specimen
presence of blood meal host organism indicated by boolean values of yes or no.
A data item that indicates whether blood in a blood meal specimen came from a specified host organism.
An organism that is the source of a blood meal.
A mosquito feeds on a human whereby the human acquires the blood meal source role for the mosquito blood meal.
Will deprecate this term in VEuPathDB ontology once in OBI.
arthropod collection process with automated identification
gravid female arthropod specimen collection process
resting flight-capable arthropod specimen collection process
daytime arthropod specimen collection by aspiration
arthropod resting in human house specimen collection by aspiration
landing arthropod specimen collection process
flying adult arthropod collection process by passive interception
device for collection of resting adult arthropods
arthropod trap containing small non-human animal bait
An evaluant role that is realized in a taxonomic diversity assessment by targeted gene survey involving sequencing a small defined region of genome amplified by PCR.
Chris Stoeckert https://orcid.org/0000-0002-5714-991X
A processed material that consists of oligonucleotides that bear a primer role.
A polymerase chain reaction assay that uses target specific probes labeled with fluorogenic chromophores.
genotyping by PCR assay to identify microsatellites, chromosomal inversions and targeted assays of known resistance loci.
A genotyping assay that uses polymerase chain reaction.
Chris Stoeckert, ORCID:0000-0002-5714-991X
Examining a patient and grading their coma status on the Blantyre or Glasgow coma scale.
A physical examination of individual that has the objective to determine the severity of coma in a patient.
An assay that detects Plasmodium gametocytes in a specimen.
An organism detection assay that detects microorganisms in a feces specimen.
An assay that has a blood specimen as evaulant.
A parasite detection assay that can quickly establish the diagnosis of P. falciparum or P. vivax malaria infection by detecting the antigens in a person's blood.
A parasite detection assay that is rapid, sensitive, and able to differentiate between P. falciparum and other malaria parasites.
An assay that has a urine specimen as evaluant.
parasite species identification by PCR assay
A parasite detection by PCR assay that identifies the species of parasite.
A parasite detection assay that uses PCR.
Jonsson developed a free-standing window trap consisting of a 16 x 20-cm perspex box, 16 cm high and divided in the middle by a 20 x 36-cm sheet of perspex (window). The two compartments of the box are filled to a depth of about 12 cm with 4-6% formalin containing a few drops of detergent; in winter ethylene glycol can be added to prevent freezing. One or two holes drilled in one side of the box at 12 cm and covered with fine netting prevent the trap overflowing after heavy rain. Traps are mounted on aluminium poles. Flying insects on hitting the transparent vertical plastic window fall into the formalin. The window trap may catch vectors that are seeking a host or moving for other purposes. [ISBN:9781402066658]
Centers for Disease Control and Prevention gravid trap
A sequence datum that is the specified output of a read mapping and is the ratio of the count of mapped reads to the total count of reads.
Administering substance in vivo where an antibiotic substance is administered to a living organism.
A data item that is the specified output of an organism detection assay.
A one dimensional Cartesian spatial coordinate datum that is the eastward component of a distance from a point on a map projection.
Easting and northing coordinates are commonly measured in meters from a horizontal datum.
A one dimensional Cartesian spatial coordinate datum that is the northward component of a distance from a point on a map projection.
A protocol that specifies processes to fulfill a specimen collection objective.
A symbol that denotes a participant under investigation.
A temperature measurement datum that is about an axilla.
organismal body temperature measurement datum
A scalar measurement datum that is the result of measuring temperature.
organismal body temperature measurement assay
Sample collection time post infection (days)
Chris Stoeckert, ORCID: 0000-0002-5714-991X
Refers to whether the mosquitoes used in the analysis of insecticide resistance were collected from an established strain or any other population kept in a laboratory under controlled conditions. (per MIRO_30000033)
A population where the collection of individuals is located and maintained in a laboratory, research, or production facility.
An assay that has a cerebrospinal fluid specimen as evaluant.
An assay that has an endotracheal aspirate specimen as evaluant.
An assay that has an induced sputum specimen as evaluant.
An assay that has a lung specimen as evaluant.
An assay that has a milk specimen as evaluant.
An assay that has a feces specimen as evaluant.
An assay that has an umbilical cord blood specimen as evaluant.
An assay that has a saliva specimen as evaluant.
An organism detection assay that detects microorganisms in a cerebrospinal fluid specimen.
Endotracheal tube aspirate microbiology test
endotracheal tube aspirate microbiology assay
An organism detection assay that detects microorganisms in an endotracheal aspirate specimen.
An organism detection assay that detects microorganisms in an induced sputum specimen.
A data item that is the specified output of a blood assay.
An organism detection datum that is the specified output of a blood microbiology assay.
A data item that is the specified output of a feces assay.
An organism detection datum that is the specified output of a feces microbiology assay.
A data item that is the specified output of a urine assay.
An organism detection datum that is the specified output of a urine microbiology assay.
A data item that is the specified output of a induced sputum assay.
biomedical laboratory organization
An organization that performs assays, processes specimens, analyses data and conducts planned processes relevant to the life sciences.
Christian Stoeckert ORCID:0000-0002-5714-991X
An organism detection datum that is the specified output of an induced sputum microbiology assay.
A data item that is the specified output of a cerebrospinal fluid assay.
An organism detection datum that is the specified output of a cerebrospinal fluid microbiology assay.
An organism detection datum that is the specified output of an endotracheal aspirate assay.
Raw test result for endotracheal tube aspirate
endotracheal tube aspirate microbiology datum
An organism detection datum that is the specified output of an endotracheal tube aspirate microbiology assay.
An organism detection datum that is the specified output of a lung microbiology assay.
Raw test result for nasopharyngeal/oropharyngeal swabs
nasopharyngeal or oropharyngeal swab microbiology datum
An organism detection datum that is the specified output of a nasopharyngeal or oropharyngeal swab microbiology assay.
An organism detection datum that is the specified output of a pleural fluid microbiology assay.
A data item that is the specified output of an umbilical cord blood assay.
Raw test result for umbilical cord blood
An organism detection datum that is the specified output of an umbilical cord blood microbiology assay.
A blood microbiology datum that is about bacteria.
A blood microbiology datum that is about a virus.
A blood microbiology datum that is about eukaryota.
A feces microbiology datum that is about bacteria.
A feces microbiology datum that is about eukaryota.
A feces microbiology datum that is about a virus.
A urine microbiology datum that is about eukaryota.
An induced sputum microbiology datum that is about bacteria.
An induced sputum microbiology datum that is about eukaryota.
An induced sputum microbiology datum that is about a virus.
bacteria in endotracheal tube aspirate datum
An endotracheal tube aspirate microbiology datum that is about bacteria.
A lung microbiology datum that is about bacteria.
A lung microbiology datum that is about eukaryota.
A lung microbiology datum that is about a virus.
Raw bacteria data for nasopharyngeal/oropharyngeal swabs
bacteria in nasopharyngeal or oropharyngeal swab datum
A nasopharyngeal or oropharyngeal swab microbiology datum that is about bacteria.
Raw eukaryota data for nasopharyngeal/oropharyngeal swabs
eukaryota in nasopharyngeal or oropharyngeal swab datum
A nasopharyngeal or oropharyngeal swab microbiology datum that is about eukaryota.
Raw virus data for nasopharyngeal/oropharyngeal swabs
virus in nasopharyngeal or oropharyngeal swab datum
A nasopharyngeal or oropharyngeal swab microbiology datum that is about a virus.
A pleural fluid microbiology datum that is about bacteria.
A pleural fluid microbiology datum that is about eukaryota.
A pleural fluid microbiology datum that is about a virus.
Raw eukaryota data for umbilical cord blood
An umbilical cord blood microbiology datum that is about eukaryota.
An organism detection assay that detects microorganisms in a lung specimen.
An organism detection assay that detects microorganisms in a pleural fluid specimen.
An organism detection assay that detects microorganisms in an umbilical cord blood specimen.
nasopharyngeal or oropharyngeal swab microbiology assay
An organism detection assay that detects microorganisms in a nasopharyngeal or oropharyngeal swab specimen.
An organism detection assay that detects microorganisms in a urine specimen.
multiplex real time polymerase chain reaction assay
A real time polymerase chain reaction assay in which multiple DNA sequences are amplified in a single cycle.
multiplexed real time polymerase chain reaction assay
multiplex real time reverse-transcription polymerase chain reaction assay
A real time reverse-transcription polymerase chain reaction assay in which multiple DNA sequences are amplified in a single cycle.
multiplexed real time reverse-transcription polymerase chain reaction assay
A device that contains blood in a membrane penetrable to mosquitoes, designed to feed mosquitoes without the need for an animal host.
Testing the effectiveness of drugs or antibodies against parasite transmission.
An assay that evaluates host-to-mosquito transmission of a parasite organism by feeding a specimen of host blood infected with the parasite organism to a collection of mosquitoes through a mosquito membrane feeding device and, after a given time, dissecting the mosquitoes and counting the number of parasite organisms within them.
modified acid-fast stain microscopy assay
A microscopy assay that uses staining to identify acid-fast organisms in a specimen and does not require heating.
antibodies from lymphocyte secretions assay
PMID: 11329444.Clin Diagn Lab Immunol. 2001 May. Development of a Novel In Vitro Assay (ALS Assay) for Evaluation of Vaccine-Induced Antibody Secretion from Circulating Mucosal Lymphocytes.
