Chris Stoeckert Cristian Cocos Jie Zheng John Judkins 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. VEuPathDB Ontology 2023-05-30 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 Person:Alan Ruttenberg Really of interest to developers only BFO CLIF specification label An alternative label used in VEuPathDB project websites. VEuPathDB alternative label definition shown on EuPathDB website obsolete EuPathDB definition true Label of terms used in Amazonia data dictionary. It is in Spanish. obsolete Amazonia data dictionary label (es) true English label used in Amazonia project for display on the website obsolete Amazonia preferred label (en) true Spanish label used in Amazonia project for display on the website obsolete Amazonia preferred label (es) true label of term used in the ontology obsolete ontological label true Label of terms used in PRISM data dictionary. It is in English. obsolete PRISM data dictionary label (en) true English label used in Prism project for display on the website obsolete PRISM preferred label (en) true Term description provided by Amazonia group obsolete Amazonia description true Term description provided by PRISM group obsolete PRISM description true 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 obsolete term type true specify ICEMR term original from which database obsolete resource ID true definition of term in ontology obsolete ontological definition true An annotation property used to specify the order of terms displayed on a website. displayOrder display order Label of terms used in Indian data dictionary. It is in English. obsolete Indian data dictionary label (en) true English label used in Indian project for display on the website obsolete Indian preferred label (en) true Term description provided by Indian group obsolete Indian description true Translated English label of terms in Amazonia data dictionary. obsolete Amazonia data dictionary label (en) true 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). column header variable The column order of variables in the original data files colOrder obsolete column order true 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. dataFile 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. codebookDescription codebook description All possible responses and their mapped terms for each variable, from the data dictionary. Useful for value mapping. codebookValues 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 termType term type Annotation property that records the ontology term IRI originally used in the study. VEuPathDB team replaces https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/185 replaces An annotation property to specify the value code used in the dataset. obsolete datafile value true Annotation property that specifies units that are associated with a variable (if any) in a human-readable format. Use abbreviations. VEuPathDB team unitLabel https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/185 unit label Annotation property that specifies the ontology term IRI of unit, generally from the unit ontology (UO). VEuPathDB team unitIRI https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/185 unit IRI Annotation property that specifies which dataset a term belongs to. VEuPathDB team dataSet https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/185 dataSet Annotation property that indicates terms that were assessed longitudinally / repeatedly over time. VEuPathDB team repeated https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/185 repeated Annotation property that specifies important terms to be highlighted. VEuPathDB team is_featured https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/185 is featured Annotation property that indicates that the term is hidden from the UI and download files. VEuPathDB team hidden https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/185 hidden Annotation property that identifies terms that are on the log scale or natural log scale, as opposed to on the linear scale. VEuPathDB team scale https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/185 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) VEuPathDB team is_temporal https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/185 is temporal Annotation property that specifies key terms with longitudinal/repeated measures in the studies. VEuPathDB team mergeKey https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/185 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 VEuPathDB team defaultDisplayRangeMin https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/185 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 VEuPathDB team defaultDisplayRangeMax https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/185 default display range max Annotation property that specifies the bin width for each term's histogram. VEuPathDB team defaultBinWidth https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/185 default bin width Annotation property used to annotate numeric terms as strings. Numeric terms annotated as strings will ALWAYS be ordinal. Study specific. VEuPathDB team forceStringType https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/185 force string type Term ID as previously used by VectorBase obsolete sourced by VectorBase ID true 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 GROUP:OBI:<http://purl.obolibrary.org/obo/obi> editor preferred term 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. PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> example of usage in branch An annotation property indicating which module the terms belong to. This is currently experimental and not implemented yet. GROUP:OBI OBI_0000277 in branch has curation status PERSON:Alan Ruttenberg PERSON:Bill Bug PERSON:Melanie Courtot has curation status 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. PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> definition 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. PERSON:Daniel Schober GROUP:OBI:<http://purl.obofoundry.org/obo/obi> editor note 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. PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> term editor 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. OBO Operations committee PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> 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). alternative label 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 PERSON:Daniel Schober Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w GROUP:OBI:<http://purl.obolibrary.org/obo/obi> definition source 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. PERSON:Alan Ruttenberg PERSON:Melanie Courtot has obsolescence reason curator note An administrative note of use for a curator but of no use for a user PERSON:Alan Ruttenberg curator note 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 Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg The 'tracker item' can associate a tracker with a specific ontology term. term tracker item ontology term requester The name of the person, project, or organization that motivated inclusion of an ontology term by requesting its addition. Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg The 'term requester' can credit the person, organization or project who request the ontology term. ontology term requester 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 is denotator type imported from For external terms/classes, the ontology from which the term was imported PERSON:Alan Ruttenberg PERSON:Melanie Courtot GROUP:OBI:<http://purl.obolibrary.org/obo/obi> imported from 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 expression to 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. Chris Mungall expand assertion to first order logic expression PERSON:Alan Ruttenberg 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 Alan Ruttenberg 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:Alan Ruttenberg PERSON:Bjoern Peters PERSON:Chris Mungall PERSON:Melanie Courtot GROUP:OBO Foundry <http://obofoundry.org/> OBO foundry unique label 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 digit count 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 Person:Alan Ruttenberg has ID range allocated to has ID policy for 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" Relating an ontology used to record id policy to the ontology namespace whose policy it manages Person:Alan Ruttenberg has ID policy for has ID prefix 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 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. Person:Alan Ruttenberg has ID prefix 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 elucidation has associated axiom(nl) Person:Alan Ruttenberg Person:Alan Ruttenberg An axiom associated with a term expressed using natural language has associated axiom(nl) has associated axiom(fol) Person:Alan Ruttenberg Person:Alan Ruttenberg An axiom expressed in first order logic using CLIF syntax has associated axiom(fol) 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" PERSON:Alan Ruttenberg Add as annotation triples in the granting ontology is allocated id range 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 has ontology root term 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 #40 VFB Edges asserting this should be annotated with to record evidence supporting the assertion and its provenance. may be identical to 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 https://github.com/geneontology/go-ontology/issues/15532 https://github.com/information-artifact-ontology/ontology-metadata/issues/32 GO ontology scheduled for obsoletion on or after has axiom id Person:Alan Ruttenberg Person:Alan Ruttenberg 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 Person:Alan Ruttenberg Person:Alan Ruttenberg Add as annotation triples in the granting ontology term replaced by 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 Person: Alejandra Gonzalez-Beltran Person: Philippe Rocca-Serra ISA tools project (http://isa-tools.org) ISA alternative term 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: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group NIAID GSCID-BRC alternative term IEDB alternative term An alternative term used by the IEDB. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IEDB alternative term This is an annotation used on an object property to indicate a logical characterstic beyond what is possible in OWL. OBO Operations call 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. defined by construct 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 2023-03-03 abbreviation A synonym type for describing ambiguous synonyms 2023-03-03 ambiguous synonym A synonym type for describing dubious synonyms 2023-03-03 dubious synonym 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 2023-03-03 layperson synonym 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 2023-03-03 plural form 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 2023-03-03 UK spelling synonym An alternative label for a class or property which has a more general meaning than the preferred name/primary label. https://github.com/information-artifact-ontology/ontology-metadata/issues/18 has broad synonym https://github.com/information-artifact-ontology/ontology-metadata/issues/18 An alternative label for a class or property which has the exact same meaning than the preferred name/primary label. https://github.com/information-artifact-ontology/ontology-metadata/issues/20 has exact synonym https://github.com/information-artifact-ontology/ontology-metadata/issues/20 An alternative label for a class or property which has a more specific meaning than the preferred name/primary label. https://github.com/information-artifact-ontology/ontology-metadata/issues/19 has narrow synonym https://github.com/information-artifact-ontology/ontology-metadata/issues/19 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. https://github.com/information-artifact-ontology/ontology-metadata/issues/21 has related synonym https://github.com/information-artifact-ontology/ontology-metadata/issues/21 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 executed by executes A relation between a medication material and a disease or symptom that it may treat. no longer in use obsolete material may be used for true obsolete manifestation of true A relation between a medication material and a disease or symptom that it may treat. obsolete may treat true A relation between a drug product and (one of) its active ingredient. obsolete has active ingredient true 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. person:Alan Ruttenberg Smith, Ceusters, Ruttenberg, 2000 years of philosophy is about An information artifact IA mentions an entity E exactly when it has a component/part that denotes E mentions A person's name denotes the person. A variable name in a computer program denotes some piece of memory. Lexically equivalent strings can denote different things, for instance "Alan" can denote different people. In each case of use, there is a case of the denotation relation obtaining, between "Alan" and the person that is being named. A primitive, instance-level, relation obtaining between an information content entity and some portion of reality. Denotation is what happens when someone creates an information content entity E in order to specifically refer to something. The only relation between E and the thing is that E can be used to 'pick out' the thing. This relation connects those two together. Freedictionary.com sense 3: To signify directly; refer to specifically 2009-11-10 Alan Ruttenberg. Old definition said the following to emphasize the generic nature of this relation. We no longer have 'specifically denotes', which would have been primitive, so make this relation primitive. g denotes r =def r is a portion of reality there is some c that is a concretization of g every c that is a concretization of g specifically denotes r person:Alan Ruttenberg 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. Alan Ruttenberg 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 Person:Alan Ruttenberg 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 Person:Alan Ruttenberg is quality measured as provides_service_consumer_with 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. provides_service_consumer_with is_supported_by_data 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 OBI OBI Philly 2011 workshop is_supported_by_data has_specified_input 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 PERSON: Bjoern Peters PERSON: Larry Hunter PERSON: Melanie Coutot has_specified_input is_specified_input_of 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. Alan Ruttenberg PERSON:Bjoern Peters is_specified_input_of has_specified_output has_specified_output The inverse property of is_specified_output_of PERSON: Alan Ruttenberg PERSON: Bjoern Peters PERSON: Larry Hunter PERSON: Melanie Courtot has_specified_output is_manufactured_by http://www.affymetrix.com/products/arrays/specific/hgu133.affx is_manufactered_by http://www.affymetrix.com/ (if we decide to use these URIs for the actual entities) c is_manufactured_by o means that there was a process p in which c was built in which a person, or set of people or machines did the work(bore the "Manufacturer Role", and those people/and or machines were members or of directed by the organization to do this. Alan Ruttenberg Liju Fan has_make has_manufacturer is_manufactured_by is_specified_output_of is_specified_output_of A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of. Alan Ruttenberg PERSON:Bjoern Peters is_specified_output_of achieves_planned_objective 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. BP, AR, PPPB branch PPPB branch derived modified according to email thread from 1/23/09 in accordince with DT and PPPB branch achieves_planned_objective has grain the relation of the cells in the finger of the skin to the finger, in which an indeterminate number of grains are parts of the whole by virtue of being grains in a collective that is part of the whole, and in which removing one granular part does not nec- essarily damage or diminish the whole. Ontological Whether there is a fixed, or nearly fixed number of parts - e.g. fingers of the hand, chambers of the heart, or wheels of a car - such that there can be a notion of a single one being missing, or whether, by contrast, the number of parts is indeterminate - e.g., cells in the skin of the hand, red cells in blood, or rubber molecules in the tread of the tire of the wheel of the car. Discussion in Karslruhe with, among others, Alan Rector, Stefan Schulz, Marijke Keet, Melanie Courtot, and Alan Ruttenberg. Definition take from the definition of granular parthood in the cited paper. Needs work to put into standard form PERSON: Alan Ruttenberg PAPER: Granularity, scale and collectivity: When size does and does not matter, Alan Rector, Jeremy Rogers, Thomas Bittner, Journal of Biomedical Informatics 39 (2006) 333-349 has grain provisions 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. GROUP: Relations branch supplies provisions has_supplier 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. PERSON: Alan Rutternberg PERSON: Cristian Cocos PERSON: Frank Gibson PERSON: Melanie Courtot has_supplier objective_achieved_by 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. OBI OBI objective_achieved_by is member of organization 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. Person:Alan Ruttenberg Person:Helen Parkinson Person:Alan Ruttenberg Person:Helen Parkinson 2009/09/28 Alan Ruttenberg. Fucoidan-use-case is member of organization has disposition to bind 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 IEDB has disposition to bind 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 Person: Jie Zheng has organization member specifies value of A relation between a value specification and an entity which the specification is about. specifies value of has value specification A relation between an information content entity and a value specification that specifies its value. PERSON: James A. Overton OBI has value specification 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. quality of a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence role of a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence has function a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence has quality 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 inverse of starts with starts inverse of ends with 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. has active pharmaceutical ingredient has active substance has active ingredient inverse of has active ingredient active ingredient in 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. affects causally upstream of or within A relationship between a material entity and a process where the material entity has some causal role that influences the process causal agent in 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. causal relation between processes depends on 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. is substance that treats the relationship between a fraction and the number above the line has numerator the relationship between a fraction and the number below the line (or divisor) has denominator has measurement value has x coordinate value has specified numeric 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. PERSON: James A. Overton OBI has specified numeric value 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. OBI has specified value Vibrio cholerae serotype Inaba Vibrio cholerae serotype Ogawa Shigella flexneri, serovar 3c Shigella flexneri, serovar 4b Tree (organism) Tree Migrant Acute pulmonary edema 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 Employment status 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. MRSA methicillin-resistant Staphylococcus aureus entity Entity 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 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 per discussion with Barry Smith An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) continuant Continuant 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 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 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]) occurrent Occurrent 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 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. per discussion with Barry Smith 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] ic IndependentContinuant 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 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] s-region SpatialRegion 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 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. per discussion with Barry Smith 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] t-region TemporalRegion 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 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 per discussion with Barry Smith 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] 2d-s-region TwoDimensionalSpatialRegion 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 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] st-region SpatiotemporalRegion 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 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 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] process Process Observation type 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 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]) (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] disposition Disposition 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 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] realizable RealizableEntity 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 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] 0d-s-region ZeroDimensionalSpatialRegion 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 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] quality Quality the ambient temperature of this portion of air the color of a tomato the length of the circumference of your waist the mass of this piece of gold. the shape of your nose the shape of your nostril a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001]) If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001]) (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] (forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001] quality 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] sdc SpecificallyDependentContinuant 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 role of being a doctor 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 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. per discussion with Barry Smith (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] role Role 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 b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001]) (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] fiat-object-part FiatObjectPart 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 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] 1d-s-region OneDimensionalSpatialRegion 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 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] object-aggregate ObjectAggregate 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 An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects 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] 3d-s-region ThreeDimensionalSpatialRegion 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 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] site Site 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 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] object Object 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 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]) gdc GenericallyDependentContinuant 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 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] function Function 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 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] p-boundary ProcessBoundary 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 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] 1d-t-region OneDimensionalTemporalRegion 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 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] material MaterialEntity 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 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] 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]) cf-boundary ContinuantFiatBoundary 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 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]) 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. (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] immaterial ImmaterialEntity 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 1d-cf-boundary OneDimensionalContinuantFiatBoundary 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 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] process-profile ProcessProfile 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 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] r-quality RelationalQuality 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. 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 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] 2d-cf-boundary TwoDimensionalContinuantFiatBoundary 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 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] 0d-cf-boundary ZeroDimensionalContinuantFiatBoundary 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 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. requested by Melanie Courtot 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] 0d-t-region ZeroDimensionalTemporalRegion 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 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] history History 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 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]) liver cell line FCL fibroblast cell line A monocarboxylic acid comprising 1,8-naphthyridin-4-one substituted by carboxylic acid, ethyl and methyl groups at positions 3, 1, and 7, respectively. An orally administered antibacterial, it is used in the treatment of lower urinary-tract infections due to Gram-negative bacteria, including the majority of E. coli, Enterobacter, Klebsiella, and Proteus species. 1-ethyl-7-methyl-4-oxo-1,4-dihydro-1,8-naphthyridine-3-carboxylic acid NALIDIXIC ACID Nalidixic acid nalidixic acid Voriconazole 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. (2R,3S)-2-(2,4-difluorophenyl)-3-(5-fluoropyrimidin-4-yl)-1-(1H-1,2,4-triazol-1-yl)butan-2-ol voriconazole voriconazole 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 Ciprofloxacin ciprofloxacin ciprofloxacin chemokine ligand 10 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. 2-(dibutylamino)-1-[(9Z)-2,7-dichloro-9-(4-chlorobenzylidene)-9H-fluoren-4-yl]ethanol lumefantrine A straight-chain, sixteen-carbon, saturated long-chain fatty acid. hexadecanoic acid hexadecanoic 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 L-DOPA L-Dopa L-dopa L-dopa 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 ARACHIDONIC ACID Arachidonic acid arachidonic acid A cinchona alkaloid that is cinchonidine in which the hydrogen at the 6-position of the quinoline ring is substituted by methoxy. (9R)-6'-methoxy-8alpha-cinchonan-9-ol Quinine quinine quinine 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. 1-chloro-4-[2,2,2-trichloro-1-(4-chlorophenyl)ethyl]benzene DDT DDT Aztreonam 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. (2S,3S)-3-{(2Z)-2-(2-ammonio-1,3-thiazol-4-yl)-2-[(2-carboxypropan-2-yloxy)imino]acetamido}-2-methyl-4-oxoazetidine-1-sulfonate aztreonam An octadec-9-enoic acid in which the double bond at C-9 has Z (cis) stereochemistry. (9Z)-octadec-9-enoic acid OLEIC ACID Oleic acid oleic acid A carbonyl group with two C-bound amine groups. The commercially available fertilizer has an analysis of 46-0-0 (N-P2O5-K2O). UREA Urea urea urea Hydrogen peroxide (H2O2) An inorganic peroxide consisting of two hydroxy groups joined by a covalent oxygen-oxygen single bond. HYDROGEN PEROXIDE Hydrogen peroxide bis(hydridooxygen)(O--O) dihydrogen peroxide dihydrogen(peroxide) dioxidane hydrogen peroxide hydrogen peroxide 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. CARBON DIOXIDE Carbon dioxide carbon dioxide dioxidocarbon methanedione carbon dioxide 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. carbohydrate carbohydrates carbohydrate 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. Peptide peptides peptide 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 chlorthion A lactam obtained by formal cyclocondensation of creatine. It is a metabolite of creatine. 2-imino-1-methylimidazolidin-4-one Creatinine creatinine creatinine 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 bilirubin bilirubin IXalpha High molecular weight, linear polymers, composed of nucleotides containing deoxyribose and linked by phosphodiester bonds; DNA contain the genetic information of organisms. Deoxyribonucleic acid deoxyribonucleic acids deoxyribonucleic acid 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. Penicillin penicillins penicillin An octadecadienoic acid in which the two double bonds are at positions 9 and 12 and have Z (cis) stereochemistry. (9Z,12Z)-octadeca-9,12-dienoic acid LINOLEIC ACID Linoleic acid linoleic acid The carbon oxoanion resulting from the removal of a proton from carbonic acid. Hydrogencarbonate hydrogen(trioxidocarbonate)(1-) hydrogencarbonate hydrogencarbonate(1-) hydrogentrioxocarbonate(1-) hydrogentrioxocarbonate(IV) hydroxidodioxidocarbonate(1-) hydrogencarbonate An organochlorine compound that is dichloro-substituted acetamide containing a nitrobenzene ring, an amide bond and two alcohol functions. 2,2-dichloro-N-[(1R,2R)-2-hydroxy-1-(hydroxymethyl)-2-(4-nitrophenyl)ethyl]acetamide CHLORAMPHENICOL Chloramphenicol chloramphenicol chloramphenicol 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 gentamycin An elemental molecule consisting of two hydrogens joined by a single bond. dihydrogen dihydrogen 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. (3R,5aS,6R,8aS,9R,10S,12R,12aR)-10-methoxy-3,6,9-trimethyldecahydro-3,12-epoxypyrano[4,3-j][1,2]benzodioxepine artemether 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 cefotaxime Compound benzoic acid Any aromatic carboxylic acid that consists of benzene in which at least a single hydrogen has been substituted by a carboxy group. benzoic acids An insecticide compound naturally occurring in plants. phytogenic insecticide 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. Cephalosporin cephalosporin Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity. molecular entity molecular entity Compound 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. drug An icosanoid comprising icosanoic acid having one C=C bond at any position. icosenoic acid A substance used to destroy fungal pests. fungicide 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. glycosides glycoside A chemical entity is a physical entity of interest in chemistry including molecular entities, parts thereof, and chemical substances. chemical entity chemical entity Strictly, a substance intended to kill members of the class Insecta. In common usage, any substance used for preventing, destroying, repelling or controlling insects. insecticide A molecular entity having a net electric charge. Ion ion ion juvenile hormone mimic 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. lactam lactams lactam A macrocyclic lactone with a ring of twelve or more members derived from a polyketide. macrolide macrolides macrolide Sulbutamol type 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). 4-[2-(tert-butylamino)-1-hydroxyethyl]-2-(hydroxymethyl)phenol Albuterol albuterol A class of neuro-active insecticides that act at the nicotinic acetylcholine receptor. neonicotinoid insectide Strictly, a substance intended to kill pests. In common usage, any substance used for controlling, preventing, or destroying animal, microbiological or plant pests. pesticide pesticide 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. phosphates phosphate pyrethroid insecticide A class of aromatic heterocyclic compounds each of which contains a benzene ring ortho fused to carbons 2 and 3 of a pyridine ring. quinolines A quinoline having a chloro group at the 7-position and an aryl amino group at the 4-position. 4-[(7-chloroquinolin-4-yl)amino]-2-[(diethylamino)methyl]phenol Amodiaquine amodiaquine 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 Amoxicillin amoxicillin Amphotericin B A macrolide antibiotic used to treat potentially life-threatening fungal infections. (1R,3S,5R,6R,9R,11R,15S,16R,17R,18S,19E,21E,23E,25E,27E,29E,31E,33R,35S,36R,37S)-33-[(3-amino-3,6-dideoxy-beta-D-mannopyranosyl)oxy]-1,3,5,6,9,11,17,37-octahydroxy-15,16,18-trimethyl-13-oxo-14,39-dioxabicyclo[33.3.1]nonatriaconta-19,21,23,25,27,29,31-heptaene-36-carboxylic acid amphotericin B An oxopurine that is the final oxidation product of purine metabolism. uric acid 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. vitamin D 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 ALPHA-LINOLENIC ACID alpha-Linolenic acid alpha-linolenic acid alpha-linolenic acid A 9-octadecenoic acid and the trans-isomer of oleic acid. (9E)-octadec-9-enoic acid Elaidic acid elaidic 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 VANCOMYCIN Vancomycin vancomycin A member of the class of acrylamides that results from the formal condensation of acrylic acid with ammonia. Acrylamide acrylamide prop-2-enamide acrylamide 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 gamma-Linolenic acid gamma-linolenic acid A hexadec-9-enoic acid in which the double bond at position C-9 has cis configuration. (9Z)-hexadec-9-enoic acid PALMITOLEIC ACID Palmitoleic acid palmitoleic acid 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. icosanoic acid icosanoic acid 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. Octadecanoic acid octadecanoic acid octadecanoic acid Tobramycin 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 Tobramycin tobramycin A C24 straight-chain saturated fatty acid. Tetracosanoic acid tetracosanoic acid tetracosanoic acid A straight-chain, fourteen-carbon, long-chain saturated fatty acid mostly found in milk fat. Tetradecanoic acid myristic acid tetradecanoic acid A straight-chain, C22, long-chain saturated fatty acid. Docosanoic acid docosanoic acid docosanoic 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 Ampicillin ampicillin 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 ceftriaxone Azithromycin 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 azithromycin A hexitol produced by a variety of organisms including bacteria, fungi, lichens and plants. mannitol mannitol 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. photon photon 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. Dodecanoic acid dodecanoic acid dodecanoic acid A C10, straight-chain saturated fatty acid. DECANOIC ACID Decanoic acid decanoic acid decanoic 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 Bifenthrin bifenthrin (1r,2R,3S,4r,5R,6S)-1,2,3,4,5,6-hexachlorocyclohexane gamma-Hexachlorocyclohexane gamma-hexachlorocyclohexane gamma-hexachlorocyclohexane A chemical entity constituting the smallest component of an element having the chemical properties of the element. atom atom A substance that kills or slows the growth of microorganisms, including bacteria, viruses, fungi and protozoans. antimicrobial agent A substance (or active part thereof) that kills or slows the growth of bacteria. antibacterial agent 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. aromatic compounds aromatic molecular entity aromatic compound 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. nucleic acids nucleic acid High molecular weight, linear polymers, composed of nucleotides containing ribose and linked by phosphodiester bonds; RNA is central to the synthesis of proteins. ribonucleic acid ribonucleic acids ribonucleic acid 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. amino-acid residue 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. macromolecule macromolecule A carbamate ester obtained by the formal condensation of 1-naphthol with methylcarbamic acid. Carbaryl carbaryl naphthalen-1-yl methylcarbamate carbaryl 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. oct-1-en-3-ol oct-1-en-3-ol 2,2-dimethyl-1,3-benzodioxol-4-yl methylcarbamate Bendiocarb bendiocarb 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. Chlorpyrifos O,O-diethyl O-(3,5,6-trichloropyridin-2-yl) phosphorothioate chlorpyrifos chlorpyrifos 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. Chlorpyrifos-methyl O,O-dimethyl O-(3,5,6-trichloropyridin-2-yl) phosphorothioate chlorpyrifos-methyl An alkenyl phosphate that is the 2,2-dichloroethenyl ester of dimethyl phosphate. 2,2-dichloroethenyl dimethyl phosphate Dichlorvos dichlorvos An organochlorine compound resulting from the epoxidation of the double bond of aldrin. It is the active metabolite of the proinsecticde aldrin. Dieldrin rel-(1R,2S,3S,6R,7R,8S,9S,11R)-3,4,5,6,13,13-hexachloro-10-oxapentacyclo[6.3.1.1(3,6).0(2,7).0(9,11)]tridec-4-ene dieldrin 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. Diflubenzuron N-[(4-chlorophenyl)carbamoyl]-2,6-difluorobenzamide diflubenzuron 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. Dimethoate O,O-dimethyl S-[2-(methylamino)-2-oxoethyl] phosphorodithioate dimethoate 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. Fenitrothion O,O-dimethyl O-(3-methyl-4-nitrophenyl)phosphorothioate fenitrothion 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. Fenthion O,O-dimethyl O-[3-methyl-4-(methylsulfanyl)phenyl] phosphorothioate fenthion Methoprene propan-2-yl (2E,4E)-11-methoxy-3,7,11-trimethyldodeca-2,4-dienoate methoprene Paraquat An organic cation that consists of 4,4'-bipyridine bearing two N-methyl substituents loctated at the 1- and 1'-positions. 1,1'-dimethyl-[4,4'-bipyridin]-1,1'-diium Paraquat paraquat 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 Permethrin permethrin 3-phenoxybenzyl 2,2-dimethyl-3-(2-methylprop-1-en-1-yl)cyclopropanecarboxylate Phenothrin phenothrin An organic thiophosphate that is ethyl mandelate in which the hydroxy group has been replaced by a (dimethoxyphosphorothioyl)sulfanediyl group. Phenthoate ethyl [(dimethoxyphosphorothioyl)sulfanyl](phenyl)acetate phenthoate A carbamate ester that is phenyl methylcarbamate substituted at position 2 by a propan-2-yloxy group. 2-(propan-2-yloxy)phenyl methylcarbamate Propoxur propoxur propoxur Cefpodoxime 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 cefpodoxime hemoglobin hemoglobin Steroid type 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. Steroid steroids steroid 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. Fatty acid fatty acids fatty acid Cephradine 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 Cephradine cephradine A lactam in which the amide bond is contained within a four-membered ring, which includes the amide nitrogen and the carbonyl carbon. beta-Lactam beta-lactam An antimicrobial agent that destroys fungi by suppressing their ability to grow or reproduce. antifungal agent Triazoles An azole in which the five-membered heterocyclic aromatic skeleton contains three N atoms and two C atoms. triazoles A phosphorus oxoanion that is the conjugate base of phosphoric acid. phosphate ion Any C22 polyunsaturated fatty acid containing six double bonds. docosahexaenoic acid docosahexaenoic acid Any straight-chain, C20 polyunsaturated fatty acid having five C=C double bonds. icosapentaenoic acid icosapentaenoic acid A drug used to treat or prevent bacterial infections. antibacterial drug Chloroquine 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. Chloroquine N(4)-(7-chloroquinolin-4-yl)-N(1),N(1)-diethylpentane-1,4-diamine chloroquine 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) co-trimoxazole Colistin 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. Colistin colistin 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. antimalarial 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. carbamate insecticide 2,2-dimethyl-2,3-dihydro-1-benzofuran-7-yl [(dibutylamino)sulfanyl](methyl)carbamate carbosulfan O-[4-(dimethylsulfamoyl)phenyl] O,O-dimethyl phosphorothioate famphur ethyl 3-methyl-4-(methylsulfanyl)phenyl N-(propan-2-yl)phosphoramidate fenamiphos fenamiphos 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 pirimiphos-methyl O-(4-bromo-2-chlorophenyl) O-ethyl S-propyl phosphorothioate profenofos 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) temephos temephos The active insecticidal constituents of Chrysanthemum cinerariifolium flowers. pyrethrins pyrethrins pyrethroid ester insecticide 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. 1-[(2-chloro-1,3-thiazol-5-yl)methyl]-3-methyl-2-nitroguanidine clothianidin 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. Spinosad spinosad 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. 2-[1-methyl-2-(4-phenoxyphenoxy)ethoxy]pyridine Pyriproxyfen pyriproxyfen 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. beta-cyfluthrin Reaction product comprising equal quantities of CHEBI:39323 and CHEBI:39327. lambda-cyhalothrin A racemate comprising equimolar amounts of (1R)-cis-(alphaS)- and (1S)-cis-(alphaR)-cypermethrin. alpha-Cypermethrin alpha-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. beta-Cypermethrin beta-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. 4-bromo-2-(4-chlorophenyl)-1-(ethoxymethyl)-5-(trifluoromethyl)-1H-pyrrole-3-carbonitrile Chlorfenapyr chlorfenapyr An aromatic ether that is the 3-phenoxybenzyl ether of 2-(4-ethoxyphenyl)-2-methylpropan-1-ol. 1-{[2-(4-ethoxyphenyl)-2-methylpropoxy]methyl}-3-phenoxybenzene etofenprox pyrethroid ether insecticide (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 tetramethrin A carboxylic ester obtained by formal condensation between 3-(2,2-dichloroethenyl)-2,2-dimethylcyclopropanecarboxylic acid and (4-fluoro-3-phenoxyphenyl)(hydroxy)acetonitrile. Cyfluthrin cyano(4-fluoro-3-phenoxyphenyl)methyl 3-(2,2-dichloroethenyl)-2,2-dimethylcyclopropanecarboxylate cyfluthrin 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. Cyhalothrin cyano(3-phenoxyphenyl)methyl 3-[(1Z)-2-chloro-3,3,3-trifluoroprop-1-en-1-yl]-2,2-dimethylcyclopropanecarboxylate cyhalothrin 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. Cypermethrin cyano(3-phenoxyphenyl)methyl 3-(2,2-dichloroethenyl)-2,2-dimethylcyclopropanecarboxylate cypermethrin An optically active form of lactic acid having (S)-configuration. (2S)-2-hydroxypropanoic acid (S)-lactic acid 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 Deltamethrin deltamethrin A tetracosenoic acid having a cis-double bond at position 15. (15Z)-Tetracosenoic acid (15Z)-tetracos-15-enoic acid (15Z)-tetracosenoic acid Fluconazole 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. 2-(2,4-difluorophenyl)-1,3-bis-(1H-1,2,4-triazol-1-yl)propan-2-ol fluconazole fluconazole A liquid that can dissolve other substances (solutes) without any change in their chemical composition. solvent Caspofungin 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. (10R,12S)-N-{(2R,6S,9S,11R,12S,14aS,15S,20S,23S,25aS)-12-[(2-aminoethyl)amino]-20-[(1R)-3-amino-1-hydroxypropyl]-23-[(1S,2S)-1,2-dihydroxy-2-(4-hydroxyphenyl)ethyl]-2,11,15-trihydroxy-6-[(1R)-1-hydroxyethyl]-5,8,14,19,22,25-hexaoxotetracosahydro-1H-dipyrrolo[2,1-c:2',1'-l][1,4,7,10,13,16]hexaazacyclohenicosin-9-yl}-10,12-dimethyltetradecanamide Caspofungin caspofungin 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. Ergometrine N-[(2S)-1-hydroxypropan-2-yl]-6-methyl-9,10-didehydroergoline-8beta-carboxamide ergometrine Any of several wide-spectrum macrolide antibiotics obtained from actinomycete Saccharopolyspora erythraea (formerly known as Streptomyces erythraeus). erythromycin 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 CLOXACILLIN Cloxacillin cloxacillin 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). 3,7-dimethyl-9-(2,6,6-trimethylcyclohex-1-en-1-yl)nona-2,4,6,8-tetraen-1-ol retinol retinol A racemate comprising equimolar amounts of (R)- and (S)-fipronil. Fipronil rac-5-amino-1-[2,6-dichloro-4-(trifluoromethyl)phenyl]-4-[(trifluoromethyl)sulfinyl]-1H-pyrazole-3-carbonitrile 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 pivmecillinam An icosatrienoic acid having three cis double bonds at positions 8, 11 and 14. (8Z,11Z,14Z)-icosa-8,11,14-trienoic acid all-cis-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)-docosa-7,10,13,16,19-pentaenoic acid (7Z,10Z,13Z,16Z,19Z)-docosapentaenoic acid Anidulafungin A semisynthetic echinocandin anti-fungal drug. It is active against Aspergillus and Candida species and is used for the treatment of invasive candidiasis. N-{(2R,6S,9S,11R,12R,14aS,15S,16S,20S,23S,25aS)-23-[(1S,2S)-1,2-dihydroxy-2-(4-hydroxyphenyl)ethyl]-2,11,12,15-tetrahydroxy-6,20-bis[(1R)-1-hydroxyethyl]-16-methyl-5,8,14,19,22,25-hexaoxotetracosahydro-1H-dipyrrolo[2,1-c:2',1'-l][1,4,7,10,13,16]hexaazacyclohenicosin-9-yl}-4''-(pentyloxy)-1,1':4',1''-terphenyl-4-carboxamide anidulafungin 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. 2-[{4-[(7-chloroquinolin-4-yl)amino]pentyl}(ethyl)amino]ethanol hydroxychloroquine An imidazolidine that is N-nitroimidazolidin-2-imine bearing a (6-chloro-3-pyridinyl)methyl substituent at position 1. 1-[(6-chloropyridin-3-yl)methyl]-N-nitroimidazolidin-2-imine Imidacloprid imidacloprid 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. (9E)-hexadec-9-enoic acid palmitelaidic acid A chemical substance is a portion of matter of constant composition, composed of molecular entities of the same type or of different types. chemical substance Micafungin 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 5.1:6-anhydro{(4R,5R)-4,5-dihydroxy-N(2)-(4-{5-[4-(pentyloxy)phenyl]isoxazol-3-yl}benzoyl)-L-ornithyl-L-threonyl-(4R)-4-hydroxy-L-prolyl-(4S)-4-hydroxy-4-[4-hydroxy-3-(sulfooxy)phenyl]-L-threonyl-(3R)-3-hydroxy-L-glutaminyl-(3S,4S)-3-hydroxy-4-methyl-L-proline} micafungin Itraconazole 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. 2-(butan-2-yl)-4-{4-[4-(4-{[(2R,4S)-2-(2,4-dichlorophenyl)-2-(1H-1,2,4-triazol-1-ylmethyl)-1,3-dioxolan-4-yl]methoxy}phenyl)piperazin-1-yl]phenyl}-2,4-dihydro-3H-1,2,4-triazol-3-one Itraconazole itraconazole itraconazole A racemate is an equimolar mixture of a pair of enantiomers. racemate Any straight-chain, C22 fatty acid having four C=C double bonds. docosatetraenoic acid A synthetic galactosylfructose disaccharide used in the treatment of constipation and hepatic encephalopathy. 4-O-beta-D-galactopyranosyl-beta-D-fructofuranose Lactulose lactulose Mefloquine 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. rac--(R)-[2,8-bis(trifluoromethyl)quinolin-4-yl][(2S)-piperidin-2-yl]methanol mefloquine Posaconazole An N-arylpiperazine that consists of piperazine carrying two 4-substituted phenyl groups at positions 1 and 4. A triazole antifungal drug. 2,5-anhydro-1,3,4-trideoxy-2-(2,4-difluorophenyl)-4-({4-[4-(4-{1-[(2S,3S)-2-hydroxypentan-3-yl]-5-oxo-1,5-dihydro-4H-1,2,4-triazol-4-yl}phenyl)piperazin-1-yl]phenoxy}methyl)-1-(1H-1,2,4-triazol-1-yl)-D-threo-pentitol posaconazole posaconazole 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. (4Z,7Z,10Z,13Z,16Z)-docosa-4,7,10,13,16-pentaenoic acid (4Z,7Z,10Z,13Z,16Z)-docosa-4,7,10,13,16-pentaenoic acid 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 malaoxon 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. Malathion rac-diethyl 2-[(dimethoxyphosphorothioyl)thio]succinate malathion A chemosterilant intended to sterilize insects. insect sterilant 1,1'-(2,2,2-trichloroethane-1,1-diyl)bis(4-methoxybenzene) Methoxychlor methoxychlor 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. azole 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. Trichlorfon dimethyl (2,2,2-trichloro-1-hydroxyethyl)phosphonate trichlorfon 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. 2-(2-methyl-5-nitro-1H-imidazol-1-yl)ethanol metronidazole A 20-carbon, polyunsaturated fatty acid having two double bonds at unspecified positions. icosadienoic acid An octadecadienoic acid containing two E (trans) double bonds at positions 9 and 12. (9E,12E)-octadeca-9,12-dienoic acid linoelaidic acid Chlorphoxim Primaquine 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. N(4)-(6-methoxyquinolin-8-yl)pentane-1,4-diamine primaquine Any antifungal agent used to prevent or treat fungal infections in humans or animals. antifungal drug 4-[(1R)-2-(tert-butylamino)-1-hydroxyethyl]-2-(hydroxymethyl)phenol (R)-salbutamol Ranitidine type A member of the class of furans used to treat peptic ulcer disease (PUD) and gastroesophageal reflux disease. (E)-N-{2-[({5-[(dimethylamino)methyl]-2-furyl}methyl)sulfanyl]ethyl}-N'-methyl-2-nitroethene-1,1-diamine ranitidine (5-benzylfuran-3-yl)methyl 2,2-dimethyl-3-(2-methylprop-1-en-1-yl)cyclopropanecarboxylate Resmethrin resmethrin Ketotifen 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. 4-(1-methylpiperidin-4-ylidene)-4,9-dihydro-10H-benzo[4,5]cyclohepta[1,2-b]thiophen-10-one ketotifen The representation of a negative conclusion of a diagnostic process for the COVID-19 coronavirus disease. negative COVID-19 diagnosis 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. cell 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). native cell A cell in vitro that is or has been maintained or propagated as part of a cell culture. cultured cell A leukocyte with abundant granules in the cytoplasm. granulocyte A red blood cell. In mammals, mature erythrocytes are biconcave disks containing hemoglobin whose function is to transport oxygen. erythrocyte 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. macrophage Myeloid mononuclear recirculating leukocyte that can act as a precursor of tissue macrophages, osteoclasts and some populations of tissue dendritic cells. monocyte An achromatic cell of the myeloid or lymphoid lineages capable of ameboid movement, found in blood or other tissue. leukocyte 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. basophil 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. neutrophil A cell that is maintained or propagated in a controlled artificial environment for use in an investigation. cell in vitro 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. diastolic blood pressure Measurement of the structure or forms of the entire body or parts of the body of an organism. body morphological measurement Hemoglobin The amount of hemoglobin in a specific volume of blood, expressed as grams per deciliter of whole blood in humans. blood hemoglobin level White blood cells The number of white blood cells in a specified volume of blood. white blood cell count BMI 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. body mass index (BMI) Fraction of forced vital capacity that is exhaled in a specific number of seconds. forced expiratory volume Respiratory rate The number of breaths taken by an organism per unit of time. respiration rate 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. partial pressure of blood oxygen (Po2) Urine protein urine protein level A disease that involving errors in metabolic processes of building or degradation of molecules. disease of metabolism A bacterial infectious disease has_material_basis_in Bacteria. bacterial sepsis 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. chikungunya A disease that is the consequence of the presence of pathogenic microbial agents, including pathogenic viruses, pathogenic bacteria, fungi, protozoa, multicellular parasites, and aberrant proteins known as prions. disease by infectious agent A 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. cutaneous mycosis A nervous system disease which is located in a part of the nervous system responsible for processing sensory information that consists of sensory receptors, neural pathways, and parts of the brain involved in sensory perception. Commonly recognized sensory systems are those for vision, hearing, somatic sensation (touch), taste and olfaction (smell). sensory system disease A respiratory system disease which involves the lower respiratory tract. lower respiratory tract disease 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. penicilliosis A bacterial infectious disease that results_in infection by bacteria as a result of their presence or activity within the normal, healthy host, and their intrinsic virulence is, in part, a necessary consequence of their need to reproduce and spread. primary bacterial infectious disease Rash A skin disease that is characterized by a rash that results from a variety of causes including bacteria, viruses, toxins, drugs and autoimmune disorders. exanthem A tuberculosis that occurs at body sites other than the lung. extrapulmonary tuberculosis 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. angular cheilitis An intestinal disease characterized by a protrusion of abdominal cavity contests through the inguinal canal. inguinal hernia 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. mastoiditis A tooth disease characterized by a localized collection of pus associated with a tooth. dental abscess A connective tissue disease that affects the structure or development of bone or causes an impairment of normal bone function. bone disease A disease that has_material_basis_in a genetic abnormality, error with embryonic development, infection or compromised intrauterine environment. physical disorder A physical disorder characterized by incomplete closure of the neural tube. neural tube defect 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. sensorineural hearing loss A bone inflammation disease that has_material_basis_in infection located_in bone or located_in bone marrow. osteomyelitis 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. mumps A parotid disease characterized by the inflammation of one or both parotid glands. parotitis A disease by infectious agent that results_in infection, has_material_basis_in Bacteria. bacterial infectious disease 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. tonsillitis 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. common cold Renal failure A kidney disease characterized by the failure of the kidneys to adequately filter waste products from the blood. kidney failure A otitis which involves inflammation of the middle ear. otitis media A mouth disease located_in the salivary gland. salivary gland disease 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. herpangina A mouth disease located_in the teeth. tooth disease 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. sickle cell anemia fetal erythroblastosis 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. meconium aspiration syndrome A lung disease characterized by inadequate gas exchange by the respiratory system. respiratory failure A primary bacterial infectious disease that results in prolonged contraction of skeletal muscle fibers, has_material_basis_in Clostridium tetani, which produces tetanospasmin, a neurotoxin, which is carried to the brain and spinal cord, where it binds irreversibly to receptors inhibiting neurotransmission. Damaged upper motor neurons cannot control reflex responses to afferent sensory stimuli. tetanus 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. pneumocystosis Acute respiratory distress syndrome A respiratory failure that results from diffuse injury to the endothelium of the lung (as in sepsis, chest trauma, massive blood transfusion, aspiration of the gastric contents, or pneumonia) and is characterized by pulmonary edema with an abnormally high amount of protein in the edematous fluid and by difficult rapid breathing and hypoxemia. adult respiratory distress syndrome A 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. bronchial disease 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. protein-energy malnutrition 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. dengue disease neutropenia Marasmus 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. marasmus Malaria 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. malaria 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. dysentery 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 rectal 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. cardiovascular system disease 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. paronychia A cystitis characterized by a sudden onset or severe symptoms. acute cystitis Diarrheal disease 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. 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. typhoid fever A typhus that has_material_basis_in Orientia tsutsugamushi, which is transmitted by trombiculid mites (Leptotrombidium deliense). The infection has symptom fever, has symptom headache, has symptom muscle pain, has symptom cough, has symptom maculopapular rash, has symptom eschar, has symptom splenomegaly and has symptom lymphadenopathy. scrub typhus Kwashiorkor 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. kwashiorkor Schistosomiasis 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. schistosomiasis 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. parasitic infectious disease Cerebral 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. cerebral malaria glossitis A primary bacterial infectious disease that is described as an acute, diarrheal illness caused by infection of the intestine with the bacterium Vibrio cholerae, which is characterized by profuse watery diarrhea, vomiting, leg cramps, circulatory collapse and shock. cholera 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. candidiasis A thoracic disease which may involve inflammation of pleura, collection of air within the pleural cavity, abnormal collection of pleural fluid, abnormal growths on the pleura (pleural tumor) and pleural plaques. The main causes of pleural diseases including pleural effusions are congestive heart failure, malignancy, parapneumonic infections and pulmonary embolism. pleural disease A skin disease characterized by skin rash notable for pale red, raised and itchy bumps, located_in the upper dermis. urticaria A disease by infectious agent that results_in infection, has_material_basis_in Fungi, which pass the resistance barriers of the human or animal body. fungal infectious disease Respiratory condition A disease of anatomical entity that located_in the respiratory system which extends from the nasal sinuses to the diaphragm. respiratory system disease A disease of anatomical entity that is located_in the integumentary system comprising the skin and its appendages. integumentary system disease A lymph node disease that is characterized by an acute or chronic inflammation of one or more lymph nodes. lymphadenitis A pleural disease that is characterized as an abnormal collection of air in the pleural space between the lung and the chest wall. pneumothorax congenital heart disease Musculoskeletal condition A disease of anatomical entity that occurs in the muscular and/or skeletal system. musculoskeletal system disease A disease of anatomical entity that is located_in kidney, ureter, bladder and urethra. urinary system disease A 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. epilepsy A hepatitis that involves viral infection causing inflammation of the liver. viral hepatitis 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. cerebral palsy 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. chronic mucocutaneous candidiasis 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. dental caries carbuncle 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. pharyngitis A primary bacterial infectious disease that involves systemic infection, has_material_basis_in Leptospira, which is transmitted by contact with water, food, or soil containing urine from the infected animals. The infection has symptom jaundice, has symptom chills, has symptom fever, has symptom muscle pain, and has symptom hepatomegaly. leptospirosis A gastrointestinal system infectious disease that involves inflammation of the lining of the stomach and small and large intestines, which is caused by viruses, bacteria, or parasites. Chemicals and drugs also cause gastroenteritis. The symptoms include diarrhea, loss of appetite, nausea, vomiting, cramps, and discomfort in the abdomen. gastroenteritis Anemia A hematopoietic system disease that is characterized by a decrease in the normal number of red blood cells. anemia 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. opportunistic mycosis A skin disease characterized by itchy, erythematous, vesicular, weeping and crusting patches of skin. dermatitis A sensory system disease that is characterized by auditory dysfunction located_in the auditory system. auditory system disease A parasitic infectious disease that is caused by parasitic protozoa which are microorganisms classified as unicellular eukaryotes. parasitic protozoa infectious disease Endocrine condition A disease of anatomical entity that is located_in endocrine glands which secretes a type of hormone directly into the bloodstream to regulate the body. endocrine system disease A 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. asthma A disease of anatomical entity that is located_in the immune system. immune system disease 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. bronchiolitis A tuberculosis that is a contagious disease located_in lungs. The infection has_symptom fever, has_symptom cough, has_symptom difficulty in breathing, has_symptom inflammatory infiltrations, has_symptom formation of tubercles, has_symptom caseation, has_symptom pleural effusion, and has_symptom fibrosis. pulmonary tuberculosis gingivitis A rectal disease located_in the anus. anus disease A nervous system disease that affects either the spinal cord (myelopathy) or brain (encephalopathy) of the central nervous system. central nervous system disease A bone disease that results_in inflammation of the located_in bone. bone inflammation disease A mouth disease that is relating to or affecting the structures surrounding and supporting the teeth. periodontal disease 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. cellulitis Skin condition An integumentary system disease that is located_in skin. skin disease 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. pleural empyema Tuberculosis A primary bacterial infectious disease that is located_in lungs, located_in lymph nodes, located_in pericardium, located_in brain, located_in pleura or located_in gastrointestinal tract, has_material_basis_in Mycobacterium tuberculosis, which is transmitted_by droplets released into the air when an infected person coughs or sneezes. tuberculosis Disease A disease is a disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism. disease A gastrointestinal system disease that is located_in the mouth. mouth disease liver disease An integumentary system disease that is located_in nail. nail disease A dermatitis that is characterized by a pyogenic infection causing the formation of pus. pyoderma 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. tinea capitis folliculitis 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. allergic rhinitis Runny nose or nasal congestion 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. rhinitis A pancreas disease that is characterized by inflammation of the pancreas. pancreatitis middle ear disease A nutrition disease that is characterized by deficiency of a nutritional element, such as a vitamin, mineral, carbohydrate, protein, fat, or general energy content. nutritional deficiency disease HIV 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. intestinal disease A tooth disease located_in dental pulp. dental pulp disease A lung disease that involves lung parenchyma or alveolar inflammation and abnormal alveolar filling with fluid (consolidation and exudation). It results from a variety of causes including infection with bacteria, viruses, fungi or parasites, and chemical or physical injury to the lungs. It is accompanied by fever, chills, cough, and difficulty in breathing. pneumonia An eye and adnexa disease that is located_in the eye. eye disease 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. bronchitis A conjunctival disease characterized by an inflammation of the conjunctiva, the outermost layer of the eye and the inner surface of the eyelids. conjunctivitis An arthritis that is an autoimmune disease which develops due to an infection located elsewhere in the body. reactive arthritis A disease that has_material_basis_in genetic variations in the human genome. genetic disease AIDS 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. acquired immunodeficiency syndrome A musculoskeletal system disease that affects tissues such as skin, tendons, and cartilage. connective tissue disease 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. inherited metabolic disorder A disease that manifests in a defined anatomical structure. disease of anatomical entity A disease of anatomical entity that has_material_basis_in hematopoietic cells. hematopoietic system disease An immune system disease that is located_in the lymphatic system. lymphatic system disease peptic ulcer disease A disease of anatomical entity that is located_in the gastrointestinal tract. gastrointestinal system disease An arthritis that involves infection by a pathogen located_in joint. septic arthritis periodontitis 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. scabies A bone marrow disease characterized by an increased number of red blood cells in the bloodstream resulting in thicker blood and reduced blood flow. polycythemia A bone inflammation disease that involves a response to irritation or injury, characterized by joint pain, swelling, stiffness located_in joint. arthritis A lower respiratory tract disease in which the function of the lungs is adversely affected by narrowing or blockage of the airways resulting in poor air flow, a loss of elasticity in the lungs that produces a decrease in the total volume of air that the lungs are able to hold, and clotting, scarring, or inflammation of the blood vessels that affect the ability of the lungs to take up oxygen and to release carbon dioxide. lung disease A 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. impetigo A pemphigoid that is characterized by large blisters. bullous pemphigoid 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. herpes zoster 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. herpes simplex 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. measles Neurological condition A disease of anatomical entity that is located_in the central nervous system or located_in the peripheral nervous system. nervous system disease 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. chickenpox viral exanthem perinatal necrotizing enterocolitis pyomyositis 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). leishmaniasis A leishmaniasis that involves skin infection caused by Leishmania species, resulting in one or more cutaneous lesions. cutaneous leishmaniasis 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. visceral leishmaniasis 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. amebiasis A mouth disease located_in the lip. lip disease rectal prolapse A disease by infectious agent that results in infection, has_material_basis_in Viruses. viral infectious disease A central nervous system disease that is located_in the brain. brain disease keratoconjunctivitis An external ear disease that involves inflammation of the outer ear and ear canal. It can be caused by active bacterial or fungal infections. otitis externa A central nervous system disease that is characterized by an inflammation of the pia-arachnoid meninges. It can be caused by growth of bacteria, fungi, or parasites within the subarachnoid space or by the growth of bacteria or viruses within the meningeal or ependymal cells. meningitis A stomatitis characterized by the repeated formation of benign and non-contagious mouth ulcers. aphthous stomatitis A bacterial conjuctivitis that is characterized by pain and tenderness in the eyeball and conjuctival discharge. ophthalmia neonatorum bacterial conjunctivitis A respiratory system disease which involves the upper respiratory tract. upper respiratory tract disease An eyelid disease that is characterized by an infection of the sebaceous glands at the base of the eyelashes. Styes are generally caused by a Staphylococcus aureus bacterial infection. hordeolum Hypoglycemia A glucose metabolism disease that is characterized by abnormally low levels of blood glucose. hypoglycemia 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 syrup amoxicillin suspension Folic acid tablet Folic acid tablet Clotrimazole cream Clotrimazole skin cream Nystatin suspension Nystatin oral drop Nystatin suspension Gentamicin solution Gentamicin injection Gentamicin injectable solution Dexamethasone injection Dexamethasone injection Chloramphenicol eye drops Chloramphenicol eye/ear drop Chloramphenicol solution for otic and ophthalmic administration Ceftriaxone injection Ceftriaxone injectable solution Metronidazole syrup Metronidazole solution Prednisolone tablet prednisolone tablet Salbutamol syrup salbutamol syrup salbutamol suspension Dornase Dornase Alfa Norsol nasal drops Sodium Chloride Nasal Solution Paracetamol syrup Acetaminophen Oral Solution Ceevit Ascorbic Acid Oral Tablet Ibruprofen syrup Ibuprofen Oral Suspension Ambrox drops Ambroxol Oral Solution Azithromycin syrup Azithromycin Oral Suspension Cefixime suspension Cefixime Oral Suspension Cetirizine alatrol Cetirizine Oral Solution Chloroquine Injectable Solution Chloroquine Oral Tablet Chlorpheniramine maleate syrup Chlorpheniramine Oral Solution Ciprofloxacin syrup Ciprofloxacin Oral Suspension Clotrimazole ear drops Clotrimazole Topical Solution Diazepam tablet Diazepam Oral Tablet Dicycloverine hydrochloride Dicyclomine Oral Solution Omidon syrup Domperidone Oral Solution Glycerine suppository Glycerin Rectal Suppository Hydroxyzine hydrochloride syrup Hydroxyzine Oral Solution Mebendazole syrup Mebendazole Oral Suspension Naproxen syrup Naproxen Oral Suspension Nitrazepam tablet Nitrazepam Oral Tablet Ondansetron syrup Ondansetron Oral Solution Oxicone Oxycodone Oral Tablet Konakion injection (vitamin K) Vitamin K 1 Injectable Solution Potassium syrup (Electro K) Potassium Chloride Oral Solution Riboflavin tablet Riboflavin Oral Tablet Flacol drops Simethicone Oral Solution Theophylline Theophylline Oral Solution Povidone ointment Povidone Topical Solution Xylometazoline drop xylometazoline Nasal Solution Tobramycin eye drops Tobramycin Ophthalmic Solution Ketoconazole shampoo Ketoconazole Medicated Shampoo Betson cream Betamethasone Topical Cream Calamine lotion Calamine Topical Lotion Miconazole Topical Cream Permethrin cream Permethrin Topical Cream Silver sulfadiazine (Burnsil) Silver Sulfadiazine Topical Cream Lactulose syrup Lactulose Oral Solution Amlexanox (Apsol gel) amlexanox Oral Paste Montelukast montelukast Oral Tablet Nitazoxanide syrup nitazoxanide Oral Solution Ranitidine syrup Ranitidine Oral Solution Miconazole oral gel Miconazole Oral Gel Tetrasol Tetracycline Topical Lotion Moxifloxacin eye drops moxifloxacin Ophthalmic Solution artesunate Injectable Solution Gentin ointment Gentamicin Sulfate (USP) / Hydrocortisone Topical Ointment Erythromycin syrup Erythromycin Oral Solution Desloratadine syrup desloratadine Oral Solution Moxclav syrup Amoxicillin / Clavulanate Oral Solution Mefenamic acid Mefenamate Oral Suspension Fexofenadine fexofenadine Oral Suspension Flucloxacillin syrup Floxacillin Oral Solution Acyclovir syrup Acyclovir Oral Solution Fluconazole syrup Fluconazole Oral Solution Aquaphen syrup Guaifenesin / Pseudoephedrine / Triprolidine Oral Solution Cotrimoxazole syrup Sulfamethoxazole / Trimethoprim Oral Solution artemether / lumefantrine Oral Tablet Cipro ear drops Ciprofloxacin Otic Solution Benzoate / Salicylic Acid Topical Cream Baby zinc tablet Zinc Sulfate 20 MG Oral Tablet Gentamicin ear drops Gentamicin Otic Solution Data access level 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. consent code data use permission Pyrethroid insecticide exposure An exposure to pyrethroid insecticide. exposure to pyrethroid insecticide administrative region A primary administrative division of a country, such as a state in the United States. first-order administrative region A subdivision of a first-order administrative division. second-order administrative region A subdivision of a second-order administrative division. third-order administrative region A subdivision of a third-order administrative division. fourth-order administrative region Country A political association with effective dominion over a geographic area. national geopolitical entity 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. canal A large expanse of saline water usually connected with an ocean. sea A body of water or other liquid of considerable size contained in a depression on a landmass. lake 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." river A watercourse which is linear and flows across the solid portion of a planetary surface. stream An artificial body of water, often contained by a dam, constructed for the purpose of water storage. reservoir 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. spring A flowing body of water. watercourse A body of water, usually of smaller size than a lake. pond A wetland ecosystem which includes communities of grasses, rushes, reeds, typhas, sedges, and other herbaceous plants (possibly with low-growing woody plants). marsh A spring through which groundwater, heated by geothermal energy, flows. hot spring A pond or lake used for the artificial culture of fish. fishpond Place or area with clustered or scattered buildings and a permanent human population. populated place 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. water body Naturally formed, subterranean open area or chamber. cave A construction that has been assembled by deliberate human effort. human construction A permanent walled and roofed construction. building An area of land which is used for the cultivation of crops or grazing of livestock, including any agricultural constructions therein. farm A landform that extends above the surrounding terrain in a limited area. mountain Area of dry or relatively dry land surrounded by water or low wetland. island An area with a high density of trees. A small forest may be called a wood. forested area Elevation A landform elevated above the surrounding area. elevated landform An elevated and comparatively level expanse of land. plateau 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. swamp ecosystem A paddy field for the cultivation of rice. rice field A speleothem projecting vertically upwards from a cave floor and formed by precipitation from drips. stalagmite A lake purposefully constructed. artificial lake Environment (biome) A biome is an ecosystem to which resident ecological communities have evolved adaptations. biome A reservoir constructed for the purpose of providing drinking water. drinking water reservoir 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. shoreline Bed The portion of the ground surface which lies below water. submerged bed City, village, or region Incorporated populated place. city 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. rock 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 soil 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. marine water body Water that has been adversely affected in quality by anthropogenic influence. waste water 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. fecal material An environmental material primarily composed of dihydrogen oxide in its liquid form. liquid water 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. sediment Particulate environmental material with diameters less than 500 micrometers. Dust occurs in and may be deposited from the atmosphere. dust 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. saline water 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. fresh water Wastewater that is contaminated with feces or urine, sewage A complex aggregation of microorganisms marked by the excretion of a protective and adhesive matrix; usually adhering to a substratum. biofilm wood Water that is found on the surface of an astronomical object. surface water wastewater treatment plant The residual semi-solid material left from domestic or industrial processes, or wastewater treatment processes. sludge beach sand Manure which has been derived from the aerobically decomposed remnants of organic materials. compost pond water A portion of soil which is found in a forested area. forest soil 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). waste material 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. hay Drinking water source Drinking water is water which may be consumed by humans with no adverse effects on their health. drinking water A material entity that has been processed by humans or their technology in any way, including intermediate products as well as final products. manufactured product tap water bore hole water A portion of soil which is part of a cropland or a rangeland biome. farm soil A portion of soil which is found in a grassland. grassland soil Soil in which trees from an orchard grow. orchard soil Soil which is found in a pasture and in which vegetation, such as the grass used for the grazing of ungulates, grows. pasture soil The narrow region of soil that is directly influenced by root secretions and associated soil microorganisms. rhizosphere Environment (material) 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. environmental material 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. surface layer Airborne solid particles (also called dust or particulate matter (PM)) or liquid droplets. Should connect to PATO as "quality of an aerosol" aerosol Anthropogenic material in or on which organisms may live. anthropogenic environmental material 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. agricultural environmental material An environmental material which is a liquid or semi-liquid mixture of water and some combination of soil, silt, and clay particles. mud A well which provides access to groundwater held in an aquifer. water well 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. sand Environmental material derived from living organisms and composed primarily of one or more biomacromolecules. organic material A system which has the disposition to environ one or more material entities. environmental system A layer is a quantity of some material which is spatially continuous, has comparable thickness, and usually covers some surface. Preliminary definition. layer 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. environmental zone 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. building part 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. room 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. concrete 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. masonry cement An exterior wall is a building wall which separates the interior of a building from the buildings surrounding environment. exterior wall 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. building roof 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. thatch 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. brick A thatched building roof is a building roof that is built by thatching (or out of thatch). thatched building roof 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. tile 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. toilet fixture 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 pit latrine A toilet fixture which uses water to flush liquid and solid excreta into a sewage containment or processing facility through a drainpipe. flush toilet fixture 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. ventilated improved pit latrine A covered pit latrine is a building which comprises a pit latrine sheltered by an outhouse. covered pit latrine A covered pit latrine with slab is a building which comprises a pit latrine with a slab floor sheltered by an outhouse. covered pit latrine with slab floor 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 Radio A device capable of receiving and/or transmitting information encoded in electromagnetic radiation through wave modulation. radio device Cassette player A cassette deck is a device capable of playing and recording audio compact cassettes. cassette player Television 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 Telephone (mobile or non-mobile) 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 Mobile phone A mobile phone is a telephone which transmits sound information to a mobile phone network via radio transmissions. mobile phone Landline phone A landline telephone is a telephone which is connected to a telephone network with wires through which electronic signals are carried. landline telephone Refrigerator 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 Table A table is a form of furniture with a flat horizontal upper surface used to support objects, for storage, show, and/or manipulation. table Chair 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 Sofa A sofa is a bench which is partially or entirely upholstered, and often fitted with springs and tailored cushions. sofa Cabinet A cabinet is a roughly cuboidal piece of furniture which is used to store miscellaneous items in compartments accessible through doors or drawers. cabinet Cupboard 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 Clock 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. Subclasses will be added by inference. 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 Bicycle A bicycle is a human-powered, pedal-driven, single-track vehicle, having two wheels attached to a frame, one behind the other. bicycle Motorcycle or scooter 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 A landmass which is part of a planet. planetary landmass Habitat 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 Dwelling type 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 Village 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 Eaves 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 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 Weather 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 Garbage disposal 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. 