An assay that evaluates a blood specimen for antibodies currently being produced by lymphocytes in the specimen, by separating peripheral blood mononuclear cells, culturing them, and then collecting the supernatant containing the antibodies secreted from those cells.
antibodies from lymphocyte supernatant assay
A data item that is the specified output of a milk assay.
Using a radioactivity detection assay as part of a tritiated thymidine incorporation assay to determine the degree to which cells are replicating by detecting radioactivity of tritiated thymidine, where radioactivity of tritiated thymidine in a cell is a proxy for cells that were actively replicating.
An assay (A) that is part of another assay (B), where the target entities of A and B are disjoint, and the target entity of A is a proxy for the target of assay B.
Glutathione S-Transferase (GST) Assay Kit: https://www.sigmaaldrich.com/deepweb/assets/sigmaaldrich/product/documents/101/301/cs0410bul.pdf
A device that consists of reagents and devices that enable the performance of a specific type of assay, which could, in addition, require specific instruments not included in the kit.
A specimen that is derived from placental blood.
A blood microbiology assay that detects microorganisms in a placental blood specimen.
An organism detection datum that is the specified output of a placental blood microbiology assay.
A placental blood microbiology datum that is about eukaryota.
A length measurement datum that is the specified output of an assay measuring the length around an upper arm, taken midway along the upper arm.
A data item that is the specified output of an antigen specific antibodies assay.
antigen specific antibodies in blood assay
An antigen specific antibodies assay that has a blood specimen as evaluant.
antigen specific antibodies in milk assay
An antigen specific antibodies assay that has a milk specimen as evaluant.
antigen specific antibodies in blood assay datum
An antigen specific antibodies assay datum that is the specified output of an antigen specific antibodies in blood assay.
antigen specific antibodies in milk assay datum
An antigen specific antibodies assay datum that is the specified output of an antigen specific antibodies in milk assay.
An arthropod trap that is designed to emit a combination of carbon dioxide, heat, water, and oct-1-en-3-ol attractants while simultaneously using suction to trap arthropods. This trap has the same design as the Mosquito Magnet Pro trap but is smaller, is more lightweight, and uses a main line electricity supply instead of propane to power itself. Both use propane to produce the arthropod attractor.
A resting arthropod trap that consists of a tent inside which an adult cow is tethered to the ground, in order to attract arthropods and collect those that rest on the interior walls of the tent.
An assay kit that is manufactured by InBios International to use ELISA to test for IgM antibodies for Orientia tsutsugamushi strains Karp, Kato, Gilliam, and TA 716, with a protein microarray that has a 96-well plate and the 56-kDa type-specific antigen.
An assay kit that is manufactured by Abbott to test for IgM antibodies for Dengue with a two-plate protein microarray. One plate contains stabilized Dengue viruses 1 through 4, and the other plate contains anti-human IgM antibody.
An assay kit that is manufactured by Abbott to detect the NS1 Dengue viral protein with a protein microarray and an anti-NS1 monoclonal antibody.
A device manufactured by Abbott for rapid detection of human IgM antibodies for Chikungunya virus in blood, using analytical chromatography.
SD Bioline Chikungunya IgM capture ELISA kit
An assay kit that is manufactured by Abbott to detect human IgM antibodies for Chikungunya with a protein microarray and ELISA.
An assay kit that is manufactured by J. Mitra to detect human IgM antibodies for Chikungunya virus with a protein microarray and double-antigen sandwich ELISA.
An assay that detects a type of organism and/or the quantity of individuals of a type of organism.
This term is a generalized version of the term previously known as 'organism identification assay', to include classification other than species and to include quantities as outputs.
ELISA measuring Orientia tsutsugamushi IgM antibody
An enzyme-linked immunosorbent assay that detects the IgM antibody that binds Orientia tsutsugamushi.
microarray assay measuring Dengue IgM antibody
A microarray assay that detects the IgM antibody that binds Dengue.
analytical chromatography measuring Chikungunya IgM antibody
Analytical chromatography that detects the IgM antibody that binds Chikungunya.
ELISA measuring Chikungunya IgM antibody
An enzyme-linked immunosorbent assay that detects the IgM antibody that binds Chikungunya.
microarray ELISA measuring Chikungunya IgM antibody
An enzyme-linked immunosorbent assay that uses a microarray as the solid support and detects the IgM antibody that binds Chikungunya.
blood plasma specimen
PMID: 18217225.Sex Transm Dis. 2008 Jan;35(1):55-60. Review.Human immunodeficiency virus viral load in blood plasma and semen: review and implications of empirical findings.
a material entity which corresponds to the liquid component of blood, in which the blood cells are suspended.
03/21/2010: BP, blood plasma is defined as the output of certain separation processes, so this is in the domain of OBI, not FMA.
PERSON: Maura Gasparetto
plasma
WEB: http://en.wikipedia.org/wiki/Blood_plasma
blood serum specimen
PMID: 18229666.Adv Med Sci. 2007;52 Suppl 1:204-6.Antioxidant activity of blood serum and saliva in patients with periodontal disease treated due to epilepsy.
A material entity which derives from blood and corresponds to blood plasma without fibrinogen or the other clotting factors.
animal
fungus
plant
virus
A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs.
10/21/09: This is a placeholder term, that should ideally be imported from the NCBI taxonomy, but the high level hierarchy there does not suit our needs (includes plasmids and 'other organisms')
13-02-2009: OBI doesn't take position as to when an organism starts or ends being an organism - e.g. sperm, foetus. This issue is outside the scope of OBI.
WEB: http://en.wikipedia.org/wiki/Organism
specimen
Biobanking of blood taken and stored in a freezer for potential future investigations stores specimen.
A material entity that has the specimen role.
GROUP: OBI Biomaterial Branch
A cultured cell population applied in an experiment: "293 cells expressing TrkA were serum-starved for 18 hours and then neurotrophins were added for 10 min before cell harvest." (Lee, Ramee, et al. "Regulation of cell survival by secreted proneurotrophins." Science 294.5548 (2001): 1945-1948). A cultured cell population maintained in vitro: "Rat cortical neurons from 15 day embryos are grown in dissociated cell culture and maintained in vitro for 8–12 weeks" (Dichter, Marc A. "Rat cortical neurons in cell culture: culture methods, cell morphology, electrophysiology, and synapse formation." Brain Research 149.2 (1978): 279-293).
A processed material comprised of a collection of cultured cells that has been continuously maintained together in culture and shares a common propagation history.
2013-6-5 MHB: This OBI class was formerly called 'cell culture', but label changed and definition updated following CLO alignment efforts in spring 2013, during which the intent of this class was clarified to refer to portions of a culture or line rather than a complete cell culture or line.
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.
bronchial alveolar lavage
solution containing lung derived T cells, eosinophils, and TNFa.
Group of biomaterials present in the bronchial aveolar space of an organism which are collected through lavage including the reagents used to for the lavage process, organisms, cells, and cellular secretions present in the bronchial aveolar space.
BAL
GROUP: IEDB
data transformation
The application of a clustering protocol to microarray data or the application of a statistical testing method on a primary data set to determine a p-value.
A planned process that produces output data from input data.
Elisabetta Manduchi
Helen Parkinson
Melanie Courtot
Richard Scheuermann
Ryan Brinkman
Tina Hernandez-Boussard
data analysis
data processing
Branch editors
data transformation objective
normalize objective
An objective specification to transformation input data into output data
Modified definition in 2013 Philly OBI workshop
PERSON: James Malone
averaging data transformation
An averaging data transformation is a data transformation that has objective averaging.
center calculation objective
A mean calculation which has center calculation objective is a data transformation in which the center of the input data is discovered through the calculation of a mean average.
A center calculation objective is a data transformation objective where the aim is to calculate the center of an input data set.
center calculation data transformation
A center calculation data transformation is a data transformation that has objective of center calculation.
PMID: 12387964.Lancet. 2002 Oct 12;360(9340):1144-9.Deficiency of antibacterial peptides in patients with morbus Kostmann: an observation study.
observation design is a study design in which subjects are monitored in the absence of any active intervention by experimentalists.
pool of specimens
A pool of specimens is a mixture of a population of samples which have been gathered from one or more sample populations, obtained by the physical process of mixing individual specimens, e.g. mixing the DNA collected from the individual fish.
check with advisors as to how to represent multiple instances of any class? a set of specimens which have been gathered from one or more sample_populations, obtained by the physical process of mixing individual specimens, e.g. mixing the DNA collected from the individual fish
chemical solution
PMID: 18289311.Anesth Analg. 2008 Apr;106(4):1078-86.Less impairment of hemostasis and reduced blood loss in pigs after resuscitation from hemorrhagic shock using the small-volume concept with hypertonic saline/hydroxyethyl starch as compared to administration of 4% gelatin or 6% hydroxyethyl starch solution.
A material entity that is made up of at least 2 scattered molecular aggregates, one playing the role of solvent and the other one playing the role of solute.
liquid chemical solution
PMID: 18373502.Transfusion. 2008 Mar 25. Solvent/detergent treatment of platelet concentrates enhances the release of growth factors.
solvent role is a role which inheres in a molecular entity capable of ensuring the dissolution of another chemical entity and realized by the process of solvation
adpated from wikipedia (http://en.wikipedia.org/wiki/Solvatation)
solvent role
PMID: 18380397.Pharmazie. 2008 Feb;63(2):113-21.Deviations of drug solubility in water-cosolvent mixtures from the Jouyban-Acree model--effect of solute structure.
solute role is a role played by a chemical entity which is dissolved by another chemical entity (the solvent) when creating a solution
adapted from wikipedia (http://en.wikipedia.org/wiki/Solute)
solute role
nucleic acid extraction using phenol chloroform
A material separation in which a desired component of an input material is separated from the remainder
Current the output of material processing defined as the molecular entity, main component in the output material entity, rather than the material entity that have grain molecular entity. 'nucleic acid extract' is the output of 'nucleic acid extraction' and has grain 'nucleic acid'. However, the output of 'nucleic acid extraction' is 'nucleic acid' rather than 'nucleic acid extract'. We are aware of this issue and will work it out in the future.
extraction
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
PMID: 18428461.Purification of oligodendrocytes and their progenitors using immunomagnetic separation and Percoll gradient centrifugation. Curr Protoc Neurosci. 2001 May;Chapter 3:Unit 3.12.
centrifugation is a process separating molecules by size or density using centrifugal forces generated by a spinning rotor. G-forces of several hundred thousand times gravity are generated in ultracentrifugation
adapted from http://www.fao.org/DOCREP/003/X3910E/X3910E06.htm
centrifugation
PMID: 18540298. Role of modified bleach method in staining of acid-fast bacilli in lymph node aspirates. Acta Cytol. 2008 May-Jun;52(3):325-8.
Staining is a process which results in the addition a class-specific (DNA, proteins, lipids, carbohydrates) dye to a substrate to qualify or quantify the presence of a specific compound.
adapted from Wikipedia: http://en.wikipedia.org/wiki/Staining
staining
PMID: 18517209. The electronic role of DNA-functionalized carbon nanotubes: efficacy for in situ polymerization of conducting polymer nanocomposites. J Am Chem Soc. 2008 Jun 25;130(25):7921-8. Epub 2008 Jun 3.
polymerization is process by which molecular entity of small mass are aggregated in motifs over the course of a chemical reaction catalyzed by enzymes or other molecular entities acting as catalyst. polymerization results in molecular entity of high molecular weight
PRS:22102008: need to import catalyst from CHEBI 35223
polymerization
PMID: 18550121.Total Prostate Specific Antigen Stability Confirmed After Long-Term Storage of Serum at -80C. J Urol. 2008 Jun 10.
A maintenance process by which material entities that are not actively metabolizing are placed in well identified location and possibly under controlled environment in ad-hoc devices/structures in order to preserve and protect them from decay/alteration and maintain availability
storage
PMID: 18555787.Quantitative analysis of DNA hybridization in a flowthrough microarray for molecular testing. Anal Biochem. 2008 May 27.
a planned process by which totally or partially complementary, single-stranded nucleic acids are combined into a single molecule called heteroduplex or homoduplex to an extent depending on the amount of complementarity.
adapted from wikipedia [http://en.wikipedia.org/wiki/Nucleic_acid_hybridization]
nucleic acid hybridization
PMID: 18549238.Theory and Application of the Two-Mode Gradient Elution in Liquid Chromatography Involving Simultaneous Changes in Temperature and Mobile-Phase Composition.Anal Chem. 2008 Jun 13.
the process of extracting one material from another by washing with a solvent to remove adsorbed material from an adsorbent (as in washing of loaded ion-exchange resins to remove captured ions)
elution
A light source is an optical subsystem that provides light for use in a distant area using a delivery system (e.g., fiber optics). Light sources may include one of a variety of lamps (e.g., xenon, halogen, mercury). Most light sources are operated from line power, but some may be powered from batteries. They are mostly used in endoscopic, microscopic, and other examination and/or in surgical procedures. The light source is part of the optical subsystem. In a flow cytometer the light source directs high intensity light at particles at the interrogation point. The light source in a flow cytometer is usually a laser.
Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253
multi-well plate
96 well plate, 48 multiwell plate
A particle deliver vessel. A multi-well plate is a vessel that can deliver multiple samples to a flow cytometer in a specified order. It must be used with a plate loader.
FG this is synonymous with microtiter plate
John Quinn
ABI 377 DNA Sequencer, ABI 310 DNA Sequencer
A DNA sequencer is an instrument that determines the order of deoxynucleotides in deoxyribonucleic acid sequences.
A device with a rapidly rotating container that applies centrifugal force to its contents
A device which is used to maintain constant contact of a liquid on an array. This can be either a glass vial or slide.
CHEF gel box, slab gel box, capillary electrophoresis
A device which holds a gel and running buffers to allow electrophoresis to be performed. A gel tank has the function to contain and to control the contained environment and transfer energy from an energy supply through the running buffers to the gel matrix and the material with charged molecules in an electric field across a porous matrix or medium with the objective to separate the charged molecules.
A AC/DC transformer that generates the reqired power for an electrophoresis apparatus
A power supply is an device or part of a device that permits the required application of a defined electrical charge to an instrument. The power supply may permit the defined application of a given amount of current for a defined length of time.
was power_pack, maps to SEP electrical_power_supply
PMID:18466942. A light and transmission electron microscope study of hepatic portal tracts in the rhesus monkey (Macacus rhesus). Tissue Cell. 2008 May 6
A microscope is an instrument which magnifies the view on objects (too small to be viewed by the naked eye) under increased resolution. A microscope can be an optical instrument but also and electronic instrument. There are various kind of optical microscopes, e.g confocal microscope, epifluoresence microscope)
PMID: 18246864.Barthold SW.Effects of cage density on behavior in young adult mice.
A processed material which has the function to define a bounded habitat which is amenable to keeping animals.
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.
eligibility criterion
PMID: 17579629 -Eligibility criteria included: untreated ED-SCLC; age >/=70 and performance status 0-2, or age <70 and PS 3.
an eligibility criterion (rule) is_a selection criterion which defines and states the requirements (positive or negative) for an entity to be considered as suitable for a given task or participation in a process.
Person: Philippe Rocca-Serra
eligibility rule
Adapted from Clinical Research Glossary Version 4.0 CDICS glossary group
human subject enrollment
enlisting familiy members of HIV patients into a study
A planned process with the objective to obtain a population of human subjects to participate in an investigation by determining eligibility of subjects and obtaining informed consent.
As with group assignment, should the specified output here be an organism which bears a role
criteria come from plan / clinical trial branch
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
administering substance in vivo
Balb/c mice received an intracameral or subconjunctival injection of trinitrophenylated spleen cells
injecting mice with 10 ug morphine intranasally, a patient taking two pills of 1 mg aspirin orally
A process by which a substance is intentionally given to an organism resulting in exposure of the organism to that substance.
2009-11-10. Tracker: https://sourceforge.net/tracker/?func=detail&aid=2893050&group_id=177891&atid=886178
Different routes and means of administration should go as children underneath this
Update the definition based on the discussion. Details see the tracker: https://sourceforge.net/p/obi/obi-terms/738/
needs roles such as perturber and perturbee (children of input role). Perturb is too strong. Host might be the name for one role. Others considered: Doner, Donated, Acceptor.
material component separation
Using a cell sorter to separate a mixture of T cells into two fractions; one with surface receptor CD8 and the other lacking the receptor, or purification
a material processing in which components of an input material become segregated in space
material portioning
pouring 50 mL aliquots of fetal calf serum into conical tubes from a 500 mL stock
a material processing in which the input substance is partitioned into a number of portions that are similar in composition.
aliquoting
apportioning
maintaining cell culture
When harvesting blood from a human, isolating T cells, and then limited dilution cloning of the cells, the maintaining_cell_culture step comprises all steps after the initial dilution and plating of the cells into culture, e.g. placing the culture into an incubator, changing or adding media, and splitting a cell culture
a protocol application in which cells are kept alive in a defined environment outside of an organism. part of cell_culturing
artificially induced reverse transcription
The use of M-MLV reverse transcriptase from the Moloney murine leukemia virus to transcribe an RNA sample into cDNA
a protocol with the objective to transcribe single-stranded RNA into complementary DNA (cDNA)
It could also be added that the reverse transcriptase is bearer of a GO:0003964 RNA-directed DNA polymerase activity, which is realized in this process.
We need to indicate the relationship between the cDNA generated and the RNA that was used as a template. This may be outside of the OBI scope
PERSON:Kevin Clancy
a process through which a new type of cell culture or cell line is created, either through the isolation and culture of one or more cells from a fresh source, or the deliberate experimental modification of an existing cell culture (e.g passaging a primary culture to become a secondary culture or line, or the immortalization or stable genetic modification of an existing culture or line).
A 'cell culture' as used here referes to a new lineage of cells in culture deriving from a single biological source.. New cultures are established through the initial isolation and culturing of cells from an organismal source, or through changes in an existing cell culture or line that result in a new culture with unique characteristics. This can occur through the passaging/selection of a primary culture into a secondary culture or line, or experimental modifications of an existing cell culture or line such as an immortalization process or other stable genetic modification. This class covers establishment of cultures of either multicellular organism cells or unicellular organisms.
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
preparative chromatography
The use of gas chromatography in order separate out from an input sample of eggs a fraction that would be enriched for pesticides.
the use of a biomaterial's preferential affinity for either the mobile phase or the stationary phase to separate it from other materials of differing affinity
PERSON:Kevin Clancy; Bjoern Peters
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
specific enzymatic cleavage
The use of a protease to digest a protein into peptides
an enzymatic cleavage that uses an enzyme with a strong affinity for specific cleavage sites in the input material
dialysis
the use of a dialysis bag of select pore size to remove salt from collagen isolated from mouse cartilage
a protocol application that uses diffusion through a semi-permeable membrane to separate an input material into two fractions of different composition
electrophoresis
Loading a mixture of proteins into a polyacrylamide gel and the application of an electrical current to the gel to separate the proteins by size and change.
a protocol application that uses an electrical potential to move material through a defined matrix in order to separate it by its resistance to movement and its charge
Need to define more terms like gel_separation, matrix,centrifugation, and the connection between the force used to separate materials and the medium or barriers.
DNA cleavage, restriction analysis
the use of the restriction enzymes SalPI and PstI to cleave DNA into fragments, assay made up of components
A specific enzymatic cleavage of DNA molecules using endonucleases that cleave DNA molecules at specific sites based on the surrounding nucleotide sequence
restriction enzyme assay
DNA restriction enzyme digestion
enzymatic amplification
the use of a polymerase chain reaction to amplify a fragment of DNA
the use of enzymes to increase the number of molecules of a biomaterial
RNA extraction
A RNA extraction is a nucleic acid extraction where the desired output material is RNA
requested by Helen Parkinson for MO
nucleic acid extraction
Phenol / chlorophorm extraction disolvation of protein content folllowed by ethanol precipitation of the nucleic acid fraction over night in the fridge followed by centrifugation to obtain a nucleic acid pellet.
a material separation to recover the nucleic acid fraction of an input material
requested by Helen Parkinson for MO. Could be defined class
assay bead
Dynabeads are commercially available magnetic beads which are precoated with antibodies specific for select cellular receptors and are used to separate cell populations.
A globular or round particle of defined physicochemical properties and size which can be exploited as either the primary substance for detection or as a secondary solid platform for the attachment of bioactive molecules.
DS: Probably better modeled as a role.
bead
the detrimental process in which an infectious agent colonizes or replicates in a host environment
infection process
is a receptor produced by cells of the adaptive immune system with the purpose of binding epitopes.
adaptive immune receptor
A cell specimen comprised of a mixed population of cells obtained by processing whole lymph node into individual cells, typically performed using a sieve. This population includes T cells, B cells, macrophages, and other cell types.
lymph node cell specimen
The process of removing an organ from its source organism
organ harvesting
Is a role borne by an agent, and realized when in contact with or inside another organism in which it is capable of replicating and causing disease
disposition to infect an organism
abnormal, harmful processes caused by or associated with a disease
pathologic process
A specimen that is derived from some bodily fluid
A specimen that is derived from some umbilical cord blood
A specimen that is derived from some erythrocytes
A representation that is either the output of a clinical history taking or a physical examination or an image finding, or some combination thereof.
A series of statements representing health-relevant qualities of a patient and of a patient's family.
A representation of a quality of a specimen that is the output of a laboratory test and that can support an inference to an assertion about some quality of the patient.
A clinically abnormal phenotype.
A measurement assay that has as input a patient-derived specimen and as output a data item that is about a quality of the specimen.
The totality of all processes through which a given disease instance is realized.
The representation of a conclusion of a diagnostic process.
TODO: Define.
A structurally anomalous part of an organism acquired during fetal development and present at birth (but not necessarily hereditary) which is hypothesized to be harmful for the 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 temporally-connected health care process that has as participants an organization or person realizing the health care provider role and a person realizing the patient role. The health care provider role and patient are realized during the health care encounter
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 data item that is about a patient and is the specified output of a health care process assay or diagnostic process
clinical data item
A role borne by some material entity which can be delivered/administrated into some organism and the role is realized during a clinical treatment process aiming to treat symptoms, signs or diagnosed disease.
A microbial phenotype related to the resistance or sensitivity of a microbe to antimicrobial agents that kill (microbiocidal) or inhibit growth (microbiostatic) of a microbe.
antimicrobial compound sensitivity phenotype
antimicrobial agent resistance phenotype
An azole compound resistance phenotype where an organism or cell is resistant to one or more azole compounds.
A social role inhering in a human being.
human social role
A role borne by an organism and that is realized by presenting to a health care provider in a clinical encounter.
patient
patient role
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 facility that bears the function to provide acute and intensive healthcare services and that is run by a hospital organization and is the bearer of a hospital function.
hospital facility
A function that inheres in a material entity and, if realized, is realized by protecting persons and their possessions from weather and by some person or group of persons habitually sleeping in at least one site that is contained by that material entity.
residence function
A role in human social processes that, if realized, is realized when the bearer provides labor or services in exchange for a wage or salary as specified by some deontic declaration.
job role
health care facility
A deontic document act that concludes an inpatient encounter.
discharge process
patient discharge
An information content entity that is about human travel.
human traveling information
A planned process in which the bearer of an employer role provides wages or salary to the bearer of an employee roll in fullfillment of the arrangements specified in some declaration
employment process
A deontic document act in which a patient is registered with a health care provider for the purpose of receiving care in an inpatient encounter.
admission process
A social identity information content entity that is about whether some person identifies as some ethnicity.
ethnic identity information content entity
A social identity information content entity that is about whether some person identifies as some gender.
gender identity information content entity
A data item that is about a person's job role and/or its realization.
employment data item
job role data item
A socio-economic data item that is about a person and their completion of an education program (and its type), where that education program is the last one in a sequence (of education programs) that the person has completed, where each education program completed except the last one is a pre-requisite to the education program completed after it.
A human social role that, if realized, is realized in providing assistance in the activities of daily living of another human being who possesses reduced capability to complete some of these activities alone.
caregiver role
A relational quality that inheres within two or more persons related as members of a domestic group, or a number of domestic groups linked through descent from a common ancestor, marriage, or adoption.
family relationship
A structured interview intended to capture detailed information about all foods and beverages (and possibly, dietary supplements) consumed by the respondent in the past 24 hours, most commonly, from midnight to midnight the previous day. A key feature of the 24HR is that, when appropriate, the respondent is asked for more detailed information than first reported. For example, a respondent reporting chicken for dinner or a sandwich for lunch would be asked about the preparation method and type of bread. This open-ended response structure is designed to prompt respondents to provide a comprehensive and detailed report of all foods and beverages consumed. A 24h can also be filled at home by the responder, and be checked during an interview to further improve it with additional details
In nutrition, diet is the sum of food consumed by a person or other organism
diet
A zero-dimensional temporal region that is the date of the first day of menstruation before a presenting illness or the advent of pregnancy-related amenorrhea. The date is used in estimating the expected date of delivery.
Uma região temporal zero-dimensional que é a data do primeiro dia da menstruação antes da apresentação de uma doença ou o advento da amenorréia relacionada à gravidez. A data é usada para estimar a data esperada de entrega.
DUM
LMP
date of last menstrual period
last menstrual period
data da última menstruação
date of last menstruation
A biological process that consists on the tear of the amniotic sac, causing the amniotic fluid to flow out through the vagina. It usually happens shortly before the birth, the expectant mother feels wetness and notices a clear odorless fluid.
Um processo biológico que consiste na ruptura do saco amniótico, fazendo com que o líquido amniótico flua para fora através da vagina. Geralmente acontece pouco antes do nascimento, a gestante sente umidade e percebe um líquido claro e inodoro.
ruptura de membranas
rupture of membranes
TO DO
história obstétrica
obstetric history
A scalar measurement that refers to the diameter of the opening of the cervix measured during the cervical dilation process.
Uma medida escalar que se refere ao diâmetro da abertura do colo do útero medida durante o processo de dilatação cervical.
cervical dilation measurement
valor da dilatação do colo do útero
cervix diameter measurement datum
medida do diâmetro do colo do útero
A time measurement datum that is the result of measurement of the gestational age of a pregnant organism.
Um dado de medida de tempo que é o resultado da medição da idade gestacional de um organismo grávido.
gestational age measurement datum
idade gestacional medida
A human parturition where the birth of a baby happens with less than 37 weeks gestational age.
Um parto onde o nascimento de um bebê acontece com menos de 37 semanas da idade gestacional.
premature birth
preterm birth
preterm labor
parto prematuro
preterm labour
A parasite lifecycle stage of sporozoa consisting of a zygote enclosed by cyst wall.
A life cycle stage where a cell differentiates into male or female sexual forms.
A parasite lifecycle stage of some sporozoans where cells divide through sporogony producing daughter cells called sporozoites that infect new hosts.
An organism living in, with, or on another organism in parasitism. Individual members of parasite species, such as Leishmania, Plasmodium, Trypanosoma, etc. are members of this class.
A parasite lifecycle stage that occurs as a result of asexual replication in the red blood cells of the host organism. For Plasmodium species these stages can include merozoites, trophozoites, and schizonts.
asexual lifecycle in host red blood cell stage
A Plasmodium that is located either in the bloodstream of the vertebrate host or midgut of mosquito vector during gametocyte stage. Gametocytes are the precursor cells of the macro- or microgametes
A time quality inhering in a bearer by virtue of how long the bearer has existed.
A luminous flux quality inhering in a bearer by virtue of the bearer's emitting longer wavelength light following the absorption of shorter wavelength radiation; fluorescence is common with aromatic compounds with several rings joined together.
A quality inhering in a substance by virtue of the amount of the bearer's there is mixed with another substance.
An organismal quality inhering in a bearer by virtue of the bearer's ability to undergo sexual reproduction in order to differentiate the individuals or types involved.
A quality of a single physical entity inhering in the bearer by virtue of the bearer's size or shape or structure.
The number of entities of this type that are part of the whole organism.
A morphology quality inhering in a bearer by virtue of the bearer's physical magnitude.
A 1-D extent quality which is equal to the distance between two points.
A physical quality that inheres in a bearer by virtue of the proportion of the bearer's amount of matter.
A physical quality of the thermal energy of a system.
A quality of a single process inhering in a bearer by virtue of the bearer's occurrence per unit time.
A biological sex quality inhering in an individual or a population that only produces gametes that can be fertilised by male gametes.
A biological sex quality inhering in an individual or a population whose sex organs contain only male gametes.
A quality denoting the lack of an entity.
A quality inhering in a bearer by virtue of the bearer's existence.
A behavioral quality of a process inhering in a bearer by virtue of the bearer's exhibiting reduced activity.
A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities.
A quality inhering in a bearer by virtue of the bearer's having susceptibilty toward an external stimulus.
A resistance quality inhering in a bearer by virtue of the bearer's resistance to a stimulus.
A quality which inheres in a continuant.
multiply inhering quality of a physical entity
A 2-D extent quality inhering in a bearer by virtue of the bearer's two dimensional extent.
A biological sex quality inhering in a population of multiple sexes.
A quality inhering in a population by virtue of the proportion of its members that are ill at a given time.
A viability quality inhering in a bearer by virtue of the bearer's condition before death.
An organismal quality inhering in a bearer by virtue of the bearer's ability to produce new life or offspring.
An organismal quality inhering in a bearer by virtue of the bearer's physical expression of sexual characteristics.
A biological sex quality inhering in an individual or a population that undergo sexual reproduction.
A quality that inheres in an entire organism or part of an organism.
A quality that inheres in an entire population or part of a population.
A quality inhering in a bearer by virtue of the severity of infectious disease caused by the bearer in a target organism.
A quality of an object that has a value that is decreased compared to normal or average.
A viviparous organism having never given birth.
A structural quality which is held by a bearer where a localized pathological or traumatic structural change, damage, deformity, or discontinuity of tissue, organ, or body part is present.
An organismal quality of having successfully reproduced.
A material entity that consists of two or more organisms, viruses, or viroids.
collection of organisms
An organismal entity that consists of one or more people who live in the same dwelling and also share at meals or living accommodation, and may consist of a single family or some other grouping of people.
household
A collection of organisms that consists of two or more organisms from at least two species.
multi-species collection of organisms
A count data item of the number of steps in the line of descent from a common ancestor for a multicellular organism.
number of generations of multicellular organism
A microbial population of parasites that is defined by shared features such as genetic markers reflecting a common origin and distinguishing the population from other related parasite populations.
parasite isolate population
A document authored by a health care provider that specifies how to realize some health care process for a particular patient.
Un document créé par un fournisseur de soin indiquant comment réaliser une partie d'un processus de santé pour un patient particulier.
health care prescription
prescription de santé
A growth phenotype which describes the resistance of individuals or populations after exposure to voriconazole. Typically, organisms are deemed resistant to a chemical if they survive at a concentration of the chemical that does not allow wild type individuals or populations to grow.
resistance to voriconazole
A growth phenotype which describes the resistance of individuals or populations after exposure to posaconazole. Typically, organisms are deemed resistant to a chemical if they survive at a concentration of the chemical that does not allow wild type individuals or populations to grow.
resistance to posaconazole
A growth phenotype which describes the resistance of individuals or populations after exposure to tebuconazole. Typically, organisms are deemed resistant to a chemical if they survive at a concentration of the chemical that does not allow wild type individuals or populations to grow.
resistance to tebuconazole
A multi-tissue plant structure (PO:0025496) that develops from a gynoecium (PO:0009062), or a single carpel (PO:0009030), and at maturity may have as parts one or more seeds (PO:0009010).
A determinate reproductive shoot system (PO:0025082) that has as part at least one carpel (PO:0009030) or at least one stamen (PO:0009029) and does not contain any other determinate shoot system (PO:0009006) as a part.
An anatomical entity that is or was part of a plant.
entidad anat&#243mica vegetal (Spanish, exact)
An amino acid chain that is produced de novo by ribosome-mediated translation of a genetically-encoded mRNA, and any derivatives thereof.
A type II interferon that is a translation product of the human IFNG gene or a 1:1 ortholog thereof. The core domain structure consists of an Interferon gamma domain (Pfam:PF00714) that is four-helical cytokine domain with an additional helix in one of the crossover connections. It is a cytokine produced by lymphocytes activated by specific antigens or mitogens that has important immunoregulatory functions.
A tumor necrosis factor, TNF-like that is a translation product of the human TNF gene or a 1:1 ortholog thereof. Tumour necrosis factor alpha (TNF) is a pleiotropic cytokine that mediates apoptosis, cell proliferation, immunomodulation, inflammation, viral replication, allergy, arthritis, septic shock, insulin resistance, autoimmune diseases, and other pathological conditions. TNF transduces these cellular responses through two distinct receptors: type I, which are expressed on all cell types, and type II, which are expressed only on cells of the immune system and endothelial cells.
tumor necrosis factor ligand superfamily member 2
An interleukin-1 that is a translation product of the human IL1B gene or a 1:1 ortholog thereof.
A protein that is a translation product of the human IL1RN gene or a 1:1 ortholog thereof.
interleukin-1 receptor antagonist protein
An interleukin-17 that is a translation product of the human IL17A gene or a 1:1 ortholog thereof. The active product is a proinflammatory cytokine produced by activated T cells. This cytokine regulates the activities of NF-kappaB and mitogen-activated protein kinases.
cytotoxic T-lymphocyte-associated antigen 8
A protein that is a translation product of the human IL7 gene or a 1:1 ortholog thereof.
A protein that is a translation product of the human IL13 gene or a 1:1 ortholog thereof. Interleukin-13 is a pleiotropic cytokine which may be important in the regulation of the inflammatory and immune responses. It inhibits inflammatory cytokine production and synergises with IL-2 in regulating interferon-gamma synthesis. The sequences of IL-4 and IL-13 are distantly related.
A protein that is a translation product of the human IL15 gene or a 1:1 ortholog thereof.
A protein that is a translation product of the human IL2 gene or a 1:1 ortholog thereof. Interleukin-2 has a dual role in maintaining tolerance and contributing to immunity.
A protein that is a translation product of the human IL4 gene or a 1:1 ortholog thereof.
A protein that is a translation product of the human IL5 gene or a 1:1 ortholog thereof.
A protein that is a translation product of the human IL6 gene or a 1:1 ortholog thereof.
A protein that is a translation product of the human CXCL8 gene or a 1:1 ortholog thereof.
monocyte-derived neutrophil chemotactic factor
monocyte-derived neutrophil-activating peptide
A protein that is a translation product of the human IL9 gene or a 1:1 ortholog thereof.
A class 2 cytokine, IL-10 type that is a translation product of the human IL10 gene or a 1:1 ortholog thereof. Active interleukin-10 inhibits the synthesis of a number of cytokines, including IFN-gamma, IL-2, IL-3, TNF and GM-CSF produced by activated macrophages and by helper T cells. Structurally, IL-10 is a protein of about 160 amino acids that contains four conserved cysteines involved in disulfide bonds.
A protein with core architecture consisting of a Small cytokines (intecrine/chemokine), interleukin-8 like (Pfam:PF00048) domain.
A protein that is a translation product of the human CD14 gene or a 1:1 ortholog thereof.
myeloid cell-specific leucine-rich glycoprotein
A C/C-C motif small inducible chemokine that is a translation product of the CCL3, CCL3L1/CCL3L3, or CCL4 gene.
A C/C-C motif small inducible chemokine that is a member of a subfamily that includes eotaxin.
A C/C-C motif small inducible chemokine that is a translation product of the human CCL5 gene or a 1:1 ortholog thereof.
An eotaxin-like cytokine that is a translation product of the human CCL2 gene or a 1:1 ortholog thereof.
monocyte chemotactic and activating factor
platelet-derived growth factor-inducible protein JE
A C-C motif chemokine 3/4 that is a translation product of the human CCL3 gene or a 1:1 ortholog thereof.
A C-C motif chemokine 3/4 that is a translation product of the human CCL4 gene or a 1:1 ortholog thereof.
An eotaxin-like cytokine that is a translation product of the human CCL11 gene or a 1:1 ortholog thereof.
A protein that is a translation product of the human CRP gene or a 1:1 ortholog thereof.
A protein that is a translation product of the human CSF2 gene or a 1:1 ortholog thereof.
granulocyte-macrophage colony-stimulating factor
A protein that is a translation product of the human CSF3 gene or a 1:1 ortholog thereof.
A protein that is a translation product of the human EGF gene or a 1:1 ortholog thereof.
A protein that is a translation product of the human MFGE8 gene or a 1:1 ortholog thereof.
A protein that is a translation product of the human MPO gene or a 1:1 ortholog thereof.
A protein that is a translation product of the human REG1B gene or a 1:1 ortholog thereof.
regenerating islet-derived protein 1-beta
A serpin that is a translation product of the human SERPINA1 gene or a 1:1 ortholog thereof.
A protein that is a translation product of the Escherichia coli K-12 aspC gene or a 1:1 ortholog thereof.
A protein that is a translation product of the Escherichia coli K-12 phoA gene or a 1:1 ortholog thereof.
A dengue virus genome polyprotein proteolytic cleavage product that is the N-terminal most non-structural protein within the dengue virus genome polyprotein. Example: UniProtKB:P29990, 776-1127, Asn-905/Asn-982, MOD:00160.
A protein that is a translation product of the human GPT or GPT2 genes, 1:1 orthologs thereof, or a semi-ortholog thereof.
An acetylcholinesterase that is a translation product of the Anopheles gambiae Ace gene or a 1:1 ortholog thereof.
A voltage-gated sodium channel subunit alpha that is a translation product of the fruit fly para gene or a 1:1 ortholog thereof.
A sodium channel protein para that has an amino acid residue that differs from the typically-observed Ser at the position equivalent to 989 of the amino acid sequence represented by UniProtKB:Q94615-1.
sodium channel protein para sequence variant at position 989
A sodium channel protein para that has an amino acid residue that differs from the typically-observed Ile at the position equivalent to 1011 of the amino acid sequence represented by UniProtKB:Q94615-1.
sodium channel protein para sequence variant at position 1011
A sodium channel protein para that has an amino acid residue that differs from the typically-observed Leu at the position equivalent to 1014 of the amino acid sequence represented by UniProtKB:Q94615-1.
sodium channel protein para sequence variant at position 1014
A sodium channel protein para that has an amino acid residue that differs from the typically-observed Val at the position equivalent to 1016 of the amino acid sequence represented by UniProtKB:Q94615-1.
sodium channel protein para sequence variant at position 1016
A sodium channel protein para that has an amino acid residue that differs from the typically-observed Ile at the position equivalent to 1532 of the amino acid sequence represented by UniProtKB:Q94615-1.
sodium channel protein para sequence variant at position 1532
A sodium channel protein para that has an amino acid residue that differs from the typically-observed Phe at the position equivalent to 1534 of the amino acid sequence represented by UniProtKB:Q94615-1.
sodium channel protein para sequence variant at position 1534
A sodium channel protein para that has an amino acid residue that differs from the typically-observed Asn at the position equivalent to 1575 of the amino acid sequence represented by UniProtKB:Q94615-1.
sodium channel protein para sequence variant at position 1575
A sodium channel protein para that has an amino acid residue that differs from the typically-observed Asp at the position equivalent to 1763 of the amino acid sequence represented by UniProtKB:Q94615-1.
sodium channel protein para sequence variant at position 1763
A sodium channel protein para sequence variant at position 1016 that has a Gly residue at the position equivalent to Val-1016 of the amino acid sequence represented by UniProtKB:Q94615-1.
A protein that is a translation product of the fruit fly Rdl gene or a 1:1 ortholog thereof.
gamma-aminobutyric acid receptor subunit beta
A sodium channel protein para sequence variant at position 1011 that has a Met residue at the position equivalent to Ile-1011 of the amino acid sequence represented by UniProtKB:Q94615-1.
A sodium channel protein para sequence variant at position 1011 that has a Val residue at the position equivalent to Ile-1011 of the amino acid sequence represented by UniProtKB:Q94615-1.
A sodium channel protein para sequence variant at position 989 that has a Pro residue at the position equivalent to Ser-989 of the amino acid sequence represented by UniProtKB:Q94615-1.
A sodium channel protein para sequence variant at position 1014 that has a Ser residue at the position equivalent to Leu-1014 of the amino acid sequence represented by UniProtKB:Q94615-1.
A sodium channel protein para sequence variant at position 1532 that has a Thr residue at the position equivalent to Ile-1532 of the amino acid sequence represented by UniProtKB:Q94615-1.
A sodium channel protein para sequence variant at position 1534 that has a Cys residue at the position equivalent to Phe-1534 of the amino acid sequence represented by UniProtKB:Q94615-1.
A sodium channel protein para sequence variant at position 1534 that has a Leu residue at the position equivalent to Phe-1534 of the amino acid sequence represented by UniProtKB:Q94615-1.
A sodium channel protein para sequence variant at position 1534 that has a Ser residue at the position equivalent to Phe-1534 of the amino acid sequence represented by UniProtKB:Q94615-1.
A sodium channel protein para sequence variant at position 1575 that has a Tyr residue at the position equivalent to Asn-1575 of the amino acid sequence represented by UniProtKB:Q94615-1.
A sodium channel protein para sequence variant at position 1763 that has a Tyr residue at the position equivalent to Asp-1763 of the amino acid sequence represented by UniProtKB:Q94615-1.
A sodium channel protein para that is resistant to some insecticide.
insecticide resistant sodium channel protein para
A sodium channel protein para sequence variant at position 1016 that has an Ile residue at the position equivalent to Val-1016 of the amino acid sequence represented by UniProtKB:Q94615-1.
An insect-type acetylcholinesterase that has an amino acid residue that differs from the typically-observed Gly at the position equivalent to 119 of the amino acid sequence represented by UniProtKB:P04058-1.
insect-type acetylcholinesterase sequence variant at position 119
An insect-type acetylcholinesterase that has an amino acid residue that differs from the typically-observed Phe at the position equivalent to 290 of the amino acid sequence represented by UniProtKB:P04058-1.
insect-type acetylcholinesterase sequence variant at position 290
An insect-type acetylcholinesterase that has an amino acid residue that differs from the typically-observed Phe at the position equivalent to 331 of the amino acid sequence represented by UniProtKB:P04058-1.
insect-type acetylcholinesterase sequence variant at position 331
An insect-type acetylcholinesterase sequence variant at position 119 that has a Ser residue at the position equivalent to Gly-119 of the amino acid sequence represented by UniProtKB:P04058-1.
A gamma-aminobutyric acid receptor subunit beta that has an amino acid residue that differs from the typically-observed Ala at the position equivalent to 296 of the amino acid sequence represented by UniProtKB:P25123-1.
gamma-aminobutyric acid receptor subunit beta sequence variant at position 296
A gamma-aminobutyric acid receptor subunit beta sequence variant at position 296 that has a Gly residue at the position equivalent to Ala-296 of the amino acid sequence represented by UniProtKB:P25123-1.
A gamma-aminobutyric acid receptor subunit beta sequence variant at position 296 that has a Ser residue at the position equivalent to Ala-296 of the amino acid sequence represented by UniProtKB:P25123-1.
An insect-type acetylcholinesterase that is resistant to some insecticide.
insecticide resistant acetylcholinesterase
A gamma-aminobutyric acid receptor subunit beta that is resistant to some insecticide.
insecticide resistant gamma-aminobutyric acid receptor subunit beta
A glutathione S-transferase epsilon that is a translation product of the Anopheles funestus GSTe2 gene or a 1:1 ortholog thereof.
A glutathione S-transferase epsilon 2 that has an amino acid residue that differs from the typically-observed Ile at the position equivalent to 114 of the amino acid sequence represented by UniProtKB:V9QKI4-1.
glutathione S-transferase epsilon 2 sequence variant at position 114
A glutathione S-transferase epsilon 2 that has an amino acid residue that differs from the typically-observed Leu at the position equivalent to 119 of the amino acid sequence represented by UniProtKB:V9QKI4-1.
glutathione S-transferase epsilon 2 sequence variant at position 119
A glutathione S-transferase epsilon 2 sequence variant at position 119 that has a Phe residue at the position equivalent to Leu-119 of the amino acid sequence represented by UniProtKB:V9QKI4-1.
A glutathione S-transferase epsilon 2 that is resistant to some insecticide.
insecticide resistant glutathione S-transferase epsilon 2
A sodium channel protein para sequence variant at position 1014 that has a Cys residue at the position equivalent to Leu-1014 of the amino acid sequence represented by UniProtKB:Q94615-1.
A sodium channel protein para sequence variant at position 1014 that has a Phe residue at the position equivalent to Leu-1014 of the amino acid sequence represented by UniProtKB:Q94615-1.
social role
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.
A region of the chromosome between the centromere and the telomere. Human chromosomes have two arms, the p arm (short) and the q arm (long) which are separated from each other by the centromere.
SSLP are a kind of sequence alteration where the number of repeated sequences in intergenic regions may differ.
A repeat_region containing repeat_units of 2 to 10 bp repeated in tandem.
A sequence of nucleotides that has been algorithmically derived from an alignment of two or more different sequences.
A region of sequence implicated in an experimental result.
A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions.
Cytosolic 16S rRNA is an RNA component of the small subunit of cytosolic ribosomes in prokaryotes.
A genome is the sum of genetic material within a cell or virion.
A genotype is a variant genome, complete or incomplete.
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 sequence variant where the structure of the gene is changed.
A physical quality which inheres to the variant by virtue of the number instances of the variant within a population.
A quality inhering in a variant by virtue of its phenotype.
A continuous nucleotide sequence is inverted in the same position.
A chromosomal inversion that does not include the centromere.
a count is a data item denoted by an integer and represented the number of instances or occurences of an entity
count
A z-score (also known as z-value, standard score, or normal score) is a measure of the divergence of an individual experimental result from the most probable result, the mean. Z is expressed in terms of the number of standard deviations from the mean value.
z-score
a subject pairing is a planned process which executes a pairing rule and results in the creation of sets of 2 subjects meeting the pairing criteria
subject pairing
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 general symptom that is characterized as an act, instance, or result of being bled or the process by which something is bled: as a the escape of blood from vessels.
A pain that is characterized by a pain situated, or occurring, in or around a joint.
Prostration is a general symptom characterized by complete physical or mental exhaustion.
A pain that is characterized by a painful throat due to inflammation of the fauces and pharynx.
A nutrition, metabolism, and development symptom that is characterized by a loss of appetite especially when prolonged.
A nervous system symptom that is characterized by an abnormal violent and involuntary contraction or series of contractions of the muscles.
A balance symptom that is characterized by a sensation of unsteadiness accompanied by a feeling of movement within the head.
A neurological and physiological symptom that is characterized by an indefinite feeling of debility or lack of health, often indicative of or accompanying the onset of an illness.
A neurological and physiological symptom that is characterized by a weariness or exhaustion from labor, exertion, or stress.
Any portion of the organ that covers that body and consists of a layer of epidermis and a layer of dermis.
An organ that is capable of transducing sensory stimulus to the nervous system.
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 head is the anterior-most division of the body [GO].
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.
The stage of development at which the animal is fully formed, including immaturity and maturity. Includes both sexually immature stage, and adult stage.
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.
A life cycle stage of holometabolous insects in which the organism is a pupa and starts with the larval-pupal apolysis and ends with pupal-adult apolysis.
proximo-distal subdivision of respiratory tract
An anatomical structure that develops from the endoderm and the mesoderm.
mixed endoderm/mesoderm-derived structure
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 cavity at the start of the digestive tract that that is enclosed by the mouth. The boundaries and contents vary depending on the species. In vertebrates, the boundaries are the oral opening, the cheeks, the palate and (if present) the palatoglossal arch - if this is not present then the mouth and pharynx form the oropharyngeal cavity. The buccal cavity contains the teeth, tongue and palate (when present).
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.
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.
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.
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 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].
Unilaminar epithelium, which consists of a single layer of columnar cells. Examples: ciliated columnar epithelium, gastric epithelium, microvillus columnar epithelium.[FMA].
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.
The brain is the center of the nervous system in all vertebrate, and most invertebrate, animals. Some primitive animals such as jellyfish and starfish have a decentralized nervous system without a brain, while sponges lack any nervous system at all. In vertebrates, the brain is located in the head, protected by the skull and close to the primary sensory apparatus of vision, hearing, balance, taste, and smell[WP].
The transparent anterior portion of the fibrous coat of the eye that serves as the chief refractory structure.
Blood analogue used by all arthropods and most mollusks that have an open circulatory system. In these animals there is no distinction between blood and interstitial fluid. The liquid fills all of the interior (the hemocoel) of the body and surrounds all cells.
Saliva-secreting exocrine glands of the oral cavity[GO].
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.
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.
A thin musculomebranous barrier that separates the abdominal and thoracic cavities. Often used for breathing control.
Muscle tissue that consists primarily of skeletal muscle fibers.
A major subdivision of an organism that is the entire part of the organism dorsal to a horizontal plane and bounded on one side by the same transverse plane. In vertebrares this includes the vertebral column..
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.
Anatomical cavity bounded by visceral and parietal peritoneum.
A clear, colorless, bodily fluid, that occupies the subarachnoid space and the ventricular system around and inside the brain and spinal cord.
The part of the forelimb extending from the shoulder to the autopod[cjm].
Skeletal element that is composed of bone tissue.
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].
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.
A muscular organ in the floor of the mouth.
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 part of the ear that projects from the head, connecting to the external acoustic meatus.
The small curved bones that extends horizontally along the lateral wall of the nasal passage.
The smooth stratified squamous epithelium that covers the outer surface of the cornea.
A thick watery refractive medium that fills the space between the lens and the cornea[WP].
The mucous membrane that lines the nasal cavity[MP].
A fluid produced in the oral cavity by salivary glands, typically used in predigestion, but also in other functions.
Organ component of neuraxis that has as its parts the medullary reticular formation, inferior olivary complex and cochlear nuclear complex, among other structures[FMA]. The medulla oblongata lies directly above the spinal cord and controls vital autonomic functions such as digestion, breathing and the control of heart rate[GO].
An emulsion of fat globules within a fluid that is secreted by the mammary gland during lactation.
Organism substance that is composed of sperm cells suspended in seminal fluid.
Organ of metabolic interchange between fetus and mother, partly of embryonic origin and partly of maternal origin[GO]. The fetal portion of the placenta is known as the villous chorion. The maternal portion is known as the decidua basalis. The two portions are held together by anchoring villi that are anchored to the decidua basalis by the cytotrophoblastic shell.
Portion of semisolid bodily waste discharged through the anus[MW,modified].
Respiration organ that develops as an outpocketing of the esophagus.
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].
An organ that aids digestion and stores bile produced by the liver[WP].
A paired organ of the urinary tract which has the production of urine as its primary function.
The middle layer of the heart, comprised mainly of striated cardiac muscle fibers.
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].
Anatomical structure of largely lymphoid tissue that functions in cell-mediated immunity by being the site where T cells develop.
The soft tissue that fills the cavities of bones.
Muscle tissue is a contractile tissue made up of actin and myosin fibers[GO].
An external caudal extension of the body. In chordates, the tail is post-anal, in other animals the anus ends in the tail.
Replacement bone that forms within cartilage.
An organ that functions as a secretory or excretory organ.
Anatomical surface structure found in many aquatic organisms. It is a respiration organ whose function is the extraction of oxygen from water and the excretion of carbon dioxide. The microscopic structure of a gill is such that it presents a very large surface area to the external environment. Gills usually consist of thin filaments of tissue, branches, or slender tufted processes which have a highly folded surface to increase surface area. A high surface area is crucial to the gas exchange of aquatic organisms as water contains only 1/20 parts dissolved Oxygen compared to air. With the exception of some aquatic insects, the filaments and lamellae (folds) contain blood or coelomic fluid, from which gases are exchanged through the thin walls. Oxygen is carried by the blood to other parts of the body. Carbon dioxide passes from the blood through the thin gill tissue into the water. Gills or gill-like organs, located in different parts of the body, are found in various groups of aquatic animals, including mollusks, crustaceans, insects, fish, and amphibians.
A distinct juvenile form 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.
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 gland that is part of a digestive tract [Automatically generated definition].
A bone that is part of a head [Automatically generated definition].
A bone that is part of a facial skeleton [Automatically generated definition].
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].
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.
Organ that is part of the hematopoietic system.
This begins with the newly hatched first-instar larva, through its maturation to the end of the last larval stage. An example of this process is found in Drosophila melanogaster.
Organ consisting of skeletal tissue. Encompasses whole bones, fused bones, cartilaginious elements, teeth, dermal denticles.
A mucosa that is part of a gastrointestinal system.
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.
A proximal-distal subdivision of the digestive tract.
A part of a wall of an organ that forms a layer.
An organ that is part of a immune system [Automatically generated definition].
Muscle structures are contractile cells, tissues or organs that are found in multicellular organisms[GO].
The avian beak is an external anatomical structure, in the head region, that is adapted for feeding self and young, catching prey, probing, etc. It encompasses, but is not restricted to, the maxilla, mandible, maxillary ramaphotheca, mandibular ramaphotheca, nostril, nasal fossa, nasal bones, egg tooth and rictus[GO]. The beak, bill or rostrum is an external anatomical structure of birds which is used for eating and for grooming, manipulating objects, killing prey, probing for food, courtship and feeding young.
An organ or element that is in the abdomen. Examples: spleen, intestine, kidney, abdominal mammary gland.
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 that part of the thoracic segment region. This region can be further subdividied chest and thoracic cavity regions.
An epithelium that lines the nasal cavity.
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.
Body substance in a liquid or semi-solid state in the eyeball which serves to refract light.
Liquid components of living organisms. includes fluids that are excreted or secreted from the body as well as body water that normally is not.
A portion of organism substance that secreted_by a respiratory system.
Any gland that is part of the digestive system.
Matter ejected from the lungs, bronchi, and trachea, through the mouth.
A pouched enlargement of the gullet of many birds that serves as a receptacle for food and for its preliminary maceration.
Simple columnar epithelium in which the luminal side of the cells bears cilia. Examples: epithelium of trachea, epithelium of uterine tube.[FMA].
Any bodily fluid that has passed through a membrane such as the capillary wall, as a result of unbalanced hydrostatic and osmotic forces.
The external junctural region between the lower part of the abdomen and the thigh.
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.
Branch or outpocketing of the digestive tract.
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.
Gland of the epithelium lining the oral cavity. The most common are the salivary glands.
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].
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
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
A major subdivision of an organism that divides an organism along its main body axis (typically anterio-posterior axis). In vertebrates, this is based on the vertebral column.
subdivision of organism along main body axis
Blood that remains in the placenta and in the attached umbilical cord after childbirth[WP].
Any of the organs or elements that are part of the digestive system. Examples: tongue, esophagus, spleen, crop, lunge feeding organ, tooth elements.
A larval stage of that is the immature stage of some invertebrates that undergoe gradual metamorphosis (hemimetabolism) before reaching its adult stage.
Any structure that is placed on one side of the left-right axis of a bilaterian.
An epithelium that is part of a camera-type eye.
A life cycle stage that starts at completion of development and growth of the sexually mature adult animal, and ends before senescence.
Any organ component layer that consists of muscle tissue.
A membranous sac in animals that serves as the receptacle of a liquid or contains gas.
Any region of epithelium that is part of a skin region.
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.
A skeletal element of the ethmoid region with complex morphology that are lined with mucuous membranes involved in either olfaction or air conditioning.
Paired, vertical, and relatively straight plates that form the anterior limit of the nasal capsule.
Left part of the organism dorsal to a horizontal plane and bounded on one side by the same transverse plane.
Right part of the organism dorsal to a horizontal plane and bounded on one side by the same transverse plane.
"A unit which is a standard measure of the distance between two points." [Wikipedia:Wikipedia]
"A unit which is a standard measure of the amount of matter/energy of a physical object." [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 standard measure of the amount of a 2-dimensional flat surface." [UOC:GVG]
"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 density unit which is a standard measure of the mass exerting an influence on a given area." [Wikipedia:Wikipedia]
"A unit which is a standard measure of the amount of space occupied by any substance, whether solid, liquid, or gas." [NIST:NIST]
"A dimensionless concentration notation which describes the amount of one substance in another. It is the ratio of the amount of the substance of interest to the amount of that substance plus the amount of the substance." [Wikipedia:Wikipedia]
"A 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 concentration unit which denotes the average cell number in a given volume." [Bioedonline:Bioedonline]
"A concentration unit which is a standard measure of the amount of the action of a catalyst in a given volume." [UOC:GVG]
"A dimensionless concentration unit which denotes the given volume of the solute in the total volume of the resulting solution." [NIST:NIST]
"A concentration unit which is a standard measure of the amount of a toxic or pharmaceutical substance administered to a recipient subject, expressed in terms of the size of the subject." [UO:PC]
a path that is located in gross anatomical part of an organism (e.g., human) and is used for administering a vaccine, a drug, fluid, poison, or other substance into the body.
An antibody function (or antigen binding function) is an infection-fighting protein molecule in blood or secretory fluids that tags, neutralizes, and helps destroy pathogenic microorganisms such as bacteria, viruses and toxins.
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.
The number of PLATELETS per unit volume in a sample of venous BLOOD.
The number of times the HEART VENTRICLES contract per unit of time, usually per minute.
The mass or quantity of heaviness of an individual at BIRTH. It is expressed by units of pounds or kilograms.
The volume of packed RED BLOOD CELLS in a blood specimen. The volume is measured by centrifugation in a tube with graduated markings, or with automated blood cell counters. It is an indicator of erythrocyte status in disease. For example, ANEMIA shows a low value; POLYCYTHEMIA, a high value.
An fasting blood glucose measurement is a measurement of glucose in the blood of a patient at some defined time point after eating.
The point in time at which an individual was born.
quantification of the content of parasites in the blood, used as a measurement of parasite load in the organism and an indication of the degree of an active parasitic infection
A condition or physical state produced by the ingestion, injection, inhalation of or exposure to a deleterious agent.
A disease that involves the genitourinary system. [database_cross_reference: MONDO:patterns/location]
Abnormal result of a diagnostic imaging test.
the ending of pregnancy by removing a fetus or embryo before it can survive outside the uterus.
A categorical household wealth index representing the bottom third of values for the numerical household wealth index.
A categorical household wealth index representing the middle third of values for the numerical household wealth index.
A categorical household wealth index representing the top third of values for the numerical household wealth index.
A information content entity created to indicate the lack of air bricks in the dwelling.
A information content entity indicating that the household eats in restaurants.
obsolete record of eating in restaurants
A information content entity indicating that the household does not cook in the dwelling.
An information content entity indicates no toilet facility in the dwelling.
An information content entity indicating that a household uses a neighbours' toilet facility.
obsolete record of using neighbours' toilet
A time of screening occurring during the initial human subject enrollment period.
obsolete time of screening during initial enrollment
A time of screening occuring after the initial enrollment period had ended and the study had begun.
obsolete time of screenng after initial enrollment
obsolete inability to comply with protocol
obsolete unable to be located for over 120 days
obsolete withdrawal of all children under care
obsolete record of unknown death location
the growth of a child during three years after birth
A unit that represents a change in length of one centimeter in one year.
centimeter per year
the increase in mass of a child during three years after birth
A unit that represents a change in mass of one kilogram in one year.
kilogram per year
An organization that manufactures mosquito traps and other mosquito control products.
A ratio unit that denotes the mean enzymatic activity of a field-collected population of specimens compared to that of a reference population, normalized by a base two logarithmic transformation.
unit of log2 ratio of specimen population mean enzymatic activity to that of reference specimen population
A ratio unit that denotes the median enzymatic activity of a field-collected population of specimens compared to that of a reference population, normalized by a base two logarithmic transformation.
unit of log2 ratio of specimen population median enzymatic activity to that of reference specimen population
A fraction unit that denotes the fraction of a population exhibiting higher enzymatic activity than the 99th percentile of a reference population.
unit of population fraction with greater enzymatic activity than 99th percentile of reference population
An organization that monitors mosquito species in the Florida Keys district, performs abatement, and is located in the Florida Keys, Florida, USA.
Florida Keys Mosquito Control district organization
A landlocked country in East Africa, bordered on the east by Kenya, the north by Sudan, on the west by the Democratic Republic of the Congo, on the southwest by Rwanda, and on the south by Tanzania. The southern part of the country includes a substantial portion of Lake Victoria, within which it shares borders with Kenya and Tanzania. Uganda is divided into 80 districts, spread across four administrative regions: Northern, Eastern, Central and Western. The districts are subdivided into counties.
example to be eventually removed
failed exploratory term
The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job
metadata complete
Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete.
organizational term
Term created to ease viewing/sort terms for development purpose, and will not be included in a release
ready for release
Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking "ready_for_release" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed "ready_for_release" will also derived from a chain of ancestor classes that are also "ready_for_release."
metadata incomplete
Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors.
uncurated
Nothing done yet beyond assigning a unique class ID and proposing a preferred term.
pending final vetting
All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor.
Core is an instance of a grouping of terms from an ontology or ontologies. It is used by the ontology to identify main classes.
obsolete_core
placeholder removed
terms merged
An editor note should explain what were the merged terms and the reason for the merge.
term imported
This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use.
term split
This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split and indicate the URIs of the new terms created.
universal
Hard to give a definition for. Intuitively a "natural kind" rather than a collection of any old things, which a class is able to be, formally. At the meta level, universals are defined as positives, are disjoint with their siblings, have single asserted parents.
A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf
defined class
A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal
"definitions", in some readings, always are given by necessary and sufficient conditions. So one must be careful (and this is difficult sometimes) to distinguish between defined classes and universal.
named class expression
A named class expression is a logical expression that is given a name. The name can be used in place of the expression.
named class expressions are used in order to have more concise logical definition but their extensions may not be interesting classes on their own. In languages such as OWL, with no provisions for macros, these show up as actuall classes. Tools may with to not show them as such, and to replace uses of the macros with their expansions
to be replaced with external ontology term
Terms with this status should eventually replaced with a term from another ontology.
requires discussion
A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues.
A manufacturer of rapid point-of-care assay devices.
A manufacturer of in vitro diagnostic assay kits in India.
A manufacturer that specializes in in vitro diagnostic devices designed to test for infectious diseases.
The term was added to the ontology on the assumption it was in scope, but it turned out later that it was not.
This obsolesence reason should be used conservatively. Typical valid examples are: un-necessary grouping classes in disease ontologies, a phenotype term added on the assumption it was a disease.
"A mass unit which is equal to one millionth of a gram or 10^[-6] g." [UOC:GVG]
"A mass unit which is equal to one thousandth of one millionth of a gram or 10^[-9] g." [UOC:GVG]
"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 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 12 months which in science is taken to be equal to 365.25 days." [Wikipedia:Wikipedia]
"A dimensionless concentration notation which denotes the amount of a given substance in a total amount of 1,000,000 regardless of the units of measure used as long as they are the same or 1 part in 10^[6]." [UOC:GVG]
"A dimensionless concentration notation which denotes the amount of a given substance in a total amount of 1,000,000,000 regardless of the units of measure as long as they are the same or 1 part in 10^[9]." [UOC:GVG]
"A dimensionless unit which denoted an irrational real number, approximately equal to 3.14159 which is the ratio of a circle's circumference to its diameter in Euclidean geometry." [Wikipedia:Wikipedia]
"A dimensionless count unit which denotes the number of molecules." [MGED:MGED]
"A dimensionless percent unit which denotes the homogeneity of a biomaterial." [MGED:MGED]
"A dimensionless percent unit which denotes the density of an attached or monolayer culture (e.g., cell culture)." [MGED:MGED]
"A temperature unit which is equal to 5/9ths of a kelvin. Negative 40 degrees Fahrenheit is equal to negative 40 degrees Celsius." [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 unit of cell concentration which is equal to one cell in a volume of 1 milliliter." [Bioedonline:Bioedonline]
"A catalytic (activity) concentration unit which is equal to 1 katal activity of a catalyst in a given volume of one cubic meter." [NIST:NIST]
"A catalytic (activity) concentration unit which is equal to 1 katal activity of a catalyst in a given volume of one thousandth of a cubic meter." [NIST:NIST]
"A volume per unit volume unit which is equal to one millionth of a liter of solute in one cubic meter of solution." [NIST:NIST]
"A volume per unit volume unit which is equal to one millionth of a liter of solute in one liter of solution." [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 mass unit density which is equal to mass of an object in milligrams divided by the volume in liters." [UOC:GVG]
"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 micrograms divided by the volume in liters." [UOC:GVG]
"A dose unit which is equal to 1 milligram of a toxic or pharmaceutical substance per square meter of surface area of the recipient subject." [UO:PC]
"An area unit which is equivalent to 1 furlong x 1 chain. This is equal to an area of 4,046.856,4224 square meters, or 43,500 square feet." [Wikipedia:Wikipedia]
"An area density unit which is equal to the mass of an object in grams divided by the surface area in meters squared." [NIST:NIST]
"A unit of mass concentration defined as the number of micrograms of a substance per 250 ml Wheaton bottle." [UOB:LTS]