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. excreta material 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 Building material A material entity used to build a dwelling or part of a dwelling. Person: Jie Zheng, Chris Stoeckert PRISM Penn Group 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. Person: Jie Zheng, Chris Stoeckert PRISM Penn Group http://en.wikipedia.org/wiki/Dwelling obsolete dwelling true Roof material A building material used in the construction of a roof. Person: Jie Zheng, Chris Stoeckert PRISM Penn Group roof material obsolete roof true Floor material A building material used in the construction of a floor Person: Jie Zheng, Chris Stoeckert PRISM Penn Group floor material Wall material A building material used in the construction of a wall. Person: Jie Zheng, Chris Stoeckert PRISM Penn Group 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. http://www.thefreedictionary.com/brick obsolete wall brick true was ICEMR PRISM household, no longer used obsolete traditional house true was ICEMR household, no longer used obsolete modern house true Household wealth index, numerical 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. Person: Jie Zheng, Chris Stoeckert PRISM Penn Group http://dhsprogram.com/topics/Wealth-Index.cfm 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. Person: Jie Zheng, Chris Stoeckert PRISM Penn Group http://en.wikipedia.org/wiki/Eaves obsolete eaves true was ICEMR PRISM, no longer used obsolete open eaves true was ICEMR PRISM household, no longer used obsolete closed eaves true Air bricks A brick with holes which is embedded in a wall to allow ventilation through it. Person: Jie Zheng, Chris Stoeckert PRISM Penn Group http://en.wiktionary.org/wiki/air_brick air brick Persons living in house count A scalar measurements datum of resident in a dwelling. Person: Jie Zheng, Chris Stoeckert PRISM Penn Group number of residents in a dwelling An information content entity to indicate whether a household has electricity in a dwelling. Person: Jie Zheng, Chris Stoeckert PRISM Penn Group obsolete household having electricity information true Cooking fuel A material entity that consists of fuel mainly used for cooking. Person: Jie Zheng, Chris Stoeckert PRISM Penn Group cooking fuel material A material entity that consists of an energy source for lighting. Person: Jie Zheng, Chris Stoeckert PRISM Penn Group obsolete lighting material true Sleeping rooms in dwelling count number of rooms in a dwelling that are used for sleeping. Person: Jie Zheng, Chris Stoeckert number of bedrooms in a dwelling PRISM Penn Group number of rooms for sleeping in a dwelling Acres A scalar measurement datum of land such as land owned by a household. Person: Jie Zheng, Chris Stoeckert PRISM Penn Group Person: Chris Stoeckert land area measurement datum Meals per day A scalar measurement datum of meals per day in a household Person: Jie Zheng, Chris Stoeckert PRISM Penn Group number of meals per day Meat meals per week A scalar measurement datum of days eating meat in a week in a household Person: Jie Zheng, Chris Stoeckert PRISM Penn Group number of days per week eating meat Food problems per week A categorical measurement datum that specifies how frequently the food needs of a household were not met. Person: Jie Zheng, Chris Stoeckert PRISM Penn Group frequency of not satisfying food needs A length measurement datum of the distance from a dwelling to the nearest health facility. Person: Jie Zheng, Chris Stoeckert Penn Group Person: Chris Stoeckert obsolete distance to health facility true ICEMR protein array obsolete date of birth true G6PD genotype A genotype information which is about the presence of certain genetic variants of glucose-6-phosphate dehydrogenase. Person: Jie Zheng, Chris Stoeckert PRISM Penn Group glucose 6 phosphate dehydrogenase genotype Alpha-thalassemia 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. Person: Jie Zheng, Chris Stoeckert PRISM Penn Group alpha thalassemia genotype HbS 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. Person: Jie Zheng, Chris Stoeckert PRISM Penn Group sickle hemoglobin genotype Malaria-related diagnosis A diagnosis that is an assertion that a patient has a parasitic infectious disease. Person: John Judkins VEuPathDB 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 http://en.wikipedia.org/wiki/Bacteremia obsolete presence of bacteria in the blood true A diagnosis of malaria without evidence of complicated malaria. Person: Jie Zheng, Chris Stoeckert, Grant Dorsey Grant Dorsey PRISM obsolete diagnosis of uncomplicated malaria true 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 http://en.wikipedia.org/wiki/Viremia obsolete presence of virus in the blood true Complicated malaria 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. Person: Jie Zheng, Chris Stoeckert, Grant Dorsey Grant Dorsey diagnosis of complicated malaria was ICEMR PRISM observation, no longer used obsolete diagnosis of complicated malaria with high parasite density true 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. Person: Jie Zheng, Chris Stoeckert, Grant Dorsey Grant Dorsey PRISM obsolete diagnoses of complicated malaria with danger signs true Severe malaria 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. Person: Jie Zheng, Chris Stoeckert, Grant Dorsey Grant Dorsey 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. Person: John Judkins Centers for Disease Control and Prevention obsolete severe malaria true Symptom or sign information that is used for the diagnosis of severe malaria based on World Health Organization (WHO) criteria. Person: Jie Zheng, Chris Stoeckert PRISM Penn Group severe malaria symptom or sign information A scalar measurement datum about the level of hemoglobin in the blood. Person: Jie Zheng, Chris Stoeckert ICEMR protein array PRISM Penn Group obsolete hemoglobin level true 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. Person: Jie Zheng, Chris Stoeckert asexual parasites present by microscopy ICEMR protein array PRISM Penn Group blood smear reading as positive or negative A planned process in which a patient is seen by a medical practitioner. Person: Jie Zheng, Chris Stoeckert PRISM Penn Group obsolete clinical visit true A clinical visit that is primarily for a regular examination. Person: Jie Zheng, Chris Stoeckert PRISM Penn Group obsolete routine clinical visit true a human being who bears a participant under investigation role Person: John Judkins human study subject EuPathDB human participant under investigation A material entity whichis part of a dwelling for providing fresh air to the dwelling. PRISM obsolete dwelling ventilation true Sub-county in Uganda A fourth-order administrative region of Uganda. Person: Jie Zheng, Chris Stoeckert PRISM VEuPathDB subcounty of Uganda was ICEMR PRISM, no longer used obsolete CDC light trap assay true 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. Person: Jie Zheng, Chris Stoeckert Penn Group obsolete medication role true blood used in transfusion for replacement blood lost during surgery or due to a serious injury. quinine used in malaria medication A material entity that is bearer of a medication role. Person: Jie Zheng, Chris Stoeckert Penn Group obsolete medication material true Antimalarial medication A medication material intended to prevent or treat malaria. Person: Jie Zheng, Chris Stoeckert Penn Group malaria medication Non-malaria medication A medication material intended to prevent or treat a disease other than malaria. Person: Jie Zheng, Chris Stoeckert Penn Group non-malaria medication A drug product that has the chemical ingredient quinine and has antipyretic (fever-reducing), antimalarial, analgesic (painkilling), and anti-inflammatory properties. Person: Jie Zheng, Chris Stoeckert quinine PRISM obsolete quinine drug product true 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. Person: Jie Zheng, Chris Stoeckert artemether-lumefantrine coartem PRISM http://en.wikipedia.org/wiki/Artemether/lumefantrine obsolete artemether-lumefantrine drug product true A dependent continuant which is either disease or phenotypic abnormality. obsolete clinical characteristics true An information content entity is about household. Person: Jie Zheng, Chris Stoeckert PRISM Penn Group household information A diagnosis of uncomplicated malaria that occurs with the first trimester of pregnancy. Person: Jie Zheng, Chris Stoeckert PRISM Penn Group obsolete diagnosis of uncomplicated malaria in the 1st trimester of pregnancy true A diagnosis based on presence of asexual parasites by microscopy in the absence of subjective fever or documented elevated temperature Person: Jie Zheng, Chris Stoeckert, Grant Dorsey PRISM Penn Group obsolete diagnosis of asymptomatic microscopic parasitemia true Malaria diagnosis A diagnosis of malaria based on positive blood smear with subjective fever or elevated temperature resulting in antimalarial treatment. Person: Jie Zheng, Chris Stoeckert, Grant Dorsey Penn Group diagnosis of symptomatic malaria Visit date A time measurement datum that specifies the date of a clinical visit. Person: Jie Zheng, Chris Stoeckert PRISM Penn Group 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 PRISM Penn Group asexual parasite density by microscope An information content entity about dwelling. Person: Jie Zheng, Chris Stoeckert PRISM Penn Group obsolete dwelling information true Household ID A symbol that denotes a specific household. Person: Jie Zheng, Chris Stoeckert PRISM Penn Group household identifier Participant ID A symbol that denotes a specific human participant under investigation. Person: Jie Zheng, Chris Stoeckert ICEMR protein array PRISM Penn Group human study subject identifier Participant An information content entity which is about features of a human participant under investigation. Person: Jie Zheng, Chris Stoeckert PRISM Penn Group study participant information Febrile elevated temperature or subjective fever Person: Jie Zheng, Chris Stoeckert ICEMR protein array PRISM Penn Group febrile A function to provide fresh air to a closed space. obsolete ventilation function true 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. Person: Jie Zheng, Chris Stoeckert PRISM Penn Group obsolete dwelling facility true Subjective fever A phenotypic abnormality of a subjective fever as reported by the study participant or their parent/guardian Person: Jie Zheng, Chris Stoeckert, Grant Dorsey Grant Dorsey PRISM subjective fever a febrile quality of an abnormally high temperature Person: John Judkins EuPathDB obsolete elevated temperature true A scalar measurement datum that is about temperature. obsolete temperature measurement datum true was in ICEMR, no longer used A ventilation function to provide fresh air to a dwelling. obsolete dwelling ventilation function true an organism that is the bearer of a partipant under investigation role Person: John Judkins study subject EuPathDB 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. Person: Jie Zheng, Chris Stoeckert Penn Group yes 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. Person: Jie Zheng, Chris Stoeckert Penn Group yes 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. Person: Jie Zheng, Chris Stoeckert Penn Group yes 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. Person: Jie Zheng, Chris Stoeckert Penn Group yes 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. yes obsolete dwelling facility role true A temperature measurement datum that is about an organism. Person: Jie Zheng, Chris Stoeckert PRISM Penn Group obsolete organismal body temperature measurement datum true 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. http://www.thefreedictionary.com/brick obsolete floor brick true An age since birth measurement datum at the time of a clinical visit. Person: Jie Zheng, Chris Stoeckert, Shon cade, Grant Dorsey ICEMR protein array PRISM Penn Group obsolete age since birth at time of visit true 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. Person: Jie Zheng, Chris Stoeckert, Shon cade, Grant Dorsey PRISM Penn Group 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. Person: Jie Zheng, Chris Stoeckert, Shon cade, Grant Dorsey PRISM Penn Group 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). Person: Jie Zheng, Chris Stoeckert, Shon cade, Grant Dorsey PRISM Penn Group 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. Person: Jie Zheng, Chris Stoeckert, Shon cade, Grant Dorsey PRISM Penn Group 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). Person: Jie Zheng, Chris Stoeckert, Shon cade, Grant Dorsey PRISM Penn Group 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. Person: Jie Zheng, Chris Stoeckert, Shon cade, Grant Dorsey PRISM Penn Group average percent of female Anopheles with Plasmodium sporozoites An age since birth measurement datum at the time of subject enrollment. Person: Jie Zheng PRISM Penn Group obsolete age since birth at time of enrollment true Total antenatal care visits A data item of the total number of clinical visits by a participant in an investigation. Person: Jie Zheng, Chris Stoeckert, Shon cade, Grant Dorsey PRISM Penn Group number of clinical visits A data item of the number of clinical visits during which the participant was diagnosed with malaria Person: Jie Zheng, Chris Stoeckert, Shon cade, Grant Dorsey PRISM Penn Group 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. Person: Jie Zheng, Chris Stoeckert, Shon cade, Grant Dorsey PRISM Penn Group 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. Person: Jie Zheng, Chris Stoeckert, Shon cade, Grant Dorsey PRISM Penn Group obsolete number of non-routine clinical visits true A data item of the total number of clinical visits which were not sheduled routine visits. Person: Jie Zheng, Chris Stoeckert, Shon cade, Grant Dorsey PRISM Penn Group obsolete number of routine clinical visits true An information content entity that is about the type of sample/specimen collected during a clinical visit. Person: Jie Zheng, Chris Stoeckert PRISM obsolete sample available information true A blood specimen that is located on a filter paper. Chris Stoeckert Jie Zheng Filter paper sample Penn Group obsolete blood specimen on filter paper true 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. Person: Jie Zheng, Chris Stoeckert PBMC specimen http://en.wikipedia.org/wiki/Peripheral_blood_mononuclear_cell peripheral blood mononuclear cell specimen A processed specimen consisting of red blood cells isolated from whole blood by centrifugation. Person: Jie Zheng, Chris Stoeckert RBC specimen erythrocyte specimen http://www.ruf.rice.edu/~bioslabs/studies/sds-page/gellab1.html obsolete red blood cell specimen true 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. Person: Jie Zheng, Chris Stoeckert, Shon cade, Grant Dorsey PRISM Penn Group obsolete average number of Plasmodium parasite-positive female Anopheles true 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. Person: Jie Zheng, Chris Stoeckert, Shon cade, Grant Dorsey PRISM Penn Group obsolete average number of female Anopheles tested for Plasmodium parasite true An average percentage value for female Anopheles mosquitoes carrying Plasmodium parasites in all female mosquitoes tested for carrying Plasmodium parasites across multiple collections. Person: Jie Zheng, Chris Stoeckert, Shon cade, Grant Dorsey PRISM Penn Group obsolete average percent of Plasmodium parasite-positive female Anopheles true A count of Anopheles mosquitoes collections performed (e.g. from a given household) in a given period. Person: Jie Zheng, Chris Stoeckert, Shon cade, Grant Dorsey PRISM Penn Group number of Anopheles collections Female Anopheles count A sum value for all species of female Anopheles mosquitoes in a given collections. Person: Jie Zheng, Chris Stoeckert, Shon cade, Grant Dorsey PRISM Penn Group sum number of female Anopheles in a collection Female Anopheles funestus count A sum value for all female Anopheles funestus mosquitoes in a given collections. Person: Jie Zheng, Chris Stoeckert, Shon cade, Grant Dorsey PRISM Penn Group sum number of female Anopheles funestus in a collection Female Anopheles gambiae count A sum value for all female Anopheles gambiae mosquitoes in a given collections. Person: Jie Zheng, Chris Stoeckert, Shon cade, Grant Dorsey PRISM Penn Group sum number of female Anopheles gambiae in a collection Observation period A time datum for the duration of a patients participation in an investigation. Person: Jie Zheng, Chris Stoeckert, Shon cade, Grant Dorsey PRISM Penn Group duration of observation of study participant An average value for the number of clinical visits of a patient based on calendar years Person: Jie Zheng, Chris Stoeckert, Shon cade, Grant Dorsey PRISM Penn Group 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. Person: Jie Zheng, Chris Stoeckert, Shon cade, Grant Dorsey PRISM Penn Group 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 Person: Jie Zheng, Chris Stoeckert, Shon cade, Grant Dorsey PRISM Penn Group 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. Person: Jie Zheng PRISM Penn Group obsolete routine clinical visit date true Household wealth index, categorical 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 PRISM http://dhsprogram.com/topics/Wealth-Index.cfm categorical household wealth index Assets An information content entity about items that a household owns such as a car, funiture, etc. Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey PRISM Penn Group 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. Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey PRISM Penn Group obsolete antimalarial therapy given outside the study since last seen information true An information content entity indicating the cause of death for a participant in the study. Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey PRISM Penn Group obsolete cause of participant death true A clinical visit occuring because of a sickness. Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey PRISM Penn Group obsolete clinical visit when sick true A covered pit latrine that does not have a latrine slab. Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey PRISM Penn Group obsolete covered pit latrine without slab true Death date A time measurement datum specifying the date of death Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey PRISM Penn Group date of death Enrollment date A time measurement datum that specified the date of participant first enrolled in a study Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey PRISM Penn Group date of participant first enrolled in a study Last date observed A time measurement datum that specified the date of participant last seen in a study Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey PRISM Penn Group 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. Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey PRISM Penn Group obsolete days since a clinical visit with a malaria diagnosis true Abdominal pain duration A time measurement datum that measures the duration of having abdominal pain. Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey PRISM Penn Group duration of abdominal pain Anorexia duration A time measurement datum that measures the duration of having anorexia. Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey PRISM Penn Group duration of anorexia Cough duration A time measurement datum that measures the duration of having a cough. Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey PRISM Penn Group duration of cough Diarrhea duration A time measurement datum that measures the duration of having diarrhea. Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey PRISM Penn Group duration of diarrhea Fatigue duration A time measurement datum that measures the duration of having fatigue. Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey PRISM Penn Group duration of fatigue Headache duration A time measurement datum that measures the duration of having a headache. Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey PRISM Penn Group duration of headache Jaundice duration A time measurement datum that measures the duration of having jaundice. Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey PRISM Penn Group duration of jaundice Joint pains duration A time measurement datum that measures the duration of having joint pains. Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey PRISM Penn Group duration of joint pains Muscle aches duration A time measurement datum that measures the duration of having muscle aches. Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey PRISM Penn Group duration of muscle aches Seizures duration A time measurement datum that measures the duration of having seizures. Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey PRISM Penn Group duration of seizures Subjective fever duration A time measurement datum that measures the duration of having subjective fever. Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey PRISM Penn Group duration of subjective fever Vomiting duration A time measurement datum that measures the duration of having vomiting. Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey PRISM Penn Group duration of vomiting Animal-drawn cart 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 PRISM Penn Group indicator of household having animal-drawn cart Bank account A household asset information indicating whether a member of a household has a bank account. Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey, John Judkins PRISM Penn Group indicator of household having bank account A household asset information indicating whether a household has a bed. Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey PRISM Penn Group obsolete household bed asset true A household asset information indicating whether a member of a household has or owns a bicycle. Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey PRISM Penn Group obsolete household bicycle asset true Boat without a motor A household asset information indicating whether a member of a household has or owns a boat without a motor. Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey, John Judkins PRISM Penn Group indicator of household having boat without a motor Car or truck A household asset information indicating whether a member of a household has or owns a car or truck. Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey, John Judkins PRISM Penn Group indicator of household having car A household asset information indicating whether a household has a cassette player. Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey PRISM Penn Group obsolete household cassette player asset true A household asset information indicating whether a household has a chair. Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey PRISM Penn Group obsolete household chair asset true A household asset information indicating whether a household has a clock. Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey PRISM Penn Group obsolete household clock asset true A household asset information indicating whether a household has a cupboard. Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey PRISM Penn Group obsolete household cupboard asset true A household asset information indicating whether a household has electricity in their dwelling. Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey PRISM Penn Group obsolete household electricity asset true A household asset information indicating whether a household has a land line or fixed location phone. Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey PRISM Penn Group obsolete household fixed phone asset true A household asset information indicating whether a household has a mobile phone. Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey PRISM Penn Group obsolete household mobile phone asset true Boat with a motor A household asset information indicating whether a member of a household has or owns a boat with a motor. Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey, John Judkins PRISM Penn Group indicator of household having motorboat A household asset information indicating whether a member of a household has or owns a motorcycle or motor scooter. Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey PRISM Penn Group obsolete household motorcycle or scooter asset true A household asset information indicating whether a household has a radio. Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey PRISM Penn Group obsolete household radio asset true A household asset information indicating whether a household has a refrigerator. Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey PRISM Penn Group obsolete household refrigerator asset true A household asset information indicating whether a household has a sofa. Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey PRISM Penn Group obsolete household sofa asset true A household asset information indicating whether a household has a table. Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey PRISM Penn Group obsolete household table asset true A household asset information indicating whether a household has a television. Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey PRISM Penn Group obsolete household television asset true Watch A household asset information indicating whether a member of a household has or owns a watch. Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey, John Judkins PRISM Penn Group indicator of household having watch An information content entity indicating whether a malaria episode occurred Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey PRISM Penn Group obsolete incident of malaria episode information true A material entity where a clinical visit took place. Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey PRISM Penn Group obsolete location of clinical visit true A material entity where a death occurred. Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey PRISM Penn Group obsolete location of death true An information content entity indicating whether medical care occurred outside the study clinic since last seen as part of the study. Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey PRISM Penn Group obsolete medical care outside the study clinic since last seen information true Time since enrollment A time measurement datum of the interval from participant enrollment in a study until the current visit. Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey, John Judkins PRISM Penn Group duration of study participation from enrollment to current visit Bloodfed Anopheles funestus count A measurement datum of the number of female Anopheles funestus with a recent blood meal in a given collection Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey PRISM Penn Group number of fed female Anopheles funestus in a collection Bloodfed Anopheles gambiae count A measurement datum of the number of female Anopheles gambiae with a recent blood meal in a given collection Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey PRISM Penn Group number of fed female Anopheles gambiae in a collection Anopheles dissected for parity count A measurement datum of the number of female Anopheles dissected for parity in a given collection. Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey PRISM Penn Group number of female Anopheles dissected for parity in a collection Anopheles nulliparous count A measurement datum of the number of female Anopheles that have never layed eggs in a given collection. Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey PRISM Penn Group number of female null parous Anopheles in a collection Anopheles parous count A measurement datum of the number of female Anopheles that have layed eggs before or are pregnant in a given collection. Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey PRISM Penn Group number of female parous Anopheles in a collection Gravid Anopheles funestus count A measurement datum of the number of gravid or semi-gravid female Anopheles funestus in a given collection Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey PRISM Penn Group number of gravid or semi-gravid Anopheles funestus in a collection Gravid Anopheles gambiae count A measurement datum of the number of gravid or semi-gravid female Anopheles gambiae in a given collection Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey PRISM Penn Group 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. Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey PRISM Penn Group obsolete number of insecticide treated mosquito net(s) per person true Other female Anopheles species count A measurement datum of the number of female Anopheles that are not gambiae nor funestus in a given collection. Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey PRISM Penn Group number of non-gambiae or funestus female Anopheles species in a collection Sleeping places count A data item of the number of sleeping spaces in a dwelling. Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey PRISM Penn Group 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 Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey PRISM Penn Group 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 Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey PRISM Penn Group number of unassessable Anopheles gambiae in a collection Unfed Anopheles funestus count A measurement datum of the number of female Anopheles funestus without a recent blood meal in a given collection Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey PRISM Penn Group number of unfed female Anopheles funestus in a collection Unfed Anopheles gambiae count A measurement datum of the number of female Anopheles gambiae without a recent blood meal in a given collection Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey PRISM Penn Group number of unfed female Anopheles gambiae in a collection An information content entity that indicates whether a plasma sample is lost or not. Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey PRISM Penn Group obsolete plasma sample lost information true Plasmodium gametocytes, by microscopy A Plasmodium gametocytes in blood by microscopy assay datum that specifies whether gametocytes were detected. Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey, John Judkins PRISM presence of Plasmodium gametocyte in blood by microscopy assay Reason for withdrawal An information content entity indicating the reason why a participant withdrew from a study. Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey PRISM Penn Group reason for participant withdrawal An information content entity that indicates whether a redraw of a symptom occurred after a clinical visit. Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey PRISM Penn Group obsolete redraw of a symptom after clinical visit information true A routine clinical visit in which a blood specimen was collected for a T-cell study. Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey PRISM Penn Group obsolete routine clinical visit for T-cell study true 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). Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey PRISM Penn Group obsolete routine clinical visit with finger prick true 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). Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey PRISM Penn Group obsolete routine clinical visit with venipuncture true A routine clinical visit in which no routine assessment was done during the visit. Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey PRISM Penn Group obsolete routine clinical visit without any routine assessment done true An air brick with a screen that can prevent some insects get in the dwelling. Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey PRISM Penn Group obsolete screened air brick true Severe anemia An anemia with hemoglobin levels less than 5 gm/dL. Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey ICEMR protein array PRISM Penn Group severe anemia ITN last night An information content entity indicating whether a person slept in an insecticide treated net the previous night. Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey PRISM Penn Group slept in an insecticide treated net last night information Anopheles tested for sporozoites count A sum value for all female Anopheles examined for sporozoites in a given collection. Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey PRISM Penn Group sum number of female Anopheles examined for sporozoites in a collection Sporozoite-pos Anopheles count A sum value for all female Anopheles with Plasmodium sporozoites in a given collection. Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey PRISM Penn Group sum number of female Anopheles with Plasmodium sporozoites in a collection Timing of enrollment An information content entity indicating whether enrollment of a human study subject occurred at the beginning of a study or during the study. Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey, John Judkins PRISM Penn Group indicator of enrollment timing A pit latrine that is not sheltered by an outhouse but has a latrine slab. Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey PRISM Penn Group obsolete uncovered pit latrine with slab true A pit latrine that is not sheltered by an outhouse and does not have a latrine slab. Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey PRISM Penn Group obsolete uncovered pit latrine without slab true An air brick without a screen to prevent insects from enetering the dwelling. Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey PRISM Penn Group obsolete unscreened air brick true Pain perceived to originate in the muscle. PRISM obsolete Muscle aches true A light source that light is produced from solar energy. Person: Jie Zheng, Chris Stoeckert obsolete solar light source true 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 Person: John Judkins VEuPathDB obsolete drinking water from open public well true 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 Person: John Judkins VEuPathDB obsolete drinking water from open well in yard true Piped into dwelling drinking water accessed through a plumbing fixture located inside a human dwelling Person: John Judkins EuPathDB drinking water from pipe into dwelling Piped into yard drinking water obtained through a plumbing fixture located in the yard of a human dwelling Person: John Judkins EuPathDB drinking water from pipe into yard was ClinEpi household, no longer used obsolete drinking water from protected public well true from ClinEpi household, no longer used obsolete drinking water from freshwater spring true ClinEpi household, no longer used obsolete drinking water from protected well in yard true 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 Person: John Judkins VEuPathDB obsolete drinking water from unprotected freshwater spring true was ICEMR PRISM household, no longer used obsolete drinking water from water truck true A centrally registered identifier symbol assigned by the American Type Culture Collection (ATCC). obsolete ATCC number true Parasite clearance half life half life datum (t 1/2) for cleaning parasite clearance half life EuPathDB parasite clearance half life Parasite clearance rate 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 Person: John Judkins clearance rate EuPathDB parasite clearance rate Parasite clearance time 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 Person: John Judkins clearance time EuPathDB duration of parasite clearance was in ICEMR Amazonia, no longer used obsolete symptomatic episode true was in EuPathDB/PlasmoDB, no longer used obsolete chloroquine resistant true was in EuPathDB/PlasmoDB, no longer used obsolete pyrimethamine and chloroquine resistant true was in EuPathDB/PlasmoDB, no longer used obsolete pyrimethamine, mefloquine and chloroquine resistant true was in EuPathDB/PlasmoDB, no longer used obsolete pyrimethamine resistant, chloroquine sensitive true was in ICEMR prism, no longer used obsolete record of unknown information true obsolete pyrimethamine,chloroquine, and mefloquine resistant true was in EuPathDB/PlasmoDB, no longer used not responsive to SAG therapy obsolete sodium antimony gluconate resistant true was EuPathDB/PlasmoDB term, no longer used Sensitive to SAG obsolete sodium antimony gluconate sensitive true was ICEMR PRISM observation, no longer used obsolete no malaria parasite infection diagnosis true Haplogroup A population of people who share a common ancestor on the patrilineal or matrilineal line. haplogroup Parasitemia start time a time measurement datum that represents the beginning of the first process in which a parasitemia is realized Person: John Judkins EuPathDB time parasitemia started Treatment outcome an information content entity that describes the success, failure, or indeterminacy of a treatment Person: John Judkins treatment outcome EuPathDB treatment outcome information was in EuPathDB/PlasmoDB, no longer used ETF obsolete early treatment failure true was in EuPathDB/PlasmoDB, no longer used LCF obsolete late clinical failure true 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 was in EuPathDB/PlasmoDB, no longer used LF obsolete late failure true Shannon Takala Harrison: LOSS probably also means the patient was lost to follow-up. Term need for annotation NIH-10K experiment, treatment outcome no longer used LOSS obsolete lost to follow-up true was in EuPathDB/PlasmoDB, no longer used LPF obsolete late parasitological failure true was in EuPathDB/PlasmoDB, no longer used LTF obsolete Late Treatment Failure true Shannon Takala Harrison: Not sure what NULL means; it could also indicate lost to follow-up. Term need for annotation NIH-10K experiment, treatment outcome was EuPathDB/PlasmoDB term, no longer used NULL obsolete unknown outcome true was ICEMR Amazonia, no longer used VIVAX obsolete have a subsequent P. vivax infection true was in EuPathDB/PlasmoDB, no longer used WTH obsolete withdrew from the study true was ICEMR, no longer used obsolete summary information about a dwelling true Dwelling facilities 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. Person: John Judkins EuPathDB information on dwelling facilities Dwelling characteristics a information content entity that is about a part of a dwelling Person: John Judkins EuPathDB information on dwelling physical characteristics Socioeconomic factors 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 Person: John Judkins EuPathDB 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 Person: John Judkins EuPathDB aggregated clinical visit information Participant genotype a genotype information that is about the genetic material of a human being Person: John Judkins EuPathDB human genotype information Participant study details 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 Person: John Judkins EuPathDB information on participant study details Hospitalization an information content entity that is about a part of a health care encounter that occurs in a hospital facility Person: John Judkins EuPathDB ICEMR protein array hospitalization information Signs and symptoms 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. Person: John Judkins EuPathDB ICEMR protein array symptom or sign information Observation details an information content entity that is about a clinical visit Person: John Judkins EuPathDB information on observation details an information content entity that specifies whether a clinical visit is scheduled or unscheduled Person: John Judkins EuPathDB 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 Person: John Judkins aggregated entomological measurement data EuPathDB 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 Person: John Judkins VEuPathDB obsolete single catch entomological measurement datum true a clinical visit that realizes the concretization of a protocol specifying the time of the visit Person: John Judkins VEuPathDB obsolete scheduled clinical visit true a clinical visit that occurs at a time that is not mentioned in a protocol that directs the time of the visit Person: John Judkins VEuPathDB obsolete unscheduled clinical visit true an information content entity that is about a malaria diagnosis and describes the severity of the disease or the basis for the diagnosis Person: John Judkins EuPathDB obsolete malaria severity and basis information true Other diagnosis A diagnosis that is an assertion that a patient, who is the subject of a diagnostic process, has a disease other than malaria. Person: John Judkins VEuPathDB diagnosis of disease other than malaria Admitting hospital an information content entity that is about a participant under investigation and specifies the hospital admitting the participant Person: John Judkins EuPathDB hospital admission information Hospital admission date 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 Person: John Judkins EuPathDB date of hospital admission Hospital discharge date 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 Person: John Judkins EuPathDB date of hospital discharge Diagnosis at discharge A diagnosis that is documented during the patient discharge process. Person: John Judkins VEuPathDB https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/357 diagnosis at patient discharge Anopheles funestus results an information content entity that is about a collection of Anopheles funestus Person: John Judkins EuPathDB Anopheles funestus related information Anopheles gambiae sensu lato results an information content entity that is about a collection of Anopheles gambiae sensu lato Person: John Judkins EuPathDB, Wikipedia 'Sensu' entry Anopheles gambiae sensu lato related information Anopheles parity an information content entity that is about a number of mosquitos that have given birth Person: John Judkins EuPathDB mosquito parity information Sporozoite testing 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 Person: John Judkins EuPathDB sporozoite testing information a data item that is the specified output of a data transformation that has only sporozoite testing information as input Person: John Judkins EuPathDB aggregated sporozoite testing information a data item that is about a collection of insects Person: John Judkins entomological measurement data EuPathDB obsolete entomological data item true was ICEMR PRISM, no longer used obsolete clinical visit information true 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 true 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 true Human waste facilities 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 Malaria diagnosis and parasite status 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. obsolete dwelling animal information true An information content entity that is about human traveling. replaced with OMRSE:00000142 obsolete human traveling information true Household vector intervention An information content entity that is about vector control intervention towards interruption of transmission of infectious diseases. vector control intervention information Employment An information content entity that is about employment. employment information Animals on property An organism that raised by people and lives in a human dwelling. domesticated animal in a human dwelling Personal bednet treatment 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. obsolete educational level information true Lifetime Plasmodium vivax infections count A count of the total times of a person who infected with P. vivax in his lifetime. Person: Chris Stoeckert, Jie Zheng 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. Person: Chris Stoeckert, Jie Zheng 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. Person: Chris Stoeckert, Jie Zheng 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. Person: Chris Stoeckert, Jie Zheng number of infections with P. falciparum in the last year Time spent in occupation every week A measurement datum of days per week spent in one's primary occupation. days per week at primary occupation Time spent in occupation 2 every week 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. https://en.wikipedia.org/wiki/Job obsolete job role true A planned process that a person participates in exchange for payment. The job role born by the person is realized in the process. obsolete economic activity true An economic activity that a person is involved in primarily. obsolete primary economic activity true Occupation 2 An occupation that a person is not involved in primarily. Person: John Judkins VEuPathDB https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/289 secondary occupation A textual entity that describes a person's primary economic activity. obsolete primary economic activity description true A textual entity that describes a person's secondary economic activity. obsolete secondary economic activity description true Additional job in the past month An information content entity about secondary economic activity a person participates in the last month. secondary economic activity in last month Occupation An information content entity that is about an activity that realizes a social role and is often performed for payment. occupation Occupation payment frequency A time measurement datum about the pay period of primary economic activity. primary economic activity pay period Occupation 2 payment frequency A time measurement datum about the pay period of secondary economic activity. secondary economic activity pay period Receive payment for occupation An information content entity about whether a person received payment from primary economic activity. Jie Zheng Chris Stoeckert https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/142 indicator of whether person received payment from primary economic activity Receive payment for occupation 2 An information content entity about whether a person received payment from secondary economic activity. Jie Zheng Chris Stoeckert https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/142 indicator of whether person received payment from secondary economic activity Occupation salary A data item of salary of primary job. salary of primary economic activity Occupation 2 salary A data item of salary of other job. salary of secondary economic activity Time spent in occupation every day A measurement datum of hours in one's primary occupation per day spent in that occupation. hours per day at primary occupation Time spent in occupation 2 every day 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. obsolete garbage disposal true A textual entity about community where a person is living. obsolete community name true A textual entity about community where a study taken place. obsolete study location name true A malaria medication that is generally taken for initial treatment of malaria. obsolete first line malaria medication true "A malaria medication that is given when first-line medication doesn't work, or stops working." obsolete second line malaria medication true was in ICEMR Amazonia, no longer used obsolete information of whether malaria medication is given true Marital status a categorical value specification that is about a human being and specifies whether that human being is joined to another human being in marriage Person: John Judkins EuPathDB, BFO's 'relational quality' examples marital status Plan to move a categorical value specification that specifies whether a human being plans to change within two years the dwelling which that human being occupies Jie Zheng Chris Stoeckert Person: John Judkins EuPathDB https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/142 indicator of whether person plans to move Relationship to household head An information content entity that specifies the relationship between a person and the head of their household. Person: John Judkins, Chris Stoeckert EuPathDB relationship to head of household Time living in dwelling a time measurement datum that represents the time a human being resides in a human dwelling Person: John Judkins EuPathDB duration of residence in dwelling Time living in settlement 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. Person: John Judkins EuPathDB duration of residence in community Common room count 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 Person: John Judkins EuPathDB number of common areas in a dwelling Covered area 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 Person: John Judkins EuPathDB covered area measured in square meter Kitchen location 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. Person: John Judkins EuPathDB area measurement datum Home ownership 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 Person: John Judkins EuPathDB information on whether occupant owns or pays rent on dwelling was ICEMR Amazonia, no longer used obsolete days of travel true was in ICEMR Amazonia, no longer used obsolete information of whether ship is taken during a trip true an information content entity that is about a geographic location in which part of a journey occurs Person: John Judkins VEuPathDB obsolete information on place visited during a trip true Traveled in last month 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 Person: John Judkins EuPathDB yes information on travel before malaria Bednet material A material entity that is used to make bed net. bed net material Last fumigation date 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 Person: John Judkins EuPathDB date of last fumigation Bednet treater an information content entity that specifies the organization that administers insecticide to a collection of bed nets Person: John Judkins EuPathDB information on organization responsible for treating bed nets Contact with malaria 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. Person: John Judkins VEuPathDB 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 Person: John Judkins VEuPathDB obsolete information on participant status at visit true was ICEMR Amazonia, no longer used obsolete information of whether address has changed true Livestock count a count of the number of instances of a domesticated animal that is raised in an agricultural setting to produce labor and commodities Person: John Judkins Wikipedia number of livestock Pet or other animal count a count of the number of instances of a domesticated animal that is kept for pleasure rather than utility Person: John Judkins EuPathDB number of pets was in ICEMR Amazonia, no longer used obsolete bed net treatment information true ITN bednet count, treated <6 months ago a count of the number of instances of a bed net to which insecticide was applied in the past six months Person: John Judkins EuPathDB number of insecticide-treated bed nets treated less than 6 months ago ITN bednet count, treated >6 months ago a count of the number of instances of a bed net to which insecticide was applied before the previous six months Person: John Judkins EuPathDB number of insecticide-treated bed nets treated more than 6 months ago Long-lasting ITN bednet count a count of the number of instances of bed net to which long last insecticide is administered Person: John Judkins EuPathDB number of long last insecticide-treated bed nets Untreated bednet count a count of the number of instances of a bed net to which insecticide has not been applied Person: John Judkins EuPathDB number of untreated bed net no longer used obsolete blood pressure measurement datum true A categorical measurement datum about proximity to case dwelling. obsolete proximity to case dwelling datum true no longer used obsolete information of whether a census form filled at enrollment true an organization that administrates a medical care center that provides healthcare services on an outpatient basis Person: John Judkins obsolete clinic organization true A geographic location where the clinic is located. obsolete clinic location true District A second-order administrative region of India. Person: John Judkins VEuPathDB district of India A textual entity about a 'division' or 'ward' being a sub-division of a city. obsolete division number true Took antimalarial medication as advised a categorical value specification that specifies whether a patient complies with a dose specification that specifies the dose of malaria medication to self-administer Jie Zheng Chris Stoeckert Person: John Judkins EuPathDB https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/142 indicator of whether participant taking antimalarial drugs as advised Took antimalarial medication an information content entity that specifies whether a participant under investigation self-administered antimalarial drugs in the past 2 weeks Jie Zheng Chris Stoeckert Person: John Judkins EuPathDB https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/142 indicator of whether participant taking antimalarial drugs in last 2 weeks Type of existing illness an information content entity that is about a human participant under investigation that has a disease and specifies the disease Person: John Judkins EuPathDB information on existing illness Existing illness an information content entity that is about a human participant under investigation and specifies whether the participant has a disease Jie Zheng Chris Stoeckert Person: John Judkins EuPathDB https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/142 indicator of whether participant having existing illness Fever treatment location 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. Person: John Judkins EuPathDB fever treatment provider information Fever duration A time measurement datum that measures the duration of having febrile. Person: Jie Zheng, Chris Stoeckert ICEMR protein array duration of being febrile was ICEMR Amazonia, no longer used obsolete information of whether a person is family head true was ICEMR Amazonia, no longer used obsolete hospital registration number true Ill now an information content entity that specifies whether a human being is manifesting a disease Jie Zheng Chris Stoeckert Person: John Judkins EuPathDB https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/142 indicator of whether person is sick now Animals indoors "An information content entity is about who are indoor residents, such as only human, or human and animals." indoor residents information Larvicide frequency a measurement datum that approximates the temporal interval between applications of larvicide at the same site Person: John Judkins EuPathDB 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 Person: John Judkins VEuPathDB obsolete information on where malaria diagnosed in last 12 months true a count of the number of instances of a parasite in a life cycle stage in which reproduction is asexual Person: John Judkins EuPathDB, Centers for Disease Control and Prevention obsolete number of asexual parasite true was ICEMR, no longer used obsolete number of sexual parasite true Plasmodium species, by microscopy A data item of which parasite species detected in a blood specimen. parasite species information Nationality A country name denote where a person was born. birth country name Plasmodium species in last year 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 Person: John Judkins EuPathDB 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 Time since last malaria diagnosis A time measurement datum of the time since the most recent diagnosis of malaria. duration since last diagnosis of malaria Treated with antimalarials An information content entity about whether antimalarial drug treated last year Jie Zheng Chris Stoeckert https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/142 indicator of whether participant treated antimalarial drugs last year Antimalarial treatment date A time measurement datum about when the antimalarial drug used last year date antimalarial drug used Antimalarial treatment An information content entity about what antimalarial drug used last year information on antimalarial drug used last year Where treated An information about who treated malaria last year information on who treated malaria last year PCR DNA sample source 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. VEuPathDB obsolete parasite species identification by PCR assay true A textual entity that denotes the public health clinic/hospital that the human subject normally uses (for non malaria illness). obsolete primary health center name true Poverty line 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 true 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. obsolete falcivax rapid diagnostic test true A laboratory test that is a rapid, sensitive malaria test that is able to differentiate between P. falciparum and other malaria parasites. VEuPathDB obsolete optimal-IT rapid diagnostic test true Personal mosquito repellent A material entity that a person uses to deter mosquitoes from approaching or settling. personal mosquito repellent Resident status "An information content entity about a person's resident status, permanent or temporary." resident status information Sprayed in the last 12 months An information content entity about repellent sprayed in last 12 months in a dwelling. information on mosquito repellent sprayed in last 12 months State of birth A text entity denotes to a state where a person was born. state name of birth On fever suppressant An information content entity that is about whether a person take fever suppressant. take fever suppressant information Taluk in India A third-order administrative region of India. Person: John Judkins VEuPathDB taluk of India Country visited A country name denote a geographic location that a person has visited. visited country name District visited A text entity denotes to a district that a person has visited. visited district name State visited A text entity denotes to a state that a person has visited. visited state name Taluk visited A taluk name denote a geographic location that a person has visited. visited taluk name Village visited A village name denote a geographic location that a person has visited. visited village name Traveled in last 2 weeks An information content entity about whether a person travelled in last 14 days. traveled information in last 14 days Typical healthcare public, private, or community funded health care Health care information that specifies the source of funding for a health care process. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/441 Sheena Tomko indicator of health care source A first-order administrative region of Mali. Person: John Judkins VEuPathDB region of Mali A text entity of a zone number denotes to a geographic location. obsolete location zone number true obsolete average mapping coverage true 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 John Judkins VEuPathDB obsolete proportion mapped reads true was in EuPathDB/PlasmoDB, no longer used obsolete number mapped reads true was EuPathDB/PlasmoDB term, no longer used obsolete average read length true was in EuPathDB/PlasmoDB, no longer used obsolete unstranded unique average mapping coverage true was in EuPathDB/PlasmoDB, no longer used obsolete unstranded unique proportion mapped reads true was EuPathDB/PlasmoDB term, no longer used obsolete unstranded unique number mapped reads true was in EuPathDB/PlasmoDB, no longer used obsolete unstranded unique average read length true was in EuPathDB/PlasmoDB, no longer used obsolete unstranded non unique average mapping coverage true was in EuPathDB/PlasmoDB, no longer used obsolete unstranded non unique proportion mapped reads true was in EuPathDB/PlasmoDB, no longer used obsolete unstranded non unique number mapped reads true was in EuPathDB/PlasmoDB, no longer used obsolete unstranded non unique average read length true was in EuPathDB/PlasmoDB, no longer used obsolete first strand unique average mapping coverage true was in EuPathDB/PlasmoDB, no longer used obsolete first strand unique proportion mapped reads true was in EuPathDB/PlasmoDB, no longer used obsolete first strand unique number mapped reads true was in EuPathDB/PlasmoDB, no longer used obsolete first strand unique average read length true was EuPathDB/PlasmoDB term, no longer used obsolete first strand non unique unstranded unique average mapping coverage true was EuPathDB/PlasmoDB term, no longer used obsolete first strand non unique unstranded unique proportion mapped reads true was EuPathDB/PlasmoDB term, no longer used obsolete first strand non unique unstranded unique number mapped reads true was EuPathDB/PlasmoDB term, no longer used obsolete first strand non unique unstranded unique average read length true was in EuPathDB/PlasmoDB, no longer used obsolete second strand unique unstranded non unique average mapping coverage true was in EuPathDB/PlasmoDB, no longer used obsolete second strand unique unstranded non unique proportion mapped reads true was in EuPathDB/PlasmoDB, no longer used obsolete second strand unique unstranded non unique number mapped reads true was in EuPathDB/PlasmoDB, no longer used obsolete second strand unique unstranded non unique average read length true was in EuPathDB/PlasmoDB, no longer used obsolete second strand non unique first strand unique average mapping coverage true was in EuPathDB/PlasmoDB, no longer used obsolete second strand non unique first strand unique proportion mapped reads true was in EuPathDB/PlasmoDB, no longer used obsolete second strand non unique first strand unique number mapped reads true was in EuPathDB/PlasmoDB, no longer used obsolete second strand non unique first strand unique average read length true was in EuPathDB/PlasmoDB, no longer used https://www.beiresources.org/Catalog/Fungi/NR-29444.aspx obsolete Candida albicans strain 12C true was in EuPathDB/PlasmoDB, no longer used https://www.beiresources.org/Catalog/Fungi/NR-29445.aspx obsolete Candida albicans strain L26 true 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 true 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. Person: Grant Dorsey, Jie Zheng obsolete diagnosis of submicroscopic parasitemia true 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 Plasmodium, by LAMP A eukaryota in blood datum that specifies whether Plasmodium was detected by loop-mediated isothermal amplification. Person: Jie Zheng, Grant Dorsey, John Judkins PRISM presence of Plasmodium in blood by loop-mediated isothermal amplification An information content entity is about blood smear not performed. Person: Jie Zheng, Grant Dorsey PRISM obsolete information on blood smear not performed true A presence of parasite that indicates that no parasite was detected in a specimen, either by loop-mediated isothermal amplification or blood smear. Person: Jie Zheng, Grant Dorsey, John Judkins PRISM obsolete negative blood smear and negative LAMP true An information content entity is about parasite status with negative blood smear and LAMP test is not performed. Person: Jie Zheng, Grant Dorsey PRISM Penn Group 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. Person: Jie Zheng, Shon cade, Grant Dorsey average number of clinical visits with asymptomatic parasitemia diagnosis per year Courses of antibiotics A count of the number of courses of antibiotics received by the human or animal. Person: Daniel Beiting, Jie Zheng microbiome number of courses of antibiotics given Family ID A symbol that denotes a specific family, rather than the physical home in which they live. Person: Daniel Beiting, Jie Zheng microbiome family identifier Dwelling ID A symbol denotes a physical structure/home/dwelling, rather than the human inhabitants. Person: Daniel Beiting, Jie Zheng microbiome dwelling identifier An information content entity that idicates whether the hive was treated with tetracyline to prevent infection with the bacterial pathogen Paenibacillus larvae. Person: Daniel Beiting, Jie Zheng microbiome obsolete information on whether hive treated with tetracyline true An information indicates that samples from child or from the mother, or both. Person: Daniel Beiting, Jie Zheng microbiome obsolete information on whether specimen from mother or child true Mom's courses of delivery antibiotics A number of courses of antibiotics given to a mother during delivery. Person: Daniel Beiting, Jie Zheng microbiome number of courses of antibiotics received by mom prior to delivery A region of the 16S rRNA gene that was PCR amplified and sequenced. Person: Daniel Beiting, Jie Zheng microbiome obsolete 16S rRNA gene region for sequencing true Lab host An organism that realizes host role in laboratory. lab host was EuPathDB/PlasmoDB term, no longer used obsolete bronchial wash specimen true was EuPathDB/PlasmoDB term, no longer used obsolete bronchoalveolar lavage fluid specimen true was EuPathDB/PlasmoDB term, no longer used obsolete lung aspirate specimen true was EuPathDB/PlasmoDB term, no longer used obsolete lung lesion specimen true was in EuPathDB/PlasmoDB, no longer used obsolete lung mold bronch specimen true was in EuPathDB/PlasmoDB, no longer used obsolete lung nodule specimen true was in EuPathDB/PlasmoDB, no longer used obsolete TGH specimen true was in EuPathDB/PlasmoDB, no longer used obsolete TGH mold iso specimen true was in EuPathDB/PlasmoDB, no longer used obsolete number of contigs true was EuPathDB/PlasmoDB term, no longer used obsolete number of genes called true was in EuPathDB/PlasmoDB, no longer used obsolete number of bases true was in EuPathDB/PlasmoDB, no longer used obsolete lesion on arm specimen true 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. https://en.wikipedia.org/wiki/Common_name obsolete common name of organism true An information content entity specify any molecular data associated with specimen source is available. Person: Jie Zheng, Chris Stoeckert ICEMR protein array information on availability of molecular data Collection type An information content entity indicates whether the specimen collection is original collection or follow up collection from same study subject. Person: Jie Zheng, Chris Stoeckert ICEMR protein array information on original or follow up specimen collection Data consent An information content entity specifies whether study subject signed informed consent for data collection and usage. Person: Jie Zheng, Chris Stoeckert ICEMR protein array information on informed consent for data collection and usage Person: Jie Zheng, Chris Stoeckert, John Judkins obsolete electrolyte disturbances true was in EuPathDB/PlasmoDB, no longer used https://www.beiresources.org/Catalog/Fungi/NR-29447.aspx obsolete Candida albicans strain P37005 true P. falciparum A categorical measurement datum that indicates whether Plasmodium falciparum were present in a specimen. Person: Jie Zheng, Chris Stoeckert ICEMR protein array presence of Plasmodium falciparum Plasmodium gametocytes A categorical measurement datum that indicates whether gametocyte were present in a specimen. Person: Jie Zheng, Chris Stoeckert ICEMR protein array presence of gametocyte P. knowlesi A categorical measurement datum that indicates whether Plasmodium knowlesi were present in a specimen. Person: Jie Zheng, Chris Stoeckert ICEMR protein array presence of Plasmodium knowlesi P. malariae A categorical measurement datum that indicates whether Plasmodium malariae were present in a specimen. Person: Jie Zheng, Chris Stoeckert ICEMR protein array presence of Plasmodium malariae P. ovale A categorical measurement datum that indicates whether Plasmodium ovale were present in a specimen. Person: Jie Zheng, Chris Stoeckert ICEMR protein array presence of Plasmodium ovale Presence of parasite species A categorical measurement datum that indicates whether parasite were present in a specimen. Person: Jie Zheng, Chris Stoeckert ICEMR protein array presence of parasite P. vivax A categorical measurement datum that indicates whether Plasmodium vivax were present in a specimen. Person: Jie Zheng, Chris Stoeckert ICEMR protein array presence of Plasmodium vivax Follow up day A time measurement datum measuring the time interval from the first specimen collection to the current specimen collection from the same study subject. Person: Jie Zheng, Chris Stoeckert, John Judkins ICEMR protein array duration of study participation from first to current specimen collection A scalar measurement datum that is about gametocyte density measured using microscopy. Person: Jie Zheng, Chris Stoeckert ICEMR protein array gametocyte density by microscope Plasmodium gametocytes, by RT-PCR result A scalar measurement datum that is about gametocyte density measured by RT-PCR. Person: Jie Zheng, Chris Stoeckert ICEMR protein array gametocyte density by RT-PCR An assay that detects parasite gametocyte in a specimen. Person: Jie Zheng, Chris Stoeckert VEuPathDB obsolete gametocyte detection assay true Plasmodium gametocytes detection method A protocol that specifies how to measure the density of parasite gametocyte. Person: Jie Zheng, Chris Stoeckert ICEMR protein array gametocyte detection protocol GPS location a site in which a global positioning system receiver produces a data item specifying the location of the site Person: Jie Zheng, Chris Stoeckert ICEMR protein array location where GPS coordinates were taken Host genetics An information content entity specify any host genetics data associated with specimen source is available. Person: Jie Zheng, Chris Stoeckert ICEMR protein array information on availabilty of host genetics data Immune responses An information content entity specify any immune response data associated with specimen source is available. Person: Jie Zheng, Chris Stoeckert ICEMR protein array information on availability of immune response data Parasite genetics An information content entity specify any parasite genetics data associated with specimen source is available. Person: Jie Zheng, Chris Stoeckert ICEMR protein array information on availability of parasite genetics data Other molecular An information content entity specify any molecular data other than host genetics, parasite genetics, and immune response, associated with specimen source is available. Person: Jie Zheng, Chris Stoeckert ICEMR protein array information on availability of other molecular data IRB number 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. Person: Jie Zheng, Chris Stoeckert ICEMR protein array IRB number Plasmodium, by PCR result A scalar measurement datum that is about parasite density measured by PCR. Person: Jie Zheng, Chris Stoeckert ICEMR protein array parasite density by PCR Plasmodium, 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 in the specimen. Person: Jie Zheng, Chris Stoeckert, John Judkins ICEMR protein array Plasmodium in blood by microscopy assay datum An assay that detects parasite in a specimen. Person: Jie Zheng, Chris Stoeckert ICEMR protein array obsolete parasite detection assay true An assay that detects parasite in a specimen using PCR. Person: Jie Zheng, Chris Stoeckert VEuPathDB obsolete parasite detection by PCR assay true Plasmodium asexual stages, by PCR A categorical measurement datum that indicates whether asexual parasite were present in a specimen using PCR. Person: Jie Zheng, Chris Stoeckert ICEMR protein array presence of asexual parasite by PCR RDT results A categorical measurement datum that is the result of rapid diagnosis test using a value of positive or negative. Person: Jie Zheng, Chris Stoeckert ICEMR protein array rapid diagnosis test result as positive or negative location of specimen collection The site where specimen collection taken place. Person: Jie Zheng, Chris Stoeckert ICEMR protein array location of specimen collection ICEMR 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 Person: Jie Zheng, Chris Stoeckert, John Judkins ICEMR protein array National Institute of Allergy and Infectious Diseases ICEMR organization An assay that detects body temperature of an organism. Person: Jie Zheng, Chris Stoeckert ICEMR protein array obsolete organismal body temperature measurement assay true An assay that is quick and easy in the diagnosis of malaria by detecting evidence of malaria parasites (antigens) in human blood. Person: Jie Zheng, Chris Stoeckert obsolete malaria rapid diagnosis test true 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 Person: Jie Zheng, Chris Stoeckert, John Judkins EuPathDB ICEMR protein array 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 Person: Jie Zheng, Chris Stoeckert, John Judkins EuPathDB ICEMR protein array Plasmodium vivax gametocyte density by microscope Plasmodium vivax gametocytes, by RT-PCR result A gametocyte density by RT-PCR that is about Plasmodium vivax. Person: Jie Zheng, Chris Stoeckert ICEMR protein array 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 Person: Jie Zheng, Chris Stoeckert, John Judkins EuPathDB ICEMR protein array 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 Person: Jie Zheng, Chris Stoeckert, John Judkins EuPathDB ICEMR protein array 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 Person: Jie Zheng, Chris Stoeckert, John Judkins EuPathDB ICEMR protein array 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 Person: Jie Zheng, Chris Stoeckert, John Judkins EuPathDB ICEMR protein array Plasmodium falciparum parasite density by PCR Future use consent An information content entity specifies whether study subject signed informed consent for future use of specimen. Person: Jie Zheng, Chris Stoeckert ICEMR protein array information on informed consent for future use of specimen was in EuPathDB/PlasmoDB, no longer used https://www.beiresources.org/Catalog/Fungi/NR-29449.aspx obsolete Candida albicans strain 19F true was in EuPathDB/PlasmoDB, no longer used https://www.beiresources.org/Catalog/Fungi/NR-29434.aspx obsolete Candida albicans strain P78048 true was in EuPathDB/PlasmoDB, no longer used https://www.beiresources.org/Catalog/Fungi/NR-29450.aspx obsolete Candida albicans strain P37037 true was in EuPathDB/PlasmoDB, no longer used https://www.beiresources.org/Catalog/Fungi/NR-29451.aspx obsolete Candida albicans strain P37039 true was in EuPathDB/PlasmoDB, no longer used obsolete Candida albicans strain SC5314 true was in EuPathDB/PlasmoDB, no longer used https://www.beiresources.org/Catalog/Fungi/NR-29435.aspx obsolete Candida albicans strain P57072 true was in EuPath/PlasmoDB, no longer used https://www.beiresources.org/Catalog/Fungi/NR-29441.aspx obsolete Candida albicans strain P76055 true was EuPathDB/PlasmoDB term, no longer used https://www.beiresources.org/Catalog/Fungi/NR-29442.aspx obsolete Candida albicans strain P76067 true was in EuPathDB/PlasmoDB, no longer used https://www.beiresources.org/Catalog/Fungi/NR-29439.aspx obsolete Candida albicans strain P57055 true was in EuPathDB/PlasmoDB, no longer used https://www.beiresources.org/Catalog/Fungi/NR-29443.aspx obsolete Candida albicans strain P78042 true was in EuPathDB/PlasmoDB, no longer used https://www.beiresources.org/Catalog/Fungi/NR-29436.aspx obsolete Candida albicans strain P34048 true was in EuPathDB/PlasmoDB, no longer used https://www.beiresources.org/Catalog/Fungi/NR-29453.aspx obsolete Candida albicans strain P87 true was in EuPathDB/PlasmoDB, no longer used https://www.beiresources.org/Catalog/Fungi/NR-29452.aspx obsolete Candida albicans strain GC75 true was in EuPathDB/PlasmoDB, no longer used https://www.beiresources.org/Catalog/Fungi/NR-29438.aspx obsolete Candida albicans strain P75016 true was in EuPathDB/PlasmoDB, no longer used https://www.beiresources.org/Catalog/Fungi/NR-29440.aspx obsolete Candida albicans strain P75063 true was in EuPathDB/PlasmoDB, no longer used https://www.beiresources.org/Catalog/Fungi/NR-29446.aspx obsolete Candida albicans strain P94015 true was in EuPathDB/PlasmoDB, no longer used https://www.beiresources.org/Catalog/Fungi/NR-29448.aspx obsolete Candida albicans strain P60002 true was EuPathDB/PlasmoDB term, no longer used https://www.beiresources.org/Catalog/Fungi/NR-29437.aspx obsolete Candida albicans strain P75010 true Parasite genotype A genotype information of parasite organism. parasite organism genotype information obsolete genetic clade of organism true Virulence Score (LDt50) 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 Person: John Judkins Wikipedia: LD50 virulence score (LDt50) Virulence Score (slope) 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 Person: John Judkins virulence score (slope) Repository ID 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 Depth 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 in days age since birth in days Antibiotic exposure An information content entity about whether child exposed to antibiotics. Jie Zheng Chris Stoeckert https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/142 indicator of whether child exposed to antibiotics Delivery mode a health care encounter in which a health care provider assists a mother in the birth of a child Person: John Judkins baby's delivery EuPathDB baby delivery Antibiotics A medication material that is used in the treatment and prevention of bacterial infections. It may either kill or inhibit the growth of bacteria. https://en.wikipedia.org/wiki/Antibiotics antibiotics Bee colony tetracycline An information content entity about whether bee colony treated with tetracycline. Jie Zheng Chris Stoeckert https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/142 indicator of whether bee colony treated with tetracycline main source of nutrition for a child child's diet Child's diet (by month) main source of nutrition for a child for each month child's diet by month Drug usage An information content entity about any drug used by a participant under investigation and the frequency of usage. drug usage information Environment information An information content entity about environmental material, environmental feature, environmental system, etc. environment information Family move household information that specifies whether the household relocated during its time under investigation Jie Zheng Chris Stoeckert Person: John Judkins EuPathDB https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/142 indicator of whether a family moved an information content entity that is about the bearer of a host role Person: John Judkins EuPathDB 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 Person: John Judkins EuPathDB host's diet An organism that has host role yes host organism Bee larval tetracycline a categorical value specification that is about a collection of bee larvae and specifies whether tetracycline was administered to the larvae Jie Zheng Chris Stoeckert Person: John Judkins EuPathDB https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/142 indicator of whether bee larvae treated with tetracycline Host total mass mass measurement datum is about a host that measured at specimen collection process host mass measurement datum at specimen collection Mother or child An information content entity which indicates that samples are from the child or from the mother, or both. Jie Zheng Daniel Beiting, Jie Zheng microbiomeDB https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/194 indicator of whether specimen from mother or child Child occupants a count that is about a dwelling and is also the result of counting the instances of a child that occupies the dwelling Person: John Judkins EuPathDB number of child occupants in a dwelling Waste disposal An information content entity about disposal of human excreta material. Person: John Judkins Waste disposal information on disposal of human excreta material Percent adult occupants 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 Person: John Judkins EuPathDB percent adult occupants in a dwelling Percent male occupants 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 Person: John Judkins EuPathDB percent male occupants in a dwelling Prenatal antibiotics (yes/no) a categorical value specification that specifies whether a mother received an antimicrobial agent Jie Zheng Chris Stoeckert Person: John Judkins EuPathDB https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/142 indicator of whether antibiotics given to mother of participant Prenatal antibotics (by class) an information content entity that is about an antimicrobial agent given to a mother and specifies the agent by chemical compound Person: John Judkins EuPathDB information on class of antibiotics given to mom Prenatal antibotics (by trimester) an information content entity that specifies the trimester of a pregnancy for which a mother receives an antimicrobial agent Person: John Judkins EuPathDB information on trimester antibiotics given to mom Presence of pets or farm animals 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 Person: John Judkins EuPathDB obsolete sequencing protocol true Sequencing batch 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 Person: John Judkins EuPathDB summary information of investigation a symbol that denotes the bearer of a participant under investigation role Person: John Judkins EuPathDB obsolete participant identifier true Weight loss in last three months an information content entity that is about weight loss occurring in a three-month period Person: John Judkins EuPathDB 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 Person: John Judkins EuPathDB obsolete specimen collection protocol true Sample an information content entity about the bearer of a specimen role Person: John Judkins EuPathDB specimen information Skin phenotype symptom or sign information that results from an examination of either the skin of the patient or a process in which the skin participates Person: John Judkins EuPathDB skin symptom or sign information Sample source an information content entity that is about a specimen collection process Person: John Judkins EuPathDB specimen source information an information content entity that specifies whether an animal is also human Person: John Judkins EuPathDB 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 Person: John Judkins EuPathDB obsolete specimen collection time post infection true Ear thickness skin symptom or sign information that is about the thickness of the ear of the patient Person: John Judkins EuPathDB ear thickness skin symptom or sign information that specifies the rate at which water passes through the epidermis of the patient into the air Person: John Judkins EuPathDB transepidermal water loss was microbiomeDB, no longer used obsolete site of ear swabbed true Skin type swabbed a categorical measurement datum that is about the skin of a human being and specifies whether the skin is either dry, moist, or sebaceous Person: John Judkins EuPathDB 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. Person: John Judkins EuPathDB skin pathology score Number of treatments a count of the number of instances of a treatment Person: John Judkins EuPathDB number of treatments skin symptom or sign information that is about increased thickness of the skin Person: John Judkins EuPathDB degree of skin thickening Lesion size skin symptom or sign information that specifies the size of a disorder on the skin of a patient Person: John Judkins EuPathDB 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 Person: John Judkins EuPathDB 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 Person: John Judkins EuPathDB 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 Person: John Judkins EuPathDB 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 Person: John Judkins EuPathDB 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 Person: John Judkins EuPathDB 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 Person: John Judkins EuPathDB 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 Person: John Judkins EuPathDB 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 Person: John Judkins EuPathDB 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 Person: John Judkins EuPathDB pinna lesion score after treatment treatment outcome information that specifies whether the treatment of a skin lesion was successful Person: John Judkins EuPathDB information on whether skin lesion cured after treatment Skin lesion duration 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 Person: John Judkins EuPathDB skin lesion duration a categorical value specification that specifies the degree of erythema Person: John Judkins EuPathDB NCIT & HP ontologies, EuPathDB 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 Person: John Judkins EuPathDB degree of skin inflammation a measurement datum that is a measurement of the hydration of the outer epidermis Person: John Judkins 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 Person: John Judkins EuPathDB degree of hairloss a skin symptom or sign information that specifies whether the patient has atopic dermatitis Person: John Judkins EuPathDB information on whether affected by atopic dermatitis Diagnosis at hospitalization A diagnosis that is documented during the hospital admission process. Person: John Judkins VEuPathDB https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/357 diagnosis at hospital admission Study group a population that is the bearer of a study group role Person: John Judkins EuPathDB study group Animal cage num in experiment a symbol that denotes a cage that has the function to keep an animal that is the bearer of a participant under investigation role Person: John Judkins EuPathDB 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 Person: John Judkins VEuPathDB obsolete mouse cage number true BMI-for-age z-score A z-score of the divergence of an experimental BMI measurement from the average BMI value for an organism of the same age. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB BMI-for-age z-score Household hygiene 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'. Person: John Judkins https://www.afro.who.int/health-topics/hygiene household hygiene information Child waste disposal An information content entity about disposal of excreta material produced by a child. Person: John Judkins Child waste disposal EuPathDB 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 stool test for microorganisms GEMS Penn Group obsolete feces microbiology assay true Household water An information content entity that is about the water usage of a household. Person: John Judkins VEuPathDB 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. Person: Jie Zheng obsolete propagation true CD36 genotype 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 Observation 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. not used MO_55 EnvironmentalHistory obsolete environmental history true A treatment to alleviate the signs and symptoms associated with malaria. malaria treatment Time to onset 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 DNA extraction date A time measurement datum that specifies when the DNA was extracted date of DNA extraction iPCR result The measurement datum generated by Inverse polymerase chain reaction (Inverse PCR). iPCR datum End of observation period A time measurement datum of duration of the observation at the end of an observation period. duration of observation period Time to first malaria diagnosed A time measurement datum of a person first diagnosed as malaria time to first malaria diagnosis Time to reinfection A time measurement datum of the duration for reinfection. time to reinfection GP60 genotype A genotype information about 60 kDa glycoprotein (gp60) gene. gp60 genotype Collection year A specimen collection time measurement datum in year. specimen collection time in year Blood smear summary An information content entity of multiple blood smear results during an observation period. information on blood smear result An organism that has pathogen role. obsolete pathogen organism true Parasite phenotype A quality inheres in parasite organism. parasite phenotype Fungal genotype A genotype information of fungus. fungal organism genotype information Fungal strain 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 obsolete Candida albicans strain true Parasite strain 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 WHO indicator subdomain 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. Person: John Judkins WHO 2018 Global Reference List of 100 Core Health Indicators World Health Organization core health indicator subdomain Household observations 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. VEuPathDB yes 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. VEuPathDB yes 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. VEuPathDB yes 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. obsolete blood meal source role true 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. Person: John Judkins LT50 VBcv:0000732 https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/77 lethal insecticide time 50 A clinical finding of a death that has been confirmed to be likely caused by COVID-19. death confirmed likely from COVID VEuPathDB 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. Person: John Judkins VEuPathDB obsolete sporozoite detection assay true An information content entity about the groups of participants that are randomized to receive an intervention in a trial. VEuPathDB study cluster information A blood microbiology datum that indicates whether some organism was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of organism in blood A cerebrospinal fluid microbiology datum that indicates whether some organism was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of organism in cerebrospinal fluid A endotracheal tube aspirate microbiology datum that indicates whether some organism was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of organism in endotracheal aspirate A feces microbiology datum that indicates whether some organism was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of organism in feces A induced sputum microbiology datum that indicates whether some organism was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of organism in induced sputum A lung microbiology datum that indicates whether some organism was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of organism in lung A nasopharyngeal or oropharyngeal swab microbiology datum that indicates whether some organism was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of organism in nasopharynx or oropharynx A pleural fluid microbiology datum that indicates whether some organism was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of organism in pleural fluid A umbilical cord blood microbiology datum that indicates whether some organism was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of organism in umbilical cord blood A urine microbiology datum that indicates whether some organism was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of organism in urine A 16S rRNA sequencing assay in which primers target the V1-V2 portion of the 16s gene. Person: John Judkins, Wojtek Bażant MicrobiomeDB https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/284 MicrobiomeDB 16S rRNA sequencing assay targeting V1-V2 region 16S rRNA sequencing assay in which primers target the V1-V3 portion of the 16s gene Person: John Judkins, Wojtek Bażant MicrobiomeDB https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/284 MicrobiomeDB 16S rRNA sequencing assay targeting V1-V3 region 16S rRNA sequencing assay in which primers target the V2 portion of the 16s gene Person: John Judkins, Wojtek Bażant MicrobiomeDB https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/284 MicrobiomeDB 16S rRNA sequencing assay targeting V2 region 16S rRNA sequencing assay in which primers target the V3-V4 portion of the 16s gene Person: John Judkins, Wojtek Bażant MicrobiomeDB https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/284 MicrobiomeDB 16S rRNA sequencing assay targeting V3-V4 region 16S rRNA sequencing assay in which primers target the V3-V5 portion of the 16s gene Person: John Judkins, Wojtek Bażant MicrobiomeDB https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/284 MicrobiomeDB 16S rRNA sequencing assay targeting V3-V5 region 16S rRNA sequencing assay in which primers target the V4 portion of the 16s gene Person: John Judkins, Wojtek Bażant MicrobiomeDB https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/284 MicrobiomeDB 16S rRNA sequencing assay targeting V4 region A placental blood microbiology datum that indicates whether some organism was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB 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. John Judkins ORCID:0000-0001-6595-0902 https://www.biorxiv.org/content/10.1101/2022.03.09.483664v1 Ann Sizemore Blevins eukaryote detection and abundance analysis using CORRAL software An information content entity that is about a health care process. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/441 Jie Zheng health care information A participant under investigation that is the female biological parent of a participant under investigation. John Judkins ORCID:0000-0001-6595-0902 http://purl.obolibrary.org/obo/GSSO_001986 https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/548 maternal participant under investigation A collecting specimen from organism in which the organism is a maternal participant under investigation. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/548 maternal specimen collection process A participant under investigation that is an offspring of a participant under investigation. http://purl.obolibrary.org/obo/NCIT_C42708 https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/548 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. John Judkins ORCID:0000-0001-6595-0902 https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/548 maternal urine microbiology datum A urine specimen that is the specified output of a maternal specimen collection process. John Judkins ORCID:0000-0001-6595-0902 https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/548 maternal urine specimen A saliva specimen that is the specified output of a maternal specimen collection process. John Judkins ORCID:0000-0001-6595-0902 maternal saliva specimen A feces specimen that is the specified output of a maternal specimen collection process. John Judkins ORCID:0000-0001-6595-0902 maternal feces specimen A feces assay that has a maternal feces specimen as evaluant. maternal feces assay Observation date a time measurement datum specifying the date of a clinical visit scheduled for sixty days after a treatment Date of observation EuPathDB 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. Jie Zheng https://orcid.org/0000-0002-2999-0103 percentage parasitemia VEuPathDB https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/416 VEuPathDB Genomics 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. Person: John Judkins MicrobiomeDB https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/208 metagenome pathway and function analysis 4th level EC metagenome abundance data 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. Person: John Judkins MicrobiomeDB https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/208 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. Person: John Judkins MicrobiomeDB https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/208 metagenome enzyme pathway abundance data Metagenome enzyme pathway coverage data A data item that is the output of a metagenome pathway and function analysis for gene coverage in a pathway defined by EC classifications. Person: John Judkins MicrobiomeDB https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/208 metagenome enzyme pathway coverage data Relative taxonomic abundance analysis A data transformation of input sequence data to obtain the fraction of relative abundance of organisms. Person: John Judkins MicrobiomeDB https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/208 relative taxonomic abundance analysis Kingdom A data item that is the output of a relative taxonomic abundance analysis for organisms grouped at the level of kingdom. Person: John Judkins MicrobiomeDB https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/208 relative abundance of kingdom data Phylum A data item that is the output of a relative taxonomic abundance analysis for organisms grouped at the level of phylum. Person: John Judkins MicrobiomeDB https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/208 relative abundance of phylum data Class A data item that is the output of a relative taxonomic abundance analysis for organisms grouped at the level of class. Person: John Judkins MicrobiomeDB https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/208 relative abundance of class data Order A data item that is the output of a relative taxonomic abundance analysis for organisms grouped at the level of order. Person: John Judkins MicrobiomeDB https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/208 relative abundance of order data Family A data item that is the output of a relative taxonomic abundance analysis for organisms grouped at the level of family. Person: John Judkins MicrobiomeDB https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/208 relative abundance of family data Genus A data item that is the output of a relative taxonomic abundance analysis for organisms grouped at the level of genus. Person: John Judkins MicrobiomeDB https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/208 relative abundance of genus data Species A data item that is the output of a relative taxonomic abundance analysis for organisms grouped at the level of species. Person: John Judkins MicrobiomeDB https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/208 relative abundance of species data Alpha diversity taxonomic analysis A data transformation of input sequence data to obtain a mean species diversity. Person: John Judkins MicrobiomeDB https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/208 alpha diversity taxonomic analysis Shannon-indexed alpha diversity data A data item that is the output of an alpha diversity taxonomic analysis based on the Shannon index of diversity. Person: John Judkins MicrobiomeDB https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/208 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. Person: John Judkins MicrobiomeDB https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/208 inverse Simpson-indexed alpha diversity data Plant taxon detected by sequence match A taxon detected by sequence match that indicates whether a plant taxon was detected. Person: John Judkins MicrobiomeDB plant taxon detected by sequence match Animal taxon detected by sequence match A taxon detected by sequence match that indicates whether an animal taxon was detected. Person: John Judkins MicrobiomeDB 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. Person: John Judkins MicrobiomeDB protist taxon detected by sequence match Taxon detected by sequence match 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. Person: John Judkins MicrobiomeDB taxon detected by sequence match Fungal taxon detected by sequence match A taxon detected by sequence match that indicates whether a fungal taxon was detected. Person: John Judkins MicrobiomeDB fungal taxon detected by sequence match 12.34 CPM (copies per million reads) A data item of the normalized number of sequences that match a specific taxon. Person: John Judkins taxon-specific sequence matches MicrobiomeDB normalized number of taxon-specific sequence matches A data transformation of input sequence data to obtain the absolute abundance of organisms. John Judkins ORCID:0000-0001-6595-0902 MicrobiomeDB https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/484 MicrobiomeDB John Brestelli 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. John Judkins ORCID:0000-0001-6595-0902 MicrobiomeDB https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/484 MicrobiomeDB 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. John Judkins ORCID:0000-0001-6595-0902 MicrobiomeDB https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/484 MicrobiomeDB 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. John Judkins ORCID:0000-0001-6595-0902 MicrobiomeDB https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/484 MicrobiomeDB 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. John Judkins ORCID:0000-0001-6595-0902 MicrobiomeDB https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/484 MicrobiomeDB 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. John Judkins ORCID:0000-0001-6595-0902 MicrobiomeDB https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/484 MicrobiomeDB 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. John Judkins ORCID:0000-0001-6595-0902 MicrobiomeDB https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/484 MicrobiomeDB 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. John Judkins ORCID:0000-0001-6595-0902 MicrobiomeDB https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/484 MicrobiomeDB 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 Matched case An information content entity that is about a subject pairing of two participants for a case-control study design Person: John Judkins, Chris Stoeckert Matched case EuPathDB information on case matching Previous diarrheal care A clinical history that is about a treatment for diarrhea. Person: John Judkins VEuPathDB previous diarrheal treatment datum Diarrheal episodes an information content entity that is about a realization of diarrhea John Judkins Diarrheal episodes EuPathDB information on diarrheal episode Rehydration therapy Treatment whose aim is to restore the normal hydration state of a living organism. Person: Cristian Cocos, Jie Zheng, Chris Stoeckert Rehydration therapy EuPathDB GEMS Penn Group rehydration treatment Dwelling environment environmental system associated with the dwelling used by humans. Person: Cristian Cocos, Jie Zheng, Chris Stoeckert GEMS Penn Group environment associated with human dwelling Administrative information study participant information that specifies details of the study design execution in which the human participant under investigation is participating John Judkins Administrative information EuPathDB study participant administrative information Eligibility criteria An information content entity that mentions an eligiblity criterion Person: John Judkins Eligibility criteria EuPathDB information on eligibility criterion Individuals related to participant 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 John Judkins Individuals related to participant EuPathDB information on relation to participant Stool characteristics A data item that is about a quality of a fecal specimen Person: John Judkins Stool characteristics EuPathDB fecal specimen quality data item Stool sample collection process Specimen collection process aimed at collecting a feces specimen. Person: Cristian Cocos, Jie Zheng, Chris Stoeckert GEMS Penn Group 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 Person: John Judkins Antibiotic administered before stool collection EuPathDB information specifying antibiotic administered before stool collection Organization that undertakes a clinical study at some point in time. Person: Cristian Cocos, Jie Zheng, Chris Stoeckert GEMS Penn Group obsolete study center true Case ID A participant identifier that denotes the bearer of a case-control study case role. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB case participant identifier Death location Site where a human life process ended. Person: Cristian Cocos, Jie Zheng, Chris Stoeckert place of death GEMS Penn Group location of death Caregiver plus participant weight 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. "caretaker" replaced with "caregiver" Person: John Judkins Weight of caretaker + child EuPathDB caregiver and participant combined mass measurement datum Caregiver weight A mass measurement datum that is the result of measuring the mass of a caregiver of a human participant under investigation. "caretaker" replaced with "caregiver" Person: John Judkins Weight of caretaker alone EuPathDB caregiver of participant mass measurement datum Height A length measurement datum that is the result of the first in a series of assays measuring the height of the same material entity. Person: John Judkins VEuPathDB first height measurement datum Height, 2nd A length measurement datum that is the result of the second in a series of assays measuring the height of the same material entity. Person: John Judkins VEuPathDB second height measurement datum Height, 3rd A length measurement datum that is the result of the third in a series of assays measuring the height of the same material entity. Person: John Judkins VEuPathDB third height measurement datum Mean height an average value that is the specified output of a data transformation that has as input only length measurement data about height John Judkins EuPathDB mean height Median height A center value that is the specified output of a median calculation that has as input only length measurement data about height Person: John Judkins EuPathDB median height MUAC 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 John Judkins MUAC, 1st The Mother and Child Health and Education Trust first mid-upper arm circumference datum MUAC, 2nd 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 John Judkins MUAC, 2nd The Mother and Child Health and Education Trust second mid-upper arm circumference datum MUAC, 3rd 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 Person: John Judkins MUAC, 3rd EuPathDB third mid-upper arm circumference datum Mean MUAC An average value of two or more mid-upper arm circumference data of the same human participant under investigation Person: John Judkins, Chris Stoeckert MUAC; mean EuPathDB mean mid-upper arm circumference Median MUAC A center value of one or more mid-upper arm circumference data of the same human participant under investigation Person: John Judkins, Chris Stoeckert MUAC; median EuPathDB median mid-upper arm circumference A temperature measurement datum that is about the temperature of an axilla John Judkins Axillary temperature EuPathDB obsolete axillary temperature measurement datum true 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 John Judkins Respiratory rate 1 Respiratory rate per minute, 1st EuPathDB yes first respiratory rate measurement datum Respiratory rate, 2nd 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 John Judkins Respiratory rate 2 Respiratory rate per minute, 2nd EuPathDB second respiratory rate measurement datum Mean respiratory rate 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 John Judkins Respiratory rate, mean EuPathDB average respiratory rate Drinking water container Container used by humans to drink water. Person: Cristian Cocos, Jie Zheng, Chris Stoeckert GEMS Penn Group water container Chlorine test result 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. Person: Cristian Cocos, Jie Zheng, Chris Stoeckert GEMS Penn Group chlorine test result Hand washing location Site where humans wash their hands. Person: Cristian Cocos, Jie Zheng, Chris Stoeckert GEMS Penn Group location of hand washing Currently receiving medication An information content entity that specifies whether a human participant under investigation is currently a medication-taking patient Jie Zheng Chris Stoeckert Person: John Judkins, Jie Zheng Currently receiving medication EuPathDB https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/142 indicator of whether participant receiving medication Date stool passed A time measurement datum of the date encompassing a defecation Person: John Judkins Date stool passed EuPathDB date of defecation Stool consistency a quality of water composition, shape, or structure that inheres in fecal material John Judkins Wikipedia: Bristol stool scale stool consistency First antibiotic administration date A time measurement datum of the date of the first in a series of antibiotic administrations to a human participant under investigation Person: John Judkins EuPathDB date of first antibiotic administration Time of 1st antibiotic administration A time measurement datum of the time of the first in a series of antibiotic administrations to a human participant under investigation Person: John Judkins Time of first antibiotic administration EuPathDB time of first antibiotic administration to human participant under investigation Diarrheal episode duration A time measurement datum that is the result of measuring the duration of a diarrheal episode Person: John Judkins, Chris Stoeckert EuPathDB duration of diarrheal episode Stool volume 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 stool volume measurement datum GEMS Penn Group feces volume measurement datum Rehydration date a time measurement datum of the date at which a dehydration treatment is administered John Judkins Person: John Judkins EuPathDB date of rehydration Rehydration time a time measurement datum of the time of day at which a dehydration treatment is administered John Judkins EuPathDB time of rehydration Hospitalization duration A time measurement datum of the duration of a health care encounter occuring in a hospital facility. Person: John Judkins VEuPathDB duration of hospitalization Symptoms in the last 7 days A symptom at enrollment information about a symptom that was experienced within seven days prior to the time of enrollment Person: John Judkins Symptoms in the last 7 days EuPathDB symptom in last seven days information Symptoms since illness began A symptom or sign information that is about a symptom experienced after a disease course has started Person: John Judkins Symptoms since illness began EuPathDB symptom since illness began information Process of feeding of babies and young children with milk from a woman's breast. Person: Cristian Cocos, Jie Zheng, Chris Stoeckert GEMS Penn Group obsolete breastfeeding process true Participant ID at 1st enrollment Child study subject identifier received upon enrolling into a healthcare study for the first time. Person: Cristian Cocos, Jie Zheng, Chris Stoeckert GEMS Penn Group child study subject identifier at first enrollment Diarrhea treatment before visit 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. Person: John Judkins Diarrhea treatment before visit EuPathDB information on diarrhea treatment before clinical visit Money source for expenses before visit an information content entity that specifies how the money was raised to cover the cost of a health care encounter John Judkins Money source for expenses before visit EuPathDB information on raising money for health care encounter Previously sought care A previous diarrheal treatment datum that is about the person or place from which the treatment is sought Person: John Judkins Previously sought care EuPathDB information on where diarrheal treatment sought Anthropometry flag A categorical value specification that specifies whether the value of an anthropometric information content entity lies outside a specified range Person: John Judkins Anthropometry flag EuPathDB 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 Person: John Judkins Diarrhea treatment given in health center EuPathDB 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 Person: John Judkins Diarrhea treatment by prescription at home EuPathDB 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. Person: John Judkins VEuPathDB diagnosis previous to two month follow-up Sex, matched case Information on case matching that denotes the sex of the case subject Person: John Judkins Sex, matched case EuPathDB information on sex of matched case Birth date, matched case The date of birth of a case subject in a case-control study Person: John Judkins EuPathDB 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. Person: John Judkins VEuPathDB eligibility criterion of diarrhea episode starting with past 7 days Eligible for enrollment A categorical value specification that specifies whether a human participant under investigation meets requirements for human subject enrollment Jie Zheng Person: John Judkins Eligibility for enrollment EuPathDB https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/142 indicator of whether participant eligible for enrollment Fever at episode >37.5 C a categorical measurement datum that is about a maximum fever temperature in Celsius and specifies whether its value is at least 37.5 John Judkins Fever at episode, temperature >37.5C EuPathDB presence of maximum fever temperature of at least 37.5 degrees 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 Adenovirus Jie Zheng Chris Stoeckert John Judkins Adenovirus ELISA performed EuPathDB https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/142 indicator of whether Adenovirus ELISA performed 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 Astrovirus Jie Zheng Chris Stoeckert John Judkins Astrovirus ELISA performed EuPathDB https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/142 indicator of whether Astrovirus ELISA performed Rotavirus 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 Jie Zheng Chris Stoeckert John Judkins Rotavirus ELISA performed EuPathDB https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/142 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 Jie Zheng Chris Stoeckert John Judkins modified acid fast staining method performed EuPathDB https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/142 indicator of whether modified acid fast staining method performed Stool test count A count of feces assays evaluating the same specimen. Person: John Judkins VEuPathDB number of feces assays Norovirus qRT-PCR performed 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 Jie Zheng Chris Stoeckert John Judkins Norovirus RT-PCR performed EuPathDB https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/142 indicator of whether Norovirus RT-PCR performed 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 Cryptosporidium Jie Zheng Chris Stoeckert John Judkins Cryptosporidium ELISA performed EuPathDB https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/142 indicator of whether Cryptosporidium ELISA performed 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 Entamoeba histolytica Jie Zheng Chris Stoeckert John Judkins Entamoeba histolytica ELISA performed EuPathDB https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/142 indicator of whether Entamoeba histolytica ELISA performed Giardia 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 Jie Zheng Chris Stoeckert John Judkins Giardia ELISA performed EuPathDB https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/142 indicator of whether Giardia ELISA performed Adenovirus, by ELISA A eukaryota in feces datum by enzyme-linked immunosorbent assay datum that specifies whether the virus was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Adenoviridae in feces by enzyme-linked immunosorbent assay Aeromonas, by bacteriology An Aeromonas in feces datum that specifies whether Aeromonas was detected, without specifying the taxon further. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Aeromonas unspecified in feces Ascaris lumbricoides, by microscopy A eukaryota in feces datum in feces that specifies whether Ascaris lumbricoides was detected by microscopy assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Ascaris lumbricoides in feces by microscopy assay Astrovirus, by ELISA An Astrovirus in feces by enzyme-linked immunosorbent assay datum that specifies whether the virus was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Astrovirus in feces by enzyme-linked immunosorbent assay Trichuris trichiura, by microscopy A eukaryota in feces datum that specifies whether Trichuris trichiura was detected by microscopy assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Trichuris trichiura in feces by microscopy assay Balantidium coli, by microscopy A eukaryota in feces datum that specifies whether Balantioides cf. coli was detected by microscopy assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Balantioides coli in feces by microscopy assay Aeromonas, by bacteriology result A bacteria in feces datum that is used to determine the presence of Aeromonas in the specimen. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB Aeromonas in feces datum Campylobacter, by ELISA result 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. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB Campylobacter in feces by enzyme-linked immunosorbent assay datum Campylobacter, by bacteriology result A bacteria in feces datum that is used to determine the presence of Campylobacter in the specimen. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB 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. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB Escherichia coli in feces datum Salmonella, by bacteriology result A bacteria in feces datum that is used to determine the presence of Salmonella in the specimen. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB Salmonella in feces datum Shigella, by bacteriology result A bacteria in feces datum that is used to determine the presence of Shigella in the specimen. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB Shigella in feces datum Vibrio, by bacteriology result A bacteria in feces datum that is used to determine the presence of Vibrio in the specimen. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB Vibrio in feces datum Chilomastix mesnili, by microscopy A eukaryota in feces datum that specifies whether Chilomastix mesnili was detected by microscopy assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Chilomastix mesnili in feces by microscopy assay Cyclospora, by microscopy A eukaryota in feces datum that specifies whether Cyclospora was detected by microscopy assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Cyclospora in feces by microscopy assay Entamoeba histolytica, by ELISA A Entamoeba histolytica in feces by enzyme-linked immunosorbent assay datum that specifies whether the organism was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Entamoeba histolytica in feces by enzyme-linked immunosorbent assay Endolimax nana, by microscopy A eukaryota in feces datum that specifies whether Endolimax nana was detected by microscopy assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Endolimax nana in feces by microscopy assay Enterobius vermicularis, by microscopy A eukaryota in feces datum that specifies whether Enterobius vermicularis was detected by microscopy assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Enterobius vermicularis in feces by microscopy assay Adenovirus, by ELISA result 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. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB Adenovirus in feces by enzyme-linked immunosorbent assay datum Astrovirus, by ELISA result 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. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB Astrovirus in feces by enzyme-linked immunosorbent assay datum Hymenolepis diminuta, by microscopy A eukaryota in feces datum that specifies whether Hymenolepis diminuta was detected by microscopy assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Hymenolepis diminuta in feces by microscopy assay Hymenolepis nana, by microscopy A eukaryota in feces datum that specifies whether Rodentolepis nana was detected by microscopy assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Rodentolepis nana in feces by microscopy assay Hookworm, by microscopy A eukaryota in feces datum that specifies whether Ancylostomatoidea was detected by microscopy assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Ancylostomatoidea in feces by microscopy assay Iodamoeba butschlii, by microscopy A eukaryota in feces datum that specified whether Iodamoeba butschlii was detected by microscopy assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Iodamoeba butschlii by microscopy assay Entamoeba coli, by microscopy A eukaryota in feces datum that specifies whether Entamoeba coli was detected by microscopy assay John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Entamoeba coli in feces by microscopy assay Norovirus, by RT-PCR A virus in feces datum that specifies whether Norovirus was detected by real time polymerase chain reaction assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Norovirus in feces by real time polymerase chain reaction assay Norovirus GI, by RT-PCR A virus in feces datum that specifies whether Norovirus GI was detected by real time polymerase chain reaction assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Norovirus GI in feces by real time polymerase chain reaction assay Norovirus GII, by RT-PCR A virus in feces datum that specifies whether Norovirus GII was detected by real time polymerase chain reaction assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Norovirus GII in feces by real time polymerase chain reaction assay Norovirus GII, by qRT-PCR 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 Norovirus GII in a feces specimen. Person: John Judkins VEuPathDB multiplex qPCR threshold cycle for Norovirus GII in feces Norovirus GI, by qRT-PCR 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 Norovirus GI in a feces specimen. Person: John Judkins VEuPathDB multiplex qPCR threshold cycle for Norovirus GI in feces Norovirus, by qRT-PCR 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 Norovirus in a feces specimen. Person: John Judkins VEuPathDB multiplex qPCR threshold cycle for Norovirus in feces Cryptosporidium, by ELISA result 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. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB 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 John Judkins Entamoeba histolytica, by ELISA EuPathDB obsolete presence of Entamoeba histolytica by ELISA true Giardia, by ELISA result 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. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB 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. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Plesiomonas shigelloides in feces Rotavirus, by ELISA A virus in feces datum that specifies whether Rotavirus was detected by enzyme-linked immunosorbent assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Rotavirus in feces by enzyme-linked immunosorbent assay Salmonella, by bacteriology A Salmonella in feces datum that specifies whether Salmonella was detected, without specifying the taxon further. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Salmonella unspecified in feces Schistosoma, by microscopy A eukaryota in feces datum that specifies whether Schistosoma was detected by microscopy assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Schistosoma in feces by microscopy assay Shigella, by bacteriology A Shigella in feces datum that specifies whether Shigella was detected, without specifying the taxon further. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB 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. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Strongyloides stercoralis in feces by microscopy assay STEC stx1-pos or stx2-pos, by PCR An Escherichia coli in feces datum that specifies whether Escherichia coli was detected by polymerase chain reaction assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Escherichia coli in feces by polymerase chain reaction assay Taenia, by microscopy A eukaryota in feces datum that specifies whether Taenia was detected by microscopy assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Taenia in feces by microscopy assay Vibrio, by bacteriology A Vibrio in feces datum that specifies whether Vibrio was detected, withou specifying the taxon further. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Vibrio unspecified in feces Yersinia enterocolitica, by bacteriology A bacteria in feces datum that specifies whether Yersinia enterocolitica was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Yersinia enterocolitica in feces Any bacteria, by any method A bacteria in feces datum that specifies whether bacteria were detected, without further specifying the taxon or assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of unspecified bacteria in feces by unspecified assay Any parasites, by any method A feces microbiology datum that specifies whether a parasite organism was detected, without further specifying the taxon or assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of unspecified parasite organism in feces by unspecified assay presence of pathogen A feces microbiology datum that specifies whether a pathogen was detected, without further specifying the taxon or assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB 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. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of any pathogen excluding Norovirus in feces by unspecified assay Bacteria count A count of species of bacteria in a feces specimen. Person: John Judkins VEuPathDB number of bacteria species in feces specimen Parasite count A count of species of parasite organisms in a feces specimen. Person: John Judkins VEuPathDB 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. Person: John Judkins VEuPathDB number of pathogen species in feces specimen Virus count A count of species of virus in a feces specimen. Person: John Judkins VEuPathDB number of virus species in feces specimen Any virus, by any method A feces microbiology datum that specifies whether a virus was detected, without further specifying the taxon or assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB 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. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB 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. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of parasite organism in feces by modified acid-fast stain microscopy assay Campylobacter, by PCR A Campylobacter in feces datum that specifies whether the organism was detected by polymerase chain reaction assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Campylobacter in feces by polymerase chain reaction assay Campylobacter, by ELISA A Campylobacter in feces by enzyme-linked immunosorbent assay datum that specifies whether the organism was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Campylobacter in feces by enzyme-linked immunosorbent assay Cryptosporidium, by ELISA A Cryptosporidium in feces by enzyme-linked immunosorbent assay datum that specifies whether the organism was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB 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. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB 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. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB Entamoeba histolytica in feces by microscopy assay datum Giardia, by ELISA A Giardia in feces by enzyme-linked immunosorbent assay datum that specifies whether the organism was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Giardia in feces by enzyme-linked immunosorbent assay Giardia lamblia, by microscopy result 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. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB Giardia lamblia in feces by microscopy assay datum Isospora, by microscopy A eukaryota in feces datum that specifies whether Isospora was detected by microscopy assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Isospora in feces by microscopy assay Myeloperoxidase A feces assay datum of the concentration of myeloperoxidase. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/505 ClinEpiDB Sheena Tomko feces myeloperoxidase concentration Blood sample collection process A collecting specimen from organism that has the objective to obtain a blood specimen. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/548 ClinEpiDB blood specimen collection process Dairy An information content entity that specifies whether a dairy food product was consumed by a study participant yesterday. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB indicator of dairy food product consumption yesterday Breastfeeding Information on process that is about suckling behavior. Person: John Judkins and Chris Stoeckert Breastfeeding EuPathDB information on suckling behavior Calories 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. Person: John Judkins Calories EuPathDB calorie intake measurement Stool intestinal inflammation test 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. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/507 ClinEpiDB Sheena Tomko feces assay to detect inflammation ALRI episodes An information content entity that is about an acute manifestation of a lower respiratory tract disease Person: John Judkins ALRI episodes EuPathDB information on acute lower respiratory tract disease A laboratory test that has a blood specimen as specified input. VEuPathDB obsolete blood test true A laboratory test that has a urine specimen as specified input. John Judkins VEuPathDB obsolete urine test true An information content entity that is about a microscopy assay Person: John Judkins VEuPathDB obsolete information on microscopy assay true Ferritin A blood assay datum of the concentration of ferritin. Person: John Judkins VEuPathDB blood ferritin concentration Blastocystis, 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 Blastocystis in a feces specimen. Person: John Judkins VEuPathDB TaqMan threshold cycle for Blastocystis in feces Clostridium difficile, 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 Clostridioides difficile in a feces specimen. Person: John Judkins VEuPathDB TaqMan threshold cycle for Clostridioides difficile in feces Entamoeba, 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 Entamoeba in a feces specimen. Person: John Judkins VEuPathDB TaqMan threshold cycle for Entamoeba in feces Hymenolepis nana, 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 Rodentolepis nana in a feces specimen. Person: John Judkins VEuPathDB 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. Person: John Judkins VEuPathDB TaqMan threshold cycle for Mycobacterium tuberculosis in feces Norovirus GI.1, 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 Norovirus GI.1 in a feces specimen. Person: John Judkins VEuPathDB TaqMan threshold cycle for Norovirus GI.1 in feces Norovirus GII.4, 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 Norovirus GII.4 in a feces specimen. Person: John Judkins VEuPathDB TaqMan threshold cycle for Norovirus GII.4 in feces Plesiomonas, 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 Plesiomonas in a feces specimen. Person: John Judkins VEuPathDB TaqMan threshold cycle for Plesiomonas in feces Schistosoma, 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 Schistosoma in a feces specimen. Person: John Judkins VEuPathDB TaqMan threshold cycle for Schistosoma in feces Retinol A blood assay datum of the concentration of retinol. Person: John Judkins VEuPathDB blood retinol concentration Entamoeba histolytica, by ELISA result 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. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB Entamoeba histolytica in feces by enzyme-linked immunosorbent assay datum Vibrio in stool A bacteria in feces datum that specifies whether Vibrio was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Vibrio in feces Virus in stool A virus in feces datum that specifies whether a virus was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of virus in feces Yersinia in stool A bacteria in feces datum that specifies whether Yersinia was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Yersinia in feces Aeromonas in stool A bacteria in feces datum that specifies whether Aeronomas was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Aeromonas in feces Bacteria in stool A bacteria in feces datum that specifies whether bacteria were detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of bacteria in feces Campylobacter in stool A bacteria in feces datum that specifies whether Campylobacter was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Campylobacter in feces Escherichia in stool A bacteria in feces datum that specifies whether Escherichia was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Escherichia in feces Plesiomonas in stool A bacteria in feces datum that specifies whether Plesiomonas was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Plesiomonas in feces Salmonella in stool A bacteria in feces datum that specifies whether Salmonella was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Salmonella in feces Shigella in stool A bacteria in feces datum that specifies whether Shigella was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Shigella in feces Norovirus GI, by qRT-PCR A virus in feces datum that specifies whether Norovirus GI was detected by real time reverse-transcription polymerase chain reaction assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Norovirus GI in feces by real time reverse-transcription polymerase chain reaction assay Norovirus GII, by qRT-PCR A virus in feces datum that specifies whether Norovirus GII was detected by real time reverse-transcription polymerase chain reaction assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Norovirus GII in feces by real time reverse-transcription polymerase chain reaction assay Charcoal Charcoal as a cooking fuel Person: John Judkins Charcoal EuPathDB charcoal cooking fuel An information content entity that mentions drinking water piped into a dwelling Person: John Judkins Piped into house EuPathDB obsolete information on drinking water piped into dwelling true An information content entity that mentions drinking water obtained through a plumbing fixture located in the yard of a human dwelling Person: John Judkins Piped into yard EuPathDB obsolete information on drinking water piped into yard true Rainwater drinking water that is derived from rainwater John Judkins Rainwater EuPathDB drinking water derived from rainwater Bore hole Drinking water that is derived from bore hole water John Judkins Bore hole EuPathDB drinking water derived from bore hole water Difficulty breathing A symptom since illness began information that mentions respiratory distress Person: John Judkins Difficulty breathing EuPathDB respiratory distress since illness began information Convulsion A symptom since illness began information that mentions convulsion Person: John Judkins Convulsion EuPathDB convulsion since illness began information ORALITE or ORS Information on diarrhea treatment before clinical visit that mentions an oral rehydration product as the treatment. Person: John Judkins VEuPathDB information on oral rehydration for diarrhea before visit Cutting down expenses from meals information on raising money for health care encounter that specifies that less money was spent on food to cover healthcare costs John Judkins Cutting down expenses from meal EuPathDB information on cutting food expenses to pay for health care Cutting down from other expenses 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 John Judkins Cutting down from other expenses EuPathDB information on cutting non-food expenses to pay for health care Using savings information on raising money for health care encounter that specifies that the money to cover healthcare costs was derived from savings John Judkins Using savings EuPathDB information on using savings to pay for health care Borrowing information on raising money for health care encounter that specifies that the money to cover healthcare costs was borrowed John Judkins Borrowing EuPathDB information on borrowing to pay for health care Selling assets 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 John Judkins Selling assets EuPathDB 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 John Judkins Asking for donations outside the household EuPathDB information on asking for donations outside the household to pay for health care Paid by relative or friend 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 John Judkins Paid by relative or friend EuPathDB information on health care paid for by relative or friend Rectal prolapse A symptom or sign information that mentions rectal prolapse Person: John Judkins Rectal prolapse EuPathDB rectal prolapse information Bipedal edema A symptom or sign information that mentions bipedal edema Person: John Judkins Bipedal edema EuPathDB bipedal edema symptom or sign information Skin has 'flaky paint' appearance A symptom or sign information that mentions flaky paint dermatosis Person: John Judkins Skin has 'flaky paint' appearance EuPathDB flaky paint dermatosis information Diarrhea A diagnosis at patient discharge that is an assertion that a patient has diarrhea. Person: John Judkins VEuPathDB diagnosis of diarrhea at patient discharge Dysentery A diagnosis at patient discharge that is an assertion that a patient has dysentery. Person: John Judkins VEuPathDB 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. Person: John Judkins VEuPathDB diagnosis of pneumonia of lower repiratory tract disease at patient discharge Malaria A diagnosis at patient discharge that is an assertion that a patient has malaria. Person: John Judkins VEuPathDB diagnosis of malaria at patient discharge Malnutrition A diagnosis at patient discharge that is an assertion that a patient has nutritional deficiency disease. Person: John Judkins VEuPathDB diagnosis of nutritional deficiency disease at patient discharge Typhoid A diagnosis at patient discharge that is an assertion that a patient has typhoid fever. Person: John Judkins VEuPathDB diagnosis of typhoid fever at patient discharge Adenovirus 40/41, by ELISA A virus in feces datum that specifies whether Human mastadenovirus F was detected by enzyme-linked immunosorbent assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Human mastadenovirus F in feces by enzyme-linked immunosorbent assay Adenovirus non-40/41, by ELISA A virus in feces datum that specifies whether Adenoviridae excluding human mastadenovirus F were detected by enzyme-linked immunosorbent assay John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Adenoviridae excluding human mastadenovirus F in feces by enzyme-linked immunosorbent assay Vibrio cholerae O1, by bacteriology A Vibrio in feces datum that specifies whether Vibrio cholerae O1 was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB 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. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB 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. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Vibrio cholerae serotype Ogawa in feces Vibrio cholerae O139, by bacteriology A Vibrio in feces datum that specifies whether Vibrio cholerae O139 was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Vibrio cholerae O139 in feces Salmonella typhi, by bacteriology A Salmonella in feces datum that specifies whether Salmonella enterica subsp. enterica serovar Typhi was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Salmonella enterica subsp. enterica serovar Typhi in feces Salmonella non-typhi, by bacteriology A Salmonella in feces datum that specifies whether Salmonella enterica enterica other than Typhi was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Salmonella enterica enterica other than Typhi Sapovirus, by RT-PCR A virus in feces datum that specifies whether Sapovirus was detected by reverse transcription polymerase chain reaction assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB 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. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB 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. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB 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. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB 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. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB 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. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB 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. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB Shigella flexneri non-typeable in feces datum Shigella non-typeable, by bacteriology A Shigella in feces datum that specifies whether Shigella non-typeable was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Shigella non-typeable in feces Vibrio cholerae, by bacteriology A Vibrio in feces datum that specifies whether Vibrio cholerae was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB 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. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Vibrio cholerae non-(O1 or O139) in feces Vibrio (other species), by bacteriology A Vibrio in feces datum that specifies whether Vibrio other than cholerae or parahaemolyticus was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Vibrio non-(cholerae or parahaemolyticus) in feces Campylobacter coli, by bacteriology A Campylobacter in feces datum that specifies whether Campylobacter coli was detected, without specifying the taxon further. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Campylobacter coli in feces Campylobacter jejuni, by bacteriology A Campylobacter in feces datum that specifies whether Campylobacter jejuni was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Campylobacter jejuni in feces Shigella flexneri, by bacteriology A Shigella in feces datum that specifies whether Shigella flexneri was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Shigella flexneri in feces Shigella boydii, by bacteriology A Shigella in feces datum that specifies whether Shigella boydii was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Shigella boydii in feces Shigella dysenteriae, by bacteriology A Shigella in feces datum that specifies whether Shigella dysenteriae was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Shigella dysenteriae in feces Vibrio parahaemolyticus, by bacteriology A Vibrio in feces datum that specifies whether Vibrio parahaemolyticus was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Vibrio parahaemolyticus in feces Shigella sonnei, by bacteriology A Shigella in feces datum that specifies whether Shigella sonnei was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB 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. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB 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. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB 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. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB 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. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB 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. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Shigella flexneri Y in feces Astrovirus, by RT-PCR A virus in feces datum that specifies whether Astrovirus was detected by reverse transcription polymerase chain reaction assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Astrovirus in feces by reverse transcription polymerase chain reaction assay Adenovirus, 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 Adenoviridae in a feces specimen. Person: John Judkins VEuPathDB TaqMan threshold cycle for Adenoviridae in feces Aeromonas 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 Aeromonas in a feces specimen. Person: John Judkins VEuPathDB TaqMan threshold cycle for Aeromonas in feces Ancylostoma, 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 Ancylostoma in a feces specimen. Person: John Judkins VEuPathDB TaqMan threshold cycle for Ancylostoma in feces Ascaris, 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 Ascaris in a feces specimen. Person: John Judkins VEuPathDB TaqMan threshold cycle for Ascaris in feces Astrovirus, 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 Astroviridae in a feces specimen. Person: John Judkins VEuPathDB TaqMan threshold cycle for Astroviridae in feces Bacteroides fragilis, 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 Bacteroides fragilis in a feces specimen. Person: John Judkins VEuPathDB TaqMan threshold cycle for Bacteroides fragilis in feces Campylobacter, 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 Campylobacter in a feces specimen. Person: John Judkins VEuPathDB TaqMan threshold cycle for Campylobacter in feces Cryptosporidium, 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 Cryptosporidium in a feces specimen. Person: John Judkins VEuPathDB TaqMan threshold cycle for Cryptosporidium in feces Cryptosporidium hominis, 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 Cryptosporidium hominis in a feces specimen. Person: John Judkins VEuPathDB TaqMan threshold cycle for Cryptosporidium hominis in feces Cryptosporidium parvum, 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 Cryptosporidium parvum in a feces specimen. Person: John Judkins VEuPathDB TaqMan threshold cycle for Cryptosporidium parvum in feces Cyclospora, 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 Cyclospora in a feces specimen. Person: John Judkins VEuPathDB TaqMan threshold cycle for Cyclospora in feces Enterocytozoon bieneusi, 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 Enterocytozoon bieneusi in a feces specimen. Person: John Judkins VEuPathDB TaqMan threshold cycle for Enterocytozoon bieneusi in feces Entamoeba histolytica, 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 Entamoeba histolytica in a feces specimen. Person: John Judkins VEuPathDB 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. Person: John Judkins VEuPathDB TaqMan threshold cycle for Encephalitozoon intestinalis in feces Giardia assemblage A, 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 Giardia intestinalis assemblage A in a feces specimen. Person: John Judkins VEuPathDB TaqMan threshold cycle for Giardia intestinalis assemblage A in feces Giardia assemblage B, 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 Giardia intestinalis assemblage B in a feces specimen. Person: John Judkins VEuPathDB TaqMan threshold cycle for Giardia intestinalis assemblage B in feces Giardia, 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 Giardia in a feces specimen. Person: John Judkins VEuPathDB TaqMan threshold cycle for Giardia in feces Helicobacter pylori, 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 Helicobacter pylori in a feces specimen. Person: John Judkins VEuPathDB TaqMan threshold cycle for Helicobacter pylori in feces Isospora, 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 Isospora in a feces specimen. Person: John Judkins VEuPathDB TaqMan threshold cycle for Isospora in feces Necator, 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 Necator in a feces specimen. Person: John Judkins VEuPathDB TaqMan threshold cycle for Necator in feces Norovirus GI, 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 Norovirus GI in a feces specimen. Person: John Judkins VEuPathDB TaqMan threshold cycle for Norovirus GI in feces Norovirus GII, 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 Norovirus GII in a feces specimen. Person: John Judkins VEuPathDB TaqMan threshold cycle for Norovirus GII in feces Rotavirus, 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 Rotavirus in a feces specimen. Person: John Judkins VEuPathDB TaqMan threshold cycle for Rotavirus in feces Rotavirus genotype G10, 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 Rotavirus G10 in a feces specimen. Person: John Judkins VEuPathDB TaqMan threshold cycle for Rotavirus G10 in feces Rotavirus genotype G12, 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 Rotavirus G12 in a feces specimen. Person: John Judkins VEuPathDB TaqMan threshold cycle for Rotavirus G12 in feces Rotavirus genotype G1, 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 Rotavirus G1 in a feces specimen. Person: John Judkins VEuPathDB TaqMan threshold cycle for Rotavirus G1 in feces Rotavirus genotype G2, 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 Rotavirus G2 in a feces specimen. Person: John Judkins VEuPathDB TaqMan threshold cycle for Rotavirus G2 in feces Rotavirus genotype G3, 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 Rotavirus G3 in a feces specimen. Person: John Judkins VEuPathDB TaqMan threshold cycle for Rotavirus G3 in feces Rotavirus genotype G4, 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 Rotavirus G4 in a feces specimen. Person: John Judkins VEuPathDB TaqMan threshold cycle for Rotavirus G4 in feces Rotavirus genotype G8, 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 Rotavirus G8 in a feces specimen. Person: John Judkins VEuPathDB TaqMan threshold cycle for Rotavirus G8 in feces Rotavirus genotype G9, 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 Rotavirus G9 in a feces specimen. Person: John Judkins VEuPathDB TaqMan threshold cycle for Rotavirus G9 in feces Rotavirus genotype P4, 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 Rotavirus A P4 in a feces specimen. Person: John Judkins VEuPathDB TaqMan threshold cycle for Rotavirus A P4 in feces Rotavirus genotype P6, 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 Human rotavirus P6 in a feces specimen. Person: John Judkins VEuPathDB TaqMan threshold cycle for Human rotavirus P6 in feces Rotavirus genotype P8, 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 Rotavirus A P8 in a feces specimen. Person: John Judkins VEuPathDB TaqMan threshold cycle for Rotavirus A P8 in feces Salmonella, 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 Salmonella in a feces specimen. Person: John Judkins VEuPathDB TaqMan threshold cycle for Salmonella in feces Sapovirus, 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 Sapovirus in a feces specimen. Person: John Judkins VEuPathDB TaqMan threshold cycle for Sapovirus in feces Strongyloides, 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 Strongyloides in a feces specimen. Person: John Judkins VEuPathDB TaqMan threshold cycle for Strongyloides in feces Trichuris trichiura, 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 Trichuris trichiura in a feces specimen. Person: John Judkins VEuPathDB TaqMan threshold cycle for Trichuris trichiura in feces Vibrio cholerae, 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 Vibrio cholerae in a feces specimen. Person: John Judkins VEuPathDB TaqMan threshold cycle for Vibrio cholerae in feces Ancylostoma duodenale, by RT-PCR A eukaryota in feces datum that specifies whether Ancylostoma duodenale was detected by real time polymerase chain reaction assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Ancylostoma duodenale in feces by real time polymerase chain reaction assay Ascaris lumbricoides, by RT-PCR A eukaryota in feces datum that specifies whether Ascaris lumbricoides was detected by real time polymerase chain reaction assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Ascaris lumbricoides in feces by real time polymerase chain reaction assay Ascaris lumbricoides, 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 Ascaris lumbricoides in the specimen. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB Ascaris lumbricoides in feces by reverse transcription polymerase chain reaction assay datum Bacteroides fragilis, by RT-PCR result 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. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB 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 John Judkins E. coli, by bacteriology EuPathDB obsolete presence of Escherichia coli by differential medium assay true Helicobacter pylori, by immunoassay A bacteria in feces datum that specifies whether Helicobacter pylori was detected by immunoassay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Helicobacter pylori in feces by immunoassay Hookworm, by RT-PCR A eukaryota in feces datum that specifies whether Ancylostomatoidea was detected by real time polymerase chain reaction assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Ancylostomatoidea in feces by real time polymerase chain reaction assay Necator americanus, by RT-PCR A eukaryota in feces datum that specifies whether Necator americanus was detected by real time polymerase chain reaction assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB 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. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB 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. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB 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. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB 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. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB 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. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB 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. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB 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. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB 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. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Shigella flexneri 3b in feces Shigella flexneri 3C, by bacteriology A Shigella in feces datum that specifies whether Shigella flexneri, serovar 3c was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Shigella flexneri, serovar 3c in feces Shigella flexneri 7A, by bacteriology A Shigella in feces datum that specifies whether Shigella flexneri 7a was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Shigella flexneri 7a in feces Stool weight A mass measurement datum of the mass of a feces specimen. Person: John Judkins Stool weight EuPathDB 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. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB Strongyloides stercoralis in feces by reverse transcription polymerase chain reaction assay datum Strongyloides stercoralis, by RT-PCR A Strongyloides stercoralis in feces by reverse transcription polymerase chain reaction assay datum that specifies whether the organism was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Strongyloides stercoralis in feces by reverse transcription polymerase chain reaction assay Test date A time measurement datum of the date encompassing a feces microbiology assay Person: John Judkins Test date EuPathDB date of feces microbiology assay Bacteroides fragilis toxin-pos, by PCR A Bacteroides fragilis in feces by reverse transcription polymerase chain reaction assay datum that specifies whether the organism was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB 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. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB 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. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB 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. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB 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. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB Vibrio cholerae Inaba or Ogawa in feces datum Diarrhea treatment A treatment information that mentions a medication that treats diarrhea. information on diarrhea treatment Bacteroides in stool A bacteria in feces datum that specifies whether Bacteroides was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Bacteroides in feces Clostridium in stool A bacteria in feces datum that specifies whether Clostridioides was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Clostridioides in feces Helicobacter in stool A bacteria in feces datum that specifies whether Helicobacter was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Helicobacter in feces Cause of death An information content entity that is about a dead human participant under investigation and specifies the process which caused the death of the participant Person: John Judkins Cause of death EuPathDB information on cause of death Aggregated illness data A data item that is the specified output of a data transformation that has multiple clinical data items as input. Person: John Judkins VEuPathDB aggregated clinical data item Plasmodium, by qPCR result 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. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB Plasmodium in blood by real time polymerase chain reaction assay datum Plasmodium ovale A Plasmodium in blood by microscopy assay datum that specifies whether Plasmodium ovale was detected by microscopy assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Plasmodium ovale in blood by microscopy assay Livestock a domesticated animal that is raised in an agricultural setting to produce labor and commodities John Judkins Livestock Wikipedia livestock animal None a categorical value specification that specifies that a bed net is not used John Judkins None EuPathDB no use of bed net Untreated a categorical value specification that specifies that a bed net is used, but it is not treated with insecticide John Judkins Untreated EuPathDB bed net not treated Regular ITN, treated >6 months ago a categorical value specification that specifies that a bed net is used, but it was last treated earlier than six months ago John Judkins Regular ITN treated >6 months ago EuPathDB bed net treated over six months ago Regular ITN, treated <6 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 John Judkins Regular ITN treated <6 months ago EuPathDB bed net treated within past six months Long-lasting ITN a categorical value specification that specifies that a bed net is used, and it was treated with long last insecticide John Judkins Long-lasting ITN EuPathDB bed net treated with long last insecticide Clinic 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 John Judkins Clinic EuPathDB information specifying fever treated at clinic in past 2 weeks Private practice 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 John Judkins Private practice EuPathDB information specifying fever treated by private practicioner in past 2 weeks Self-treated 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 John Judkins (Fever treatment location) Self-treated EuPathDB information specifying fever self-treated in past 2 weeks Not treated 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 John Judkins Not treated EuPathDB information specifying untreated fever in past two weeks Negative 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 John Judkins (Plasmodium species, by microscopy) Negative EuPathDB no Plasmodium by microscopy Plasmodium falciparum A Plasmodium in blood by microscopy assay datum that specifies whether Plasmodium falciparum was detected by microscopy assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Plasmodium falciparum in blood by microscopy assay Plasmodium vivax A Plasmodium in blood by microscopy assay datum that specifies whether Plasmodium vivax was detected by microscopy assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Plasmodium vivax by microscopy assay Plasmodium malariae A Plasmodium in blood by microscopy assay datum that specifies whether Plasmodium malariae was detected by microscopy assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Plasmodium malariae by microscopy assay Microscopy performed a categorical value specification that specifies whether a microscopy assay was performed Jie Zheng Chris Stoeckert John Judkins Microscopy performed EuPathDB https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/142 indicator of whether microscopy assay performed Plasmodium falciparum 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 John Judkins (Plasmodium species in last year) Plasmodium falciparum EuPathDB Plasmodium falciparum diagnosis within past year Plasmodium vivax 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 John Judkins (Plasmodium species in last year) Plasmodium vivax EuPathDB Plasmodium vivax diagnosis within past year Plasmodium malariae 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 John Judkins (Plasmodium species in last year) Plasmodium malariae EuPathDB Plasmodium malariae diagnosis within past year Can't remember 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 John Judkins (Plasmodium species in last year) Can't remember EuPathDB forgot which Plasmodium species in diagnosis within past year Artesunate information on antimalarial drug used last year that specifies artesunate as the drug administered as the most recent treatment John Judkins Artesunate EuPathDB information specifying Artesunate as antimalarial drug as most recent treatment within past year Can't remember 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. John Judkins (Antimalarial medications used) Can't remember EuPathDB forgot which antimalarial in most recent treatment Artesunate/pyrimethamine/sulphadoxine 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 John Judkins Artesunate/pyrimethamine/sulphadoxine EuPathDB artesunate/pyrimethamine/sulphadoxine combination as most recent malaria treatment Chloroquine/primaquine information on antimalarial drug used last year that specifies chloroquine or primaquine as the drugs administered as the most recent treatment John Judkins Chloroquine/primaquine EuPathDB chloroquine or primaquine as most recent malaria treatment Pyrimethamine/sulphadoxine information on antimalarial drug used last year that specifies pyrimethamine or sulphadoxine as the drugs administered as the most recent treatment John Judkins Pyrimethamine/sulphadoxine EuPathDB pyrimethamine or sulphadoxine as most recent malaria treatment Quinine/quinidine information on antimalarial drug used last year that specifies quinine or quinidine as the drugs administered as the most recent treatment John Judkins Quinine/quinidine EuPathDB quinine or quinidine as most recent malaria treatment Tetracycline/doxycycline information on antimalarial drug used last year that specifies tetracycline or doxycycline as the drugs administered as the most recent treatment John Judkins Tetracycline/doxycycline EuPath tetracycline or doxycycline as most recent malaria treatment Clinic or hospital 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 Jie Zheng Chris Stoeckert John Judkins Clinic/hospital EuPathDB https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/142 indicator of whether treated in clinic Private doctor 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 Jie Zheng Chris Stoeckert John Judkins Private doctor EuPathDB https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/142 indicator of whether treated by private practice Self-treated A categorical value specification that specifies whether a treatment to alleviate an episode of malaria was self-administered Jie Zheng Person: John Judkins (Where treated) Self-treated EuPathDB https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/142 indicator of whether malaria self-treated Can't remember 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. Jie Zheng Chris Stoeckert John Judkins (Where treated) Can't remember EuPathDB https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/142 indicator of whether participant forgot treatment location within past year Negative 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 John Judkins (Plasmodium species, by qPCR) Negative EuPathDB no Plasmodium by blood sample PCR Plasmodium falciparum 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 John Judkins (Plasmodium species, by qPCR) Plasmodium falciparum EuPathDB presence of Plasmodium falciparum by blood sample PCR Plasmodium vivax 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 John Judkins (Plasmodium species, by qPCR) Plasmodium vivax EuPathDB presence of Plasmodium vivax by blood sample PCR Plasmodium malariae 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 John Judkins (Plasmodium species, by qPCR) Plasmodium malariae EuPathDB presence of Plasmodium malariae by blood sample PCR Plasmodium ovale 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 John Judkins Plasmodium ovale EuPathDB presence of Plasmodium ovale by blood sample PCR Plasmodium falciparum a presence of Plasmodium falciparum that is the specified output of a falcivax rapid diagnostic test and specifies that Plasmodium falciparum was detected John Judkins (Plasmodium species, by FalciVax RDT) Plasmodium falciparum EuPathDB presence of Plasmodium falciparum by falcivax Plasmodium vivax a presence of Plasmodium vivax that is the specified output of a falcivax rapid diagnostic test and specifies that Plasmodium vivax was detected John Judkins (Plasmodium species, by FalciVax RDT) Plasmodium vivax EuPathDB presence of Plasmodium vivax by falcivax Negative a presence of parasite that is the specified output of a falcivax rapid diagnostic test and indicates that no Plasmodium was detected John Judkins (Plasmodium species, by FalciVax RDT) Negative EuPathDB no presence of Plasmodium by falcivax FalciVax RDT performed a categorical value specification that specifies whether a falcivax rapid diagnostic test was performed Jie Zheng Chris Stoeckert John Judkins FalciVax RDT performed EuPathDB https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/142 indicator of whether falcivax performed Plasmodium falciparum a presence of Plasmodium falciparum that is the specified output of a optimal-IT rapid diagnostic test and specifies that Plasmodium falciparum was detected John Judkins (Plasmodium species, by OptiMAL RDT) Plasmodium falciparum EuPathDB presence of Plasmodium falciparum by optimal-IT Pan Plasmodium 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 John Judkins Pan Plasmodium EuPathDB presence of pan-Plasmodium antigen by optimal-IT Negative a presence of parasite that is the specified output of an optimal-IT rapid diagnostic test and specifies that no Plasmodium was detected John Judkins (Plasmodium species, by OptiMAL RDT) Negative EuPathDB no Plasmodium by optimal-IT OptiMAL RDT performed a categorical value specification that specifies whether an optimal-IT rapid diagnostic test was performed Jie Zheng Chris Stoeckert John Judkins OptiMAL RDT performed EuPathDB https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/142 indicator of whether optimal-IT performed Can't remember 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 Jie Zheng Chris Stoeckert John Judkins (Personal mosquito repellent) Can't remember EuPathDB https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/142 information on participant forgetting whether used personal mosquito repellent Can't remember an information content entity that specifies that a human participant under investigation does not remember whether insecticide was applied in the previous 12 months John Judkins (Sprayed in the last 12 months) Can't remember EuPathDB no knowledge of insecticide spraying in last 12 months Public healthcare information that specifies that the organization that typically provides the healthcare is funded by a government rather than funded independently John Judkins Public EuPathDB public healthcare information Private healthcare information that specifies that the organization that typically provides the healthcare is funded independently of any government John Judkins Private EuPathDB, New Oxford American Dictionary entry for 'private' private healthcare information Indoor plumbing water accessed through a plumbing fixture located inside a human dwelling John Judkins Indoor plumbing EuPathDB water piped into dwelling Stream or river water derived from water that is part of either a stream or a river John Judkins Stream/river EuPath stream water A blood specimen that is located in a vacutainer. Chris Stoeckert Jie Zheng Vacutainer sample VEuPathDB obsolete blood specimen in vacutainer true Electricity A household asset information indicating whether a household has electricity. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB indicator of household having electricity Household data collection date a time measurement datum of the day that encompasses a process that has as specified output a data item about a household John Judkins EuPathDB date of household data collection Any signs 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 Jie Zheng Chris Stoeckert John Judkins Any signs EuPathDB, based on definition for 'sign' in OGMS https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/142 indicator of whether participant has sign Any symptoms 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 Jie Zheng Chris Stoeckert John Judkins Any symptoms EuPathDB, based on definition for 'sign' in OGMS https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/142 indicator of whether participant has symptom Fever in last 48 hours a categorical value specification that specifies whether a human participant under investigation was febrile in the previous 48 hours Jie Zheng Chris Stoeckert John Judkins Fever in last 48 hours EuPathDB https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/142 indicator of whether participant had fever in last 48 hours Antimalarial medication in last 2 weeks a categorical value specification that specifies whether medication to treat malaria was administered in the past two weeks to a human participant under investigation John Judkins Malaria medication in last 2 weeks EuPathDB information on whether given malaria medication in past 2 weeks State A first-order administrative region of India. Person: John Judkins VEuPathDB state of India Fever in last 2 weeks a categorical value specification that specifies whether a human participant under investigation was febrile in the previous two weeks Jie Zheng Chris Stoeckert John Judkins Fever in last 2 weeks EuPathDB https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/142 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 John Judkins EuPathDB obsolete immediate clinical history true Medication provided An information content entity that specifies whether medication material was administered during a health care encounter. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB indicator of medication administered during health care encounter Typhus in blood A bacteria in blood datum that specifies whether a typhus group virus was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of typhus group in blood Chikungunya in blood A virus in blood datum that specifies whether the Chikungunya virus was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Chikungunya virus in blood Dengue in blood A virus in blood datum that specifies whether the Dengue virus was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Dengue virus in blood A virus in blood datum that specifies whether Orthohepadnavirus was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Orthohepadnavirus in blood Salmonella typhi, by PCR A bacteria in blood datum that specifies whether Salmonella enterica subsp. enterica serovar Typhi was detected by polymerase chain reaction assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Salmonella enterica subsp. enterica serovar Typhi in blood by polymerase chain reaction assay Alanine aminotransferase A blood assay datum of the concentration of alanine aminotransferase. Person: John Judkins VEuPathDB blood alanine aminotransferase concentration Alkaline phosphatase A blood assay datum of the concentration of alkaline phosphatase. Person: John Judkins VEuPathDB blood alkaline phosphatase concentration Chikungunya A diagnosis at patient discharge that is an assertion that a patient has chikungunya. Person: John Judkins VEuPathDB diagnosis of chikungunya at patient discharge Chikungunya, by any method A virus in blood datum that specifies whether Chikungunya virus was detected, by an unspecified assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Chikungunya virus in blood by unspecified assay Dengue A diagnosis at patient discharge that is an assertion that a patient has dengue disease. Person: John Judkins VEuPathDB diagnosis of dengue disease at patient discharge Dengue, by any method A virus in blood datum that specifies whether Dengue virus was detected by an unspecified assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Dengue virus in blood by unspecified assay Gastrointestinal infection A diagnosis at patient discharge that is an assertion that a patient has a gastrointestinal infection. Person: John Judkins VEuPathDB diagnosis of gastrointestinal infection at patient discharge Hepatitis C, by any method A virus in blood datum that specifies whether Hepacivirus C was detected by an unspecified assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Hepacivirus C in blood by unspecified assay Hepatitis B, by surface antigen test A virus in blood datum that specifies whether Hepatitis B virus was detected by HBV surface antigen assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Hepatitis B virus in blood by surface antigen assay HIV, by any method A virus in blood datum that specifies whether Human immunodeficiency virus 1 was detected by an unspecified assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Human immunodeficiency virus 1 in blood by unspecified assay Leptospirosis A diagnosis at patient discharge that is an assertion that a patient has leptospirosis. Person: John Judkins VEuPathDB diagnosis of leptospirosis at patient discharge Phosphate A blood assay datum of the concentration of phosphate. Person: John Judkins VEuPathDB blood phosphate concentration Scrub typhus A diagnosis at patient discharge that is an assertion that a patient has scrub typhus. Person: John Judkins VEuPathDB diagnosis of scrub typhus at patient discharge Urea A blood assay datum of the concentration of urea. Person: John Judkins VEuPathDB blood urea concentration Uric acid A blood assay datum of the concentration of uric acid. Person: John Judkins VEuPathDB blood uric acid concentration Viral hepatitis A diagnosis at patient discharge that is an assertion that a patient has viral hepatitis. Person: John Judkins VEuPathDB diagnosis of viral hepatitis at patient discharge Lentivirus in blood A virus in blood datum that specifies whether Lentivirus was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Lentivirus in blood Hepacivirus in blood A virus in blood datum that specifies whether Hepacivirus was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Hepacivirus in blood Settlement a geographic location that is either a city or an area containing settlements where the inhabitants share a common trait John Judkins Wikipedia community External wall material a wall material used to build an exterior wall John Judkins EuPathDB external wall material Internal wall material a wall material used to build a wall between rooms John Judkins EuPathDB internal wall material Beds with bednets count a count of the number of beds in the dwelling of a household that have a bed net hung over them John Judkins Beds with bednet (#) EuPathDB number of beds with bednet Freezer A household asset information indicating whether a household has a freezer. John Judkins Freezer EuPathDB indicator of household having freezer Blender A household asset information indicating whether a household has an electrical appliance that has the function of mixing food or drink. John Judkins Blender EuPathDB indicator of household having blender Electric stove 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. John Judkins Electric stove EuPathDB indicator of household having electric stove 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 natural gas. John Judkins Gas stove EuPathDB indicator of household having gas stove 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 kerosene. John Judkins Kerosene stove EuPathDB indicator of household having kerosene stove Coal 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. John Judkins Coal stove EuPathDB indicator of household having coal stove Black and white television A household asset information indicating whether a household has a television set that is capable of producing grayscale images but not color images. John Judkins Black and white TV EuPathDB indicator of household having black and white television Color television A household asset information indicating whether a household has a television set that is capable of producing color images. John Judkins Color TV EuPathDB indicator of household having color television DVD A household asset information indicating whether a household has a device capable of playing a DVD. John Judkins DVD EuPathDB indicator of household having DVD player Stereo A household asset information indicating whether a household has a sound system. John Judkins Stereo EuPathDB indicator of household having sound system Cows A household asset information indicating whether a household has any cows. John Judkins Cows EuPathDB indicator of household having cow Goats A household asset information indicating whether a household has a goat. John Judkins Goats EuPathDB indicator of household having goat Chicks A household asset information indicating whether a household has any sexually immature domesticated birds. John Judkins Chicks EuPathDB indicator of household having chick Hens A household asset information indicating whether a household has a domesticated female bird. John Judkins Hens EuPathDB indicator of household having hen Roosters A household asset information indicating whether a household has a rooster. John Judkins Roosters EuPathDB indicator of household having roosters Turkeys A household asset information indicating whether a household has a turkey. John Judkins Turkeys EuPathDB indicator of household having turkeys Ducks A household asset information indicating whether a household has a duck. John Judkins Ducks EuPathDB indicator of household having duck Parakeets A household asset information indicating whether a household has a small parrot with a long tail. John Judkins Parakeets EuPathDB indicator of household having parakeet Parrots A household asset information indicating whether a household has a parrot. John Judkins Parrots EuPathDB indicator of household having parrot Monkeys A household asset information indicating whether a household has a monkey. John Judkins Monkeys EuPathDB indicator of household having monkey Pigs A household asset information indicating whether a household has a pig. John Judkins Pigs EuPathDB indicator of household having pig Rabbits A household asset information indicating whether a household has a rabbit. John Judkins Rabbits EuPathDB indicator of household having rabbits Dogs A household asset information indicating whether a household has a dog. John Judkins Dogs EuPathDB indicator of household having dog Cats A household asset information indicating whether a household has a cat. John Judkins Cats EuPathDB indicator of household having cat Turtles A household asset information indicating whether a household has a turtle. John Judkins Turtles EuPathDB 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 John Judkins Traveled in the 2 weeks before most recent malaria episode EuPath 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 John Judkins Traveled in the 2 weeks before second most recent malaria episode EuPath 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 John Judkins Traveled in the 2 weeks before third most recent malaria episode EuPath 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 John Judkins Traveled in the 2 weeks before fourth most recent malaria episode EuPath traveled within two weeks earlier than fourth most recent malaria episode Most recent trip duration a time measurement datum of the duration of the most recent journey of a human participant under investigation John Judkins Length of most recent trip (days) EuPathDB duration of most recent trip Second most recent trip duration a time measurement datum of the duration of the second most recent journey of a human participant under investigation John Judkins Length of second most recent trip (days) EuPathDB duration of second most recent trip Third most recent trip duration a time measurement datum of the duration of the third most recent journey of a human participant under investigation John Judkins Length of third most recent trip (days) EuPathDB duration of third most recent trip Fourth most recent trip duration a time measurement datum of the duration of the fourth most recent journey of a human participant under investigation John Judkins Length of fourth most recent trip (days) EuPathDB duration of fourth most recent trip River traveled on most recent trip an information content entity that specifies which rivers were visited during the most recent journey of a human participant under investigation John Judkins River traveled on most recent trip EuPathDB rivers traveled on most recent trip Settlement visited on most recent trip human traveling information that specifies the community to which a human participant under investigation has most recently traveled John Judkins EuPathDB 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 John Judkins EuPathDB 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 John Judkins EuPathDB 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 John Judkins EuPathDB community visited on fourth most recent trip Time at occupation a time measurement datum of the time since the beginning of the most significant occupation of a human participant under investigation John Judkins Length of main occupation (years) EuPathDB duration of current main occupation Time at occupation 2 a time measurement datum of the time since the beginning of the second most significant occupation of a human participant under investigation John Judkins Length of secondary occupation (years) EuPathDB duration of current secondary occupation Present at visit 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 Jie Zheng Chris Stoeckert John Judkins Present at visit EuPathDB https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/142 indicator of whether participant present for clinical visit Most recent travel 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 John Judkins Most recent travel EuPathDB information on most recent travel Second 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 John Judkins Second most recent travel EuPathDB information on second most recent travel Reason for sample collection 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 John Judkins Reason for specimen collection EuPathDB information on whether specimen collection prompted by sign of fever Other reason for sample collection 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 John Judkins Other reason for specimen collection EuPathDB reason besides fever for specimen collection Plasmodium vivax, by qPCR result 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. Person: John Judkins VEuPathDB qPCR threshold cycle for Plasmodium vivax in blood Plasmodium falciparum, by qPCR result 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. Person: John Judkins VEuPathDB qPCR threshold cycle for Plasmodium falciparum in blood Last bednet treatment a time measurement datum of the last time insecticide was applied to the bednets used by a household John Judkins Last bednet treatment EuPath time of most recent bednet treatment Parasites, by microscopy A eukaryota in feces datum that specifies whether a parasite organism was detected by microscopy assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of parasite organism in feces by microscopy assay Plasmodium gametocytes, by qPCR A eukaryota in blood datum that specifies whether a Plasmodium gametocyte was detected by real time polymerase chain reaction assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Plasmodium gametocyte in blood by real time polymerase chain reaction assay Shotgun A household asset information indicating whether a household has a shotgun. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB indicator of household having shotgun Total area A measurement datum of the total area of a land lot on which a dwelling is built. Person: John Judkins VEuPathDB https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/149 dwelling lot area measurement datum an information content entity that is about the relocation of the household of a human participant under investigation John Judkins Relocation details EuPathDB relocation information Enrollment time a time measurement datum of the time point at which a human subject enrollment is complete John Judkins Enrollment time EuPath time of participant first enrolled in a study Bacteria, by microscopy A bacteria in blood datum that specifies whether bacteria were detected by microscopy assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of bacteria in blood by microscopy assay Bicarbonate A blood assay datum of the concentration of hydrogencarbonate. Person: John Judkins VEuPathDB blood hydrogencarbonate concentration Blantyre coma score - total 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 Person: John Judkins Blantyre coma score - total Wikipedia Blantyre coma score sum BUN A scalar measurement datum of the concentration of urea nitrogen in blood that is the specified output of a blood test. John Judkins BUN (mg/dL) EuPathDB blood urea nitrogen concentration Creatinine A blood assay datum of the concentration of creatinine. Person: John Judkins VEuPathDB blood creatinine concentration Take 2nd antimalarial medication a categorical value specification that specifies whether a human participant under investigation was administered malaria medication a second time while in hospital Jie Zheng Chris Stoeckert John Judkins Take second antimalarial medication EuPathDB https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/142 indicator of whether participant taking second antimalarial medication Discharged a categorical value specification that specifies whether a human participant under investigation was discharged from hospital Jie Zheng Chris Stoeckert John Judkins Discharged EuPathDB https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/142 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. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB Plasmodium gametocytes in blood by microscopy assay datum Take 3rd antimalarial medication a categorical value specification that specifies whether a human participant under investigation was administered malaria medication a third time while in hospital Jie Zheng Chris Stoeckert John Judkins Take third antimalarial medication EuPathDB https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/142 indicator of whether participant taking third antimalarial medication Hemoglobin, at hospital A hemoglobin level in g per dl that is the specified output of an assay that occurs in a hospital facility Person: John Judkins Hemoglobin, from hospital EuPathDB hemoglobin concentration measured in hospital Moved in last 12 months a categorical value specification that specifies whether a human participant under investigation moved to a different dwelling in the previous twelve months Jie Zheng Chris Stoeckert John Judkins Moved in last 12 months EuPathDB https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/142 indicator of whether participant moved in past twelve months Moved in last month a categorical value specification that specifies whether a human participant under investigation moved to a different dwelling in the previous month Jie Zheng Chris Stoeckert John Judkins Moved in last month EuPathDB https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/142 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 Person: John Judkins P. falciparum parasitemia, microscopy EuPathDB 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 Person: John Judkins P. malariae parasitemia, microscopy EuPathDB 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 Person: John Judkins P. vivax parasitemia, microscopy EuPathDB Plasmodium vivax parasitemia measurement datum Plasmodium species, by FalciVax RDT at hospital a falcivax rapid diagnostic test that occurs in a hospital facility John Judkins Parasite species, FalciVax RDT from hospital EuPathDB 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. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB 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. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Plasmodium in blood by thin smear microscopy assay Sample collection time A specimen collection time measurement datum that specifies the time of day without the date. Person: John Judkins VEuPathDB specimen collection time of day measurement datum Initiated antimalarial treatment a categorical value specification that specifies whether a human participant under investigation is receiving treatment to alleviate symptoms of malaria Jie Zheng Chris Stoeckert John Judkins Initiated antimalarial treatment EuPathDB https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/142 indicator of whether participant taking initial antimalarial medication State moved from in last month 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. Person: John Judkins State moved from in last month EuPathDB subnational region relocated from within past month State visited in last month human traveling information that specifies which subnational regions a human participant under investigation had visited within one month previous John Judkins State visited in last month EuPath subnational region visited within past month States moved from in last 12 months 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. Person: John Judkins States moved from in last 12 months EuPathDB subnational region relocated from within past 12 months Take 4th antimalarial medication a categorical value specification that specifies whether a human participant under investigation was administered malaria medication a fourth time while in hospital Jie Zheng Chris Stoeckert John Judkins Take fourth antimalarial medication EuPathDB https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/142 indicator of whether participant taking fourth antimalarial medication Take 5th antimalarial medication a categorical value specification that specifies whether a human participant under investigation was administered malaria medication a fifth time while in hospital Jie Zheng Chris Stoeckert John Judkins Take fifth antimalarial medication EuPathDB https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/142 indicator of whether participant taking fifth antimalarial medication States visited in last 12 months human traveling information that specifies which subnational regions a human participant under investigation had visited within twelve months previous John Judkins States visited in last 12 months EuPath subnational region visited within past 12 months Treatment start date a time measurement datum of the date during which a treatment starts John Judkins EuPath date treatment started Treatment start time a time measurement datum of the time point at which a treatment starts John Judkins Treatment start time EuPath time treatment started Observation time a time measurement datum specifying the time (of day) of a clinical visit scheduled for sixty days after a treatment John Judkins Time of observation EuPathDB time of 60-day follow up Total bilirubin A blood assay datum of the concentration of bilirubin IXalpha. Person: John Judkins VEuPathDB blood bilirubin IXalpha concentration Traveled in last 12 months a categorical value specification that is about a human participant under investigation and specifies whether the participant had traveled within twelve months previous John Judkins Traveled in last 12 months EuPathDB information on participant travel in the last twelve months Tribal affiliation a categorical value specification that specifies whether a human participant under investigation self-identifies as a member of a tribe Jie Zheng Chris Stoeckert John Judkins Tribal affilliation EuPathDB https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/142 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 Jie Zheng Chris Stoeckert John Judkins Died EuPathDB https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/142 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. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/445 ClinEpiDB Sheena Tomko duration since bed net treatment Time owned personal bednet A time measurement datum of the duration a human being has owned a bed net. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/446 Sheena Tomko duration of bed net ownership Diarrhea A diagnosis that is an assertion that a patient has diarrhea. Person: John Judkins VEuPathDB diagnosis of diarrhea Pneumonia A diagnosis that is an assertion that a patient has pneumonia. Person: John Judkins VEuPathDB diagnosis of pneumonia Upper respiratory tract infection A diagnosis that is an assertion that a patient has upper respiratory tract disease. Person: John Judkins VEuPathDB diagnosis of upper respiratory tract disease Medication The first mention of a medication that is administered as part of a treatment. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/501 Sheena Tomko first medication in treatment Plasmodium, by qPCR A Plasmodium in blood by real time polymerase chain reaction assay datum that specifies whether the organism was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Plasmodium in blood by real time polymerase chain reaction assay Malaria A diagnosis that is an assertion that a patient has malaria. Person: John Judkins VEuPathDB 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. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/445 ClinEpiDB Sheena Tomko 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. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/446 ClinEpiDB Sheena Tomko categorical duration of bed net ownership Subdistrict in Thailand A third-order administrative region of Thailand. Person: John Judkins VEuPathDB subdistrict of Thailand District in Thailand A second-order administrative region of Thailand. Person: John Judkins VEuPathDB district of Thailand Province in Thailand A first-order administrative region of Thailand. Person: John Judkins VEuPathDB province of Thailand Plasmodium, by microscopy A Plasmodium in blood by microscopy assay datum that specifies whether the organism was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Plasmodium in blood by microscopy assay Parish in Uganda A fifth-order administrative region of Uganda. Person: John Judkins VEuPathDB parish of Uganda Assay that subjects a urine specimen to a test for microorganisms. John Judkins urine microbiology test VEuPathDB obsolete urine microbiology assay true Eukaryota in stool A eukaryota in feces datum that specifies whether a eukaryote was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of eukaryote in feces Schistosoma mansoni, by microscopy A eukaryota in feces datum that specifies whether Schistosoma mansoni was detected by microscopy assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Schistosoma mansoni in feces by microscopy assay Schistosoma in urine A eukaryota in urine datum that specifies whether Schistosoma was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Schistosoma in urine Schistosoma haematobium, by microscopy A eukaryota in urine datum that specifies whether Schistosoma haematobium was detected by microscopy assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Schistosoma haematobium in urine by microscopy assay Eukaryota in urine A eukaryota in urine datum that specifies whether a eukaryote was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of eukaryote in urine Assay that subjects an induced sputum specimen to a test for microorganisms. John Judkins induced sputum microbiology test VEuPathDB obsolete induced sputum microbiology assay true Bacteria in induced sputum A bacteria in induced sputum datum that specifies whether bacteria were detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of bacteria in induced sputum Eukaryota in induced sputum A eukaryota in induced sputum datum that specifies whether a eukaryote was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of eukaryote in induced sputum Virus in induced sputum A virus in induced sputum datum that specifies whether a virus was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB obsolete virus in induced sputum datum true Assay that subjects a pleural fluid specimen to a test for microorganisms. John Judkins pleural fluid microbiology test VEuPathDB obsolete pleural fluid microbiology assay true Bacteria in pleural fluid A bacteria in pleural fluid datum that specifies whether bacteria were detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of bacteria in pleural fluid Eukaryota in pleural fluid A eukaryota in pleural fluid datum that specifies whether a eukaryote was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of eukaryote in pleural fluid Virus in pleural fluid A virus in pleural fluid datum that specifies whether a virus was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of virus in pleural fluid Bacteria in lung aspirate A bacteria in lung datum that specifies whether bacteria were detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of bacteria in lung Eukaryota in lung aspirate A eukaryota in lung datum that specifies whether a eukaryote was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of eukaryote in lung Virus in lung aspirate A virus in lung datum that specifies whether a virus was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of virus in lung Bacteria in nasopharyngeal/oropharyngeal swabs A bacteria in nasopharyngeal or oropharyngeal swab datum that specifies whether bacteria were detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB 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. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB 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. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of virus in nasopharynx or oropharynx Assay that subjects a endotracheal aspirate specimen to a test for microorganisms. John Judkins endotracheal aspirate microbiology test VEuPathDB obsolete endotracheal aspirate microbiology assay true Haemophilus in lung aspirate A bacteria in lung datum that specifies whether Haemophilus was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Haemophilus in lung Moraxella in lung aspirate A bacteria in lung datum that specifies whether Moraxella was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Moraxella in lung Staphylococcus in lung aspirate A bacteria in lung datum that specifies whether Staphylococcus was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Staphylococcus in lung Streptococcus in lung aspirate A bacteria in lung datum that specifies whether Streptococcus was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Streptococcus in lung Acinetobacter, by bacteriology A bacteria in blood datum that specifies whether Acinetobacter was detected, without specifying the taxon further. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Acinetobacter unspecified in blood Any bacteria, by bacteriology A bacteria in blood datum that specifies whether unspecified bacteria were detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of unspecified bacteria in blood Enterobacter cloacae, by bacteriology A bacteria in blood datum that specifies whether Enterobacter cloacae was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Enterobacter cloacae in blood Enterobacteriaceae, by bacteriology A bacteria in blood datum that specifies whether Enterobacteriaceae was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Enterobacteriaceae in blood Enterococcus faecium, by bacteriology A bacteria in blood datum that specifies whether Enterococcus faecium was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Enterococcus faecium in blood Escherichia coli, by bacteriology A bacteria in blood datum that specifies whether Escherichia coli was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Escherichia coli in blood Haemophilus influenzae, by bacteriology A bacteria in blood datum that specifies whether Haemophilus influenzae was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Haemophilus influenzae in blood Klebsiella pneumoniae, by bacteriology A bacteria in blood datum that specifies whether Klebsiella pneumoniae was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Klebsiella pneumoniae in blood Moraxella catarrhalis (Branhamella catarrhalis), by bacteriology A bacteria in blood datum that specifies whether Moraxella catarrhalis was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Moraxella catarrhalis in blood Neisseria meningitidis, by bacteriology A bacteria in blood datum that specifies whether Neisseria meningitidis was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Neisseria meningitidis in blood Pseudomonas aeruginosa, by bacteriology A bacteria in blood datum that specifies whether Pseudomonas aeruginosa was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Pseudomonas aeruginosa in blood Salmonella Paratyphi A, by bacteriology A bacteria in blood datum that specifies whether Salmonella enterica enterica serovar Paratyphi A was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB 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. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Salmonella enterica enterica non-(Typhi or Paratyphi-A) in blood Salmonella typhi, by bacteriology A bacteria in blood datum that specifies whether Salmonella enterica enterica serovar Typhi was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Salmonella enterica enterica serovar Typhi in blood Salmonella, by bacteriology A bacteria in blood datum that specifies whether Salmonella was detected, without specifying the taxon further. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Salmonella unspecified in blood Staphylococcus aureus, by bacteriology A bacteria in blood datum that specifies whether Staphylococcus aureus was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB 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. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Staphylococcus group A in blood Streptococcus pneumoniae, by bacteriology A bacteria in blood datum that specifies whether Streptococcus pneumoniae was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Streptococcus pneumoniae in blood Acinetobacter baumannii, by bacteriology An Acinetobacter baumannii in induced sputum datum that specifies whether the organism was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB 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. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Acinetobacter calcoaceticus in induced sputum Acinetobacter lwoffii, by bacteriology An Acinetobacter in induced sputum datum that specifies whether Acinetobacter lwoffii was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Acinetobacter lwoffii in induced sputum Acinetobacter, by bacteriology An Acinetobacter in induced sputum datum that specifies whether the organism was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Acinetobacter in induced sputum Aeromonas hydrophila, by bacteriology An Aeromonas hydrophila in induced sputum datum that specifies whether the organism was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB 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. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB 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. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB 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. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB 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. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB 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. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Bordetella pertussis in induced sputum by multiplex real time polymerase chain reaction assay Burkholderia cepacia, by bacteriology A Burkholderia cepacia in induced sputum datum that specifies whether the organism was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB 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. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Chlamydia pneumoniae in induced sputum by multiplex real time polymerase chain reaction assay Citrobacter braakii, by bacteriology A Citrobacter braakii in induced sputum datum that specifies whether the organism was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Citrobacter braakii in induced sputum Citrobacter freundii, by bacteriology A Citrobacter freundii in induced sputum datum that specifies whether the organism was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB 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. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Coagulase-Negative Staphylococcus in induced sputum Coliform bacilli, by bacteriology A bacteria in induced sputum datum that specifies whether Coliform bacilli was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Coliform bacilli in induced sputum Corynebacterium, by bacteriology A Corynebacterium in induced sputum datum that specifies whether the organism was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB 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. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Cronobacter sakazakii in induced sputum Enterobacter asburiae, by bacteriology A Enterobacter asburiae in induced sputum datum that specifies whether the organism was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Enterobacter asburiae in induced sputum Enterobacter cloacae, by bacteriology A Enterobacter cloacae in induced sputum datum that specifies whether the organism was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Enterobacter cloacae in induced sputum Enterobacter, by bacteriology An Enterobacter in induced sputum datum that specifies whether the organism was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Enterobacter in induced sputum Enterococcus faecalis, by bacteriology A Enterobacter in induced sputum datum that specifies whether Enterococcus faecalis was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Enterococcus faecalis in induced sputum Enterococcus, by bacteriology An Enterococcus in induced sputum datum that specifies whether the organism was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Enterococcus in induced sputum Escherichia coli, by bacteriology A Escherichia coli in induced sputum datum that specifies whether the organism was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB 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. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB 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. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB 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. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Haemophilus influenzae serotype b in induced sputum by multiplex real time polymerase chain reaction assay Haemophilus influenzae, by bacteriology A Haemophilus influenzae in induced sputum datum that specifies whether the organism was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB 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. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB 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. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB 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. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB 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. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Haemophilus parainfluenzae in induced sputum Haemophilus, by bacteriology A Haemophilus in induced sputum datum that specifies whether the organism was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Haemophilus in induced sputum Kingella, by bacteriology A Kingella in induced sputum datum that specifies whether the organism was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB 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. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Klebsiella aerogenes in induced sputum Klebsiella oxytoca, by bacteriology A Klebsiella oxytoca in induced sputum datum that specifies whether the organism was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Klebsiella oxytoca in induced sputum Klebsiella pneumoniae, by bacteriology A Klebsiella pneumoniae in induced sputum datum that specifies whether the organism was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Klebsiella pneumoniae in induced sputum Klebsiella, by bacteriology A Klebsiella in induced sputum datum that specifies whether the organism was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Klebsiella in induced sputum Legionella, by multiplexed qPCR A bacteria in induced sputum datum that specifies whether Legionella was detected by multiplex real time polymerase chain reaction assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB 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. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Mixed gram-negative rods in induced sputum Moraxella catarrhalis (Branhamella catarrhalis), by bacteriology A Moraxella catarrhalis in induced sputum datum that specifies whether the organism was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB 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. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB 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. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Moraxella nonliquefaciens in induced sputum Moraxella, by bacteriology A Moraxella in induced sputum datum that specifies whether the organism was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB 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. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Mycoplasmoides pneumoniae in induced sputum by multiplex real time polymerase chain reaction assay Neisseria meningitidis, by bacteriology A Neisseria meningitidis in induced sputum datum that specifies whether the organism was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Neisseria meningitidis in induced sputum Proteus mirabilis, by bacteriology A Proteus mirabilis in induced sputum datum that specifies whether the organism was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Proteus mirabilis in induced sputum Pseudomonas aeruginosa, by bacteriology A Pseudomonas aeruginosa in induced sputum datum that specifies whether the organism was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB 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. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Pseudomonas fluorescens in induced sputum Pseudomonas, by bacteriology A Pseudomonas in induced sputum datum that specifies whether the organism was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Pseudomonas in induced sputum Pseudomonas stutzeri, by bacteriology A Stutzerimonas stutzeri in induced sputum datum that specifies whether the organism was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Stutzerimonas stutzeri in induced sputum Salmonella, by bacteriology A Salmonella in induced sputum datum that specifies whether the organism was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Salmonella in induced sputum Salmonella, by multiplexed qPCR A Salmonella in induced sputum datum that specifies whether Salmonella was detected by multiplex real time polymerase chain reaction assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Salmonella in induced sputum by multiplex real time polymerase chain reaction assay Salmonella typhi, by bacteriology A Salmonella in induced sputum datum that specifies whether Salmonella enterica subsp. enterica serovar Typhi was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Salmonella enterica subsp. enterica serovar Typhi in induced sputum Serratia marcescens, by bacteriology A Serratia marcescens in induced sputum datum that specifies whether the organism was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Serratia marcescens in induced sputum Serratia, by bacteriology A Serratia in induced sputum datum that specifies whether the organism was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Serratia in induced sputum Staphylococcus aureus, by bacteriology A Staphylococcus aureus in induced sputum datum that specifies whether the organism was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB 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. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB 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. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB 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. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB 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. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Streptococcus anginosus group in induced sputum Streptococcus group A (Streptococcus pyogenes), by bacteriology A Streptococcus sp. group A in induced sputum datum that specifies whether the organism was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Streptococcus group A in induced sputum Streptococcus group C, by bacteriology A Streptococcus sp. group C in induced sputum datum that specifies whether the organism was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Streptococcus group C in induced sputum Streptococcus group G, by bacteriology A Streptococcus sp. group G in induced sputum datum that specifies whether the organism was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Streptococcus group G in induced sputum A laboratory test that has an induced sputum specimen as specified input. John Judkins VEuPathDB obsolete induced sputum test true A laboratory test that has a endotracheal aspirate specimen as specified input. John Judkins VEuPathDB obsolete endotracheal aspirate test true Streptococcus pneumoniae, by bacteriology A Streptococcus pneumoniae in induced sputum datum that specifies whether the organism was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB 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. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Streptococcus pneumoniae in induced sputum by multiplex real time polymerase chain reaction assay Streptococcus, by bacteriology A Streptococcus in induced sputum datum that specifies whether the organism was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB 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. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB 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. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB 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. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB Acinetobacter calcoaceticus in induced sputum datum Acinetobacter, by bacteriology result A bacteria in induced sputum datum that is used to determine the presence of Acinetobacter in the specimen. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB 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. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB 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. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB 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. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB 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. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB 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. Person: John Judkins VEuPathDB 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. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB 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. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB 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. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB 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. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB 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. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB Coliform Bacteria in induced sputum datum Corynebacterium, by bacteriology result A bacteria in induced sputum datum that is used to determine the presence of Corynebacterium in the specimen. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB 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. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB 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. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB 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. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB Enterobacter cloacae in induced sputum datum Enterobacter, by bacteriology result A bacteria in induced sputum datum that is used to determine the presence of Enterobacter in the specimen. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB Enterobacter in induced sputum datum Enterococcus, by bacteriology result A bacteria in induced sputum datum that is used to determine the presence of Enterococcus in the specimen. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB Enterococcus in induced sputum datum Escherichia coli, by bacteriology result A bacteria in induced sputum datum that is used to determine the presence of Escherichia coli in the specimen. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB 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. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB 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. Person: John Judkins VEuPathDB 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. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB 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. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB 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. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB 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. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB Haemophilus parainfluenzae in induced sputum datum Haemophilus, by bacteriology result A bacteria in induced sputum datum that is used to determine the presence of Haemophilus in the specimen. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB Haemophilus in induced sputum datum Kingella, by bacteriology result A bacteria in induced sputum datum that is used to determine the presence of Kingella in the specimen. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB 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. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB 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. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB 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. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB Klebsiella pneumoniae in induced sputum datum Klebsiella, by bacteriology result A bacteria in induced sputum datum that is used to determine the presence of Klebsiella in the specimen. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB Klebsiella in induced sputum datum Legionella, 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 Legionella in an induced sputum specimen. Person: John Judkins VEuPathDB 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. Person: John Judkins VEuPathDB 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. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB 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. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB Moraxella nonliquefaciens in induced sputum datum Moraxella, by bacteriology result A bacteria in induced sputum datum that is used to determine the presence of Moraxella in the specimen. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB 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. Person: John Judkins VEuPathDB 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. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB 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. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB 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. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB 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. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB Pseudomonas fluorescens in induced sputum datum Pseudomonas, by bacteriology result A bacteria in induced sputum datum that is used to determine the presence of Pseudomonas in the specimen. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB 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. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB Stutzerimonas stutzeri in induced sputum datum Salmonella, 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 Salmonella in an induced sputum specimen. Person: John Judkins VEuPathDB multiplex qPCR threshold cycle for Salmonella in induced sputum Salmonella, by bacteriology result A bacteria in induced sputum datum that is used to determine the presence of Salmonella in the specimen. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB 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. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB Serratia marcescens in induced sputum datum Serratia, by bacteriology result A bacteria in induced sputum datum that is used to determine the presence of Serratia in the specimen. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB 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. Person: John Judkins VEuPathDB 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. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB 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. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB 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. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB 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. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB 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. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB 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. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB 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. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB 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. Person: John Judkins VEuPathDB 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. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB Streptococcus pneumoniae in induced sputum datum Streptococcus, by bacteriology result A bacteria in induced sputum datum that is used to determine the presence of Streptococcus in the specimen. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB 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. Person: John Judkins VEuPathDB multiplex qPCR threshold cycle for Pneumocystis jirovecii in induced sputum Adenovirus, 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 Adenoviridae in an induced sputum specimen. Person: John Judkins VEuPathDB 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. Person: John Judkins VEuPathDB 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. Person: John Judkins VEuPathDB 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. Person: John Judkins VEuPathDB 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. Person: John Judkins VEuPathDB 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. Person: John Judkins VEuPathDB 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. Person: John Judkins VEuPathDB 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. Person: John Judkins VEuPathDB 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. Person: John Judkins VEuPathDB multiplex qPCR threshold cycle for Respiratory syncytial virus in induced sputum Influenza A, 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 Influenza A virus in an induced sputum specimen. Person: John Judkins VEuPathDB multiplex qPCR threshold cycle for Influenza A virus in induced sputum Influenza 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 Influenza B virus in an induced sputum specimen. Person: John Judkins VEuPathDB multiplex qPCR threshold cycle for Influenza B virus in induced sputum Influenza C, 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 Influenza C virus in an induced sputum specimen. Person: John Judkins VEuPathDB 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. Person: John Judkins VEuPathDB 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. Person: John Judkins VEuPathDB 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. Person: John Judkins VEuPathDB 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. Person: John Judkins VEuPathDB 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. Person: John Judkins VEuPathDB multiplex qPCR threshold cycle for Enterovirus or Parechovirus in induced sputum Rhinovirus, 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 Rhinovirus in an induced sputum specimen. Person: John Judkins VEuPathDB multiplex qPCR threshold cycle for Rhinovirus in induced sputum Adenovirus, by multiplexed qPCR A virus in induced sputum datum that specifies whether Adenoviridae were detected by multiplex real time polymerase chain reaction assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Adenoviridae in induced sputum by multiplex real time polymerase chain reaction assay Any virus, by multiplexed qPCR A virus in induced sputum datum that specifies whether a virus was detected by multiplex real time polymerase chain reaction assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of virus in induced sputum by multiplex real time polymerase chain reaction assay Coronavirus 229, by multiplexed qPCR A virus in induced sputum datum that specifies whether Human coronavirus 229E was detected by multiplex real time polymerase chain reaction assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of human coronavirus 229E in induced sputum by multiplex real time polymerase chain reaction assay Coronavirus 43, by multiplexed qPCR A virus in induced sputum datum that specifies whether Human coronavirus OC43 was detected by multiplex real time polymerase chain reaction assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Human coronavirus OC43 in induced sputum by multiplex real time polymerase chain reaction assay Coronavirus 63, by multiplexed qPCR A virus in induced sputum datum that specifies whether Human coronavirus NL63 was detected by multiplex real time polymerase chain reaction assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Human coronavirus NL63 in induced sputum by multiplex real time polymerase chain reaction assay Coronavirus HKU, by multiplexed qPCR A virus in induced sputum datum that specifies whether Human coronavirus HKU1 was detected by multiplex real time polymerase chain reaction assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Human coronavirus HKU1 in induced sputum by multiplex real time polymerase chain reaction assay Cytomegalovirus, by multiplexed qPCR A virus in induced sputum datum that specifies whether Cytomegalovirus was detected by multiplex real time polymerase chain reaction assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Cytomegalovirus in induced sputum by multiplex real time polymerase chain reaction assay Human bocavirus, by multiplexed qPCR A virus in induced sputum datum that specifies whether Human bocavirus was detected by multiplex real time polymerase chain reaction assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB 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. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB 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. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Human orthopneumovirus in induced sputum by multiplex real time polymerase chain reaction assay Influenza A, by multiplexed qPCR A virus in induced sputum datum that specifies whether Influenza A virus was detected by multiplex real time polymerase chain reaction assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Influenza A virus in induced sputum by multiplex real time polymerase chain reaction assay Influenza B, by multiplexed qPCR A virus in induced sputum datum that specifies whether Influenza B virus was detected by multiplex real time polymerase chain reaction assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Influenza B virus in induced sputum by multiplex real time polymerase chain reaction assay Influenza C, by multiplexed qPCR A virus in induced sputum datum that specifies whether Influenza C virus was detected by multiplex real time polymerase chain reaction assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Influenza C virus in induced sputum by multiplex real time polymerase chain reaction assay Parainfluenza 1, by multiplexed qPCR A virus in induced sputum datum that specifies whether Human respirovirus 1 was detected by multiplex real time polymerase chain reaction assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Human respirovirus 1 in induced sputum by multiplex real time polymerase chain reaction assay Parainfluenza 2, by multiplexed qPCR A virus in induced sputum datum that specifies whether Human orthorubulavirus 2 was detected by multiplex real time polymerase chain reaction assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Human orthorubulavirus 2 in induced sputum by multiplex real time polymerase chain reaction assay Parainfluenza 3, by multiplexed qPCR A virus in induced sputum datum that specifies whether Human respirovirus 3 was detected by multiplex real time polymerase chain reaction assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Human respirovirus 3 in induced sputum by multiplex real time polymerase chain reaction assay Parainfluenza 4, by multiplexed qPCR A virus in induced sputum datum that specifies whether Human orthorubulavirus 4 was detected by multiplex real time polymerase chain reaction assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB 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. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Picornaviridae in induced sputum by multiplex real time polymerase chain reaction assay Rhinovirus, by multiplexed qPCR A virus in induced sputum datum that specifies whether Rhinovirus was detected by multiplex real time polymerase chain reaction assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB 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. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB Streptococcus pneumoniae serotype 2 in induced sputum datum Any noncontaminant bacteria, by multiplexed qPCR A bacteria in lung datum that specifies whether bacteria were detected by multiplex real time polymerase chain reaction assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of bacteria in lung by multiplex real time polymerase chain reaction assay Bordetella pertussis, by multiplexed qPCR A bacteria in lung datum that specifies whether Bordetella pertussis was detected by multiplex real time polymerase chain reaction assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Bordetella pertussis in lung by multiplex real time polymerase chain reaction assay Chlamydophila pneumoniae, by multiplexed qPCR A bacteria in lung datum that specifies whether Chlamydia pneumoniae was detected by multiplex real time polymerase chain reaction assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Chlamydia pneumoniae in lung by multiplex real time polymerase chain reaction assay Coagulase-negative Staphylococcus, by bacteriology A bacteria in lung datum that specifies whether Coagulase-Negative Staphylococcus was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Coagulase-Negative Staphylococcus in lung Haemophilus influenzae type B, by multiplexed qPCR A bacteria in lung datum that specifies whether Haemophilus influenzae serotype b was detected by multiplex real time polymerase chain reaction assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Haemophilus influenzae serotype b in lung by multiplex real time polymerase chain reaction assay Haemophilus influenzae, by bacteriology A bacteria in lung datum that specifies whether Haemophilus influenzae was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Haemophilus influenzae in lung Haemophilus influenzae, by multiplexed qPCR A bacteria in lung datum that specifies whether Haemophilus influenzae was detected by multiplex real time polymerase chain reaction assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Haemophilus influenzae in lung by multiplex real time polymerase chain reaction assay Haemophilus parahaemolyticus, by multiplexed qPCR A bacteria in lung datum that specifies whether Haemophilus parahaemolyticus was detected by multiplex real time polymerase chain reaction assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Haemophilus parahaemolyticus in lung by multiplex real time polymerase chain reaction assay Legionella, by multiplexed qPCR A bacteria in lung datum that specifies whether Legionella was detected by multiplex real time polymerase chain reaction assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Legionella in lung by multiplex real time polymerase chain reaction assay Moraxella catarrhalis (Branhamella catarrhalis), by bacteriology A bacteria in lung datum that specifies whether Moraxella catarrhalis was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Moraxella catarrhalis in lung Moraxella catarrhalis (Branhamella catarrhalis), by multiplexed qPCR A bacteria in lung datum that specifies whether Moraxella catarrhalis was detected by multiplex real time polymerase chain reaction assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Moraxella catarrhalis in lung by multiplex real time polymerase chain reaction assay Mycoplasma pneumoniae, by multiplexed qPCR A bacteria in lung datum that specifies whether Mycoplasmoides pneumoniae was detected by multiplex real time polymerase chain reaction assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Mycoplasmoides pneumoniae in lung by multiplex real time polymerase chain reaction assay Salmonella, by multiplexed qPCR A bacteria in lung datum that specifies whether Salmonella was detected by multiplex real time polymerase chain reaction assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Salmonella in lung by multiplex real time polymerase chain reaction assay Staphylococcus aureus, by bacteriology A bacteria in lung datum that specifies whether Staphylococcus aureus was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Staphylococcus aureus in lung Staphylococcus aureus, by multiplexed qPCR A bacteria in lung datum that specifies whether Staphylococcus aureus was detected by multiplex real time polymerase chain reaction assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Staphylococcus aureus in lung by multiplex real time polymerase chain reaction assay Streptococcus pneumoniae, by bacteriology A bacteria in lung datum that specifies whether Streptococcus pneumoniae was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Streptococcus pneumoniae in lung Streptococcus pneumoniae, by multiplexed qPCR A bacteria in lung datum that specifies whether Streptococcus pneumoniae was detected by multiplex real time polymerase chain reaction assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Streptococcus pneumoniae in lung by multiplex real time polymerase chain reaction assay Pneumocystis jiroveci, by multiplexed qPCR A eukaryota in lung datum that specifies whether Pneumocystis jirovecii was detected by multiplex real time polymerase chain reaction assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Pneumocystis jirovecii in lung by multiplex real time polymerase chain reaction assay 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 lung specimen. Person: John Judkins VEuPathDB 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. Person: John Judkins VEuPathDB multiplex qPCR threshold cycle for Chlamydia pneumoniae in lung 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 lung specimen. Person: John Judkins VEuPathDB multiplex qPCR threshold cycle for Haemophilus influenzae in lung Legionella, 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 Legionella in an lung specimen. Person: John Judkins VEuPathDB multiplex qPCR threshold cycle for Legionella in lung 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 lung specimen. Person: John Judkins VEuPathDB multiplex qPCR threshold cycle for Moraxella catarrhalis in lung 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 lung specimen. Person: John Judkins VEuPathDB multiplex qPCR threshold cycle for Mycoplasmoides pneumoniae in lung Salmonella, 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 Salmonella in an lung specimen. Person: John Judkins VEuPathDB multiplex qPCR threshold cycle for Salmonella in lung 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 lung specimen. Person: John Judkins VEuPathDB multiplex qPCR threshold cycle for Staphylococcus aureus in lung 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 lung specimen. Person: John Judkins VEuPathDB multiplex qPCR threshold cycle for Streptococcus pneumoniae in lung 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 lung specimen. Person: John Judkins VEuPathDB multiplex qPCR threshold cycle for Pneumocystis jirovecii in lung Adenovirus, 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 Adenoviridae in an lung specimen. Person: John Judkins VEuPathDB multiplex qPCR threshold cycle for Adenoviridae in lung 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 lung specimen. Person: John Judkins VEuPathDB multiplex qPCR threshold cycle for Human coronavirus 229E in lung 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 lung specimen. Person: John Judkins VEuPathDB multiplex qPCR threshold cycle for Human coronavirus OC43 in lung 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 lung specimen. Person: John Judkins VEuPathDB multiplex qPCR threshold cycle for Human coronavirus NL63 in lung 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 lung specimen. Person: John Judkins VEuPathDB multiplex qPCR threshold cycle for Human coronavirus HKU1 in lung 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 lung specimen. Person: John Judkins VEuPathDB multiplex qPCR threshold cycle for Cytomegalovirus in lung 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 lung specimen. Person: John Judkins VEuPathDB 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. Person: John Judkins VEuPathDB multiplex qPCR threshold cycle for Human metapneumovirus in lung 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 lung specimen. Person: John Judkins VEuPathDB multiplex qPCR threshold cycle for Respiratory syncytial virus in lung Influenza A, 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 Influenza A virus in an lung specimen. Person: John Judkins VEuPathDB multiplex qPCR threshold cycle for Influenza A virus in lung Influenza 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 Influenza B virus in an lung specimen. Person: John Judkins VEuPathDB multiplex qPCR threshold cycle for Influenza B virus in lung Influenza C, 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 Influenza C virus in an lung specimen. Person: John Judkins VEuPathDB multiplex qPCR threshold cycle for Influenza C virus in lung 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 lung specimen. Person: John Judkins VEuPathDB multiplex qPCR threshold cycle for Human respirovirus 1 in lung 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 lung specimen. Person: John Judkins VEuPathDB multiplex qPCR threshold cycle for Human orthorubulavirus 2 in lung 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 lung specimen. Person: John Judkins VEuPathDB multiplex qPCR threshold cycle for Human respirovirus 3 in lung 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 lung specimen. Person: John Judkins VEuPathDB multiplex qPCR threshold cycle for Human orthorubulavirus 4 in lung 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 lung specimen. Person: John Judkins VEuPathDB multiplex qPCR threshold cycle for Enterovirus or Parechovirus in lung Rhinovirus, 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 Rhinovirus in an lung specimen. Person: John Judkins VEuPathDB multiplex qPCR threshold cycle for Rhinovirus in lung Adenovirus, by multiplexed qPCR A virus in lung datum that specifies whether Adenoviridae were detected by multiplex real time polymerase chain reaction assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Adenoviridae in lung by multiplex real time polymerase chain reaction assay Any virus, by multiplexed qPCR A virus in lung datum that specifies whether a virus was detected by multiplex real time polymerase chain reaction assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of virus in lung by multiplex real time polymerase chain reaction assay Coronavirus 229, by multiplexed qPCR A virus in lung datum that specifies whether Human coronavirus 229E was detected by multiplex real time polymerase chain reaction assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Human coronavirus 229E in lung by multiplex real time polymerase chain reaction assay Coronavirus 43, by multiplexed qPCR A virus in lung datum that specifies whether Human coronavirus OC43 was detected by multiplex real time polymerase chain reaction assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Human coronavirus OC43 in lung by multiplex real time polymerase chain reaction assay Coronavirus 63, by multiplexed qPCR A virus in lung datum that specifies whether Human coronavirus NL63 was detected by multiplex real time polymerase chain reaction assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Human coronavirus NL63 in lung by multiplex real time polymerase chain reaction assay Coronavirus HKU, by multiplexed qPCR A virus in lung datum that specifies whether Human coronavirus HKU1 was detected by multiplex real time polymerase chain reaction assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Human coronavirus HKU1 in lung by multiplex real time polymerase chain reaction assay Cytomegalovirus, by multiplexed qPCR A virus in lung datum that specifies whether Cytomegalovirus was detected by multiplex real time polymerase chain reaction assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Cytomegalovirus in lung by multiplex real time polymerase chain reaction assay Human bocavirus, by multiplexed qPCR A virus in lung datum that specifies whether Human bocavirus was detected by multiplex real time polymerase chain reaction assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB 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. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Human metapneumovirus in lung by multiplex real time polymerase chain reaction assay Human respiratory syncytial viruses A/B, by multiplexed qPCR A virus in lung datum that specifies whether Human orthopneumovirus was detected by multiplex real time polymerase chain reaction assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Human orthopneumovirus in lung by multiplex real time polymerase chain reaction assay Influenza A, by multiplexed qPCR A virus in lung datum that specifies whether Influenza A virus was detected by multiplex real time polymerase chain reaction assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Influenza A virus in lung by multiplex real time polymerase chain reaction assay Influenza B, by multiplexed qPCR A virus in lung datum that specifies whether Influenza B virus was detected by multiplex real time polymerase chain reaction assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Influenza B virus in lung by multiplex real time polymerase chain reaction assay Influenza C, by multiplexed qPCR A virus in lung datum that specifies whether Influenza C virus was detected by multiplex real time polymerase chain reaction assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Influenza C virus in lung by multiplex real time polymerase chain reaction assay Parainfluenza 1, by multiplexed qPCR A virus in lung datum that specifies whether Human respirovirus 1 was detected by multiplex real time polymerase chain reaction assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Human respirovirus 1 in lung by multiplex real time polymerase chain reaction assay Parainfluenza 2, by multiplexed qPCR A virus in lung datum that specifies whether Human orthorubulavirus 2 was detected by multiplex real time polymerase chain reaction assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Human orthorubulavirus 2 in lung by multiplex real time polymerase chain reaction assay Parainfluenza 3, by multiplexed qPCR A virus in lung datum that specifies whether Human respirovirus 3 was detected by multiplex real time polymerase chain reaction assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Human respirovirus 3 in lung by multiplex real time polymerase chain reaction assay Parainfluenza 4, by multiplexed qPCR A virus in lung datum that specifies whether Human orthorubulavirus 4 was detected by multiplex real time polymerase chain reaction assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Human orthorubulavirus 4 in lung by multiplex real time polymerase chain reaction assay Parechovirus/Enterovirus, by multiplexed qPCR A virus in lung datum that specifies whether Picornaviridae was detected by multiplex real time polymerase chain reaction assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Picornaviridae in lung by multiplex real time polymerase chain reaction assay Rhinovirus, by multiplexed qPCR A virus in lung datum that specifies whether Rhinovirus was detected by multiplex real time polymerase chain reaction assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Rhinovirus in lung by multiplex real time polymerase chain reaction assay Bordetella pertussis, by multiplexed qPCR A bacteria in nasopharyngeal or oropharyngeal swab datum that specifies whether Bordetella pertussis was detected by multiplex real time polymerase chain reaction assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Bordetella pertussis in nasopharynx or oropharynx by multiplex real time polymerase chain reaction assay Chlamydophila pneumoniae, by multiplexed qPCR A bacteria in nasopharyngeal or oropharyngeal swab datum that specifies whether Chlamydia pneumoniae was detected by multiplex real time polymerase chain reaction assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Chlamydia pneumoniae in nasopharynx or oropharynx by multiplex real time polymerase chain reaction assay Haemophilus influenzae, by multiplexed qPCR A bacteria in nasopharyngeal or oropharyngeal swab datum that specifies whether Haemophilus influenzae was detected by multiplex real time polymerase chain reaction assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Haemophilus influenzae in nasopharynx or oropharynx by multiplex real time polymerase chain reaction assay Legionella, by multiplexed qPCR A bacteria in nasopharyngeal or oropharyngeal swab datum that specifies whether Legionella was detected by multiplex real time polymerase chain reaction assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Legionella in nasopharynx or oropharynx by multiplex real time polymerase chain reaction assay Moraxella catarrhalis (Branhamella catarrhalis), by multiplexed qPCR A bacteria in nasopharyngeal or oropharyngeal swab datum that specifies whether Moraxella catarrhalis was detected by multiplex real time polymerase chain reaction assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Moraxella catarrhalis in nasopharynx or oropharynx by multiplex real time polymerase chain reaction assay Mycoplasma pneumoniae, by multiplexed qPCR A bacteria in nasopharyngeal or oropharyngeal swab datum that specifies whether Mycoplasmoides pneumoniae was detected by multiplex real time polymerase chain reaction assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Mycoplasmoides pneumoniae in nasopharynx or oropharynx by multiplex real time polymerase chain reaction assay Salmonella, by multiplexed qPCR A bacteria in nasopharyngeal or oropharyngeal swab datum that specifies whether Salmonella was detected by multiplex real time polymerase chain reaction assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Salmonella in nasopharynx or oropharynx by multiplex real time polymerase chain reaction assay Staphylococcus aureus, by multiplexed qPCR A bacteria in nasopharyngeal or oropharyngeal swab datum that specifies whether Staphylococcus aureus was detected by multiplex real time polymerase chain reaction assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Staphylococcus aureus in nasopharynx or oropharynx by multiplex real time polymerase chain reaction assay Streptococcus pneumoniae serotype 2, by bacteriology result A bacteria in nasopharyngeal or oropharyngeal swab datum that is used to determine the presence of Streptococcus pneumoniae serotype 2 in the specimen. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB 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. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB 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. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB Streptococcus pneumoniae serotype 4 in nasopharyngeal or oropharyngeal swab datum Streptococcus pneumoniae, by multiplexed qPCR A bacteria in nasopharyngeal or oropharyngeal swab datum that specifies whether Streptococcus pneumoniae was detected by multiplex real time polymerase chain reaction assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Streptococcus pneumoniae in nasopharynx or oropharynx by multiplex real time polymerase chain reaction assay Pneumocystis jiroveci, by multiplexed qPCR A eukaryota in nasopharyngeal or oropharyngeal swab datum that specifies whether Pneumocystis jirovecii was detected by multiplex real time polymerase chain reaction assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Pneumocystis jirovecii in nasopharynx or oropharynx by multiplex real time polymerase chain reaction assay 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 a nasopharyngeal or oropharyngeal swab specimen. Person: John Judkins VEuPathDB multiplex qPCR threshold cycle for Bordetella pertussis in nasopharynx or oropharynx 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 a nasopharyngeal or oropharyngeal swab specimen. Person: John Judkins VEuPathDB multiplex qPCR threshold cycle for Chlamydia pneumoniae in nasopharynx or oropharynx 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 a nasopharynx specimen or oropharynx specimen. Person: John Judkins VEuPathDB multiplex qPCR threshold cycle for Haemophilus influenzae in nasopharynx or oropharynx Legionella, 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 Legionella in a nasopharyngeal or oropharyngeal swab specimen. Person: John Judkins VEuPathDB multiplex qPCR threshold cycle for Legionella in nasopharynx or oropharynx 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 a nasopharyngeal or oropharyngeal swab specimen. Person: John Judkins VEuPathDB multiplex qPCR threshold cycle for Moraxella catarrhalis in nasopharynx or oropharynx 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 a nasopharyngeal or oropharyngeal swab specimen. Person: John Judkins VEuPathDB multiplex qPCR threshold cycle for Mycoplasmoides pneumoniae in nasopharynx or oropharynx Salmonella, 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 Salmonella in a nasopharyngeal or oropharyngeal swab specimen. Person: John Judkins VEuPathDB multiplex qPCR threshold cycle for Salmonella in nasopharynx or oropharynx 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 a nasopharyngeal or oropharyngeal swab specimen. Person: John Judkins VEuPathDB multiplex qPCR threshold cycle for Staphylococcus aureus in nasopharynx or oropharynx 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 a nasopharyngeal or oropharyngeal swab specimen. Person: John Judkins VEuPathDB multiplex qPCR threshold cycle for Streptococcus pneumoniae in nasopharynx or oropharynx 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 a nasopharyngeal or oropharyngeal swab specimen. Person: John Judkins VEuPathDB multiplex qPCR threshold cycle for Pneumocystis jirovecii in nasopharynx or oropharynx Adenovirus, 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 Adenoviridae in a nasopharyngeal or oropharyngeal swab specimen. Person: John Judkins VEuPathDB multiplex qPCR threshold cycle for Adenoviridae in nasopharynx or oropharynx 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 a nasopharyngeal or oropharyngeal swab specimen. Person: John Judkins VEuPathDB multiplex qPCR threshold cycle for Human coronavirus 229E in nasopharynx or oropharynx 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 a nasopharyngeal or oropharyngeal swab specimen. Person: John Judkins VEuPathDB multiplex qPCR threshold cycle for Human coronavirus OC43 in nasopharynx or oropharynx 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 a nasopharyngeal or oropharyngeal swab specimen. Person: John Judkins VEuPathDB multiplex qPCR threshold cycle for Human coronavirus NL63 in nasopharynx or oropharynx 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 a nasopharyngeal or oropharyngeal swab specimen. Person: John Judkins VEuPathDB multiplex qPCR threshold cycle for Human coronavirus HKU1 in nasopharynx or oropharynx 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 a nasopharyngeal or oropharyngeal swab specimen. Person: John Judkins VEuPathDB multiplex qPCR threshold cycle for Cytomegalovirus in nasopharynx or oropharynx 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 a nasopharyngeal or oropharyngeal swab specimen. Person: John Judkins VEuPathDB multiplex qPCR threshold cycle for Human bocavirus in nasopharynx or oropharynx 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 a nasopharyngeal or oropharyngeal swab specimen. Person: John Judkins VEuPathDB multiplex qPCR threshold cycle for Human metapneumovirus in nasopharynx or oropharynx 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 Human orthopneumovirus in a nasopharyngeal or oropharyngeal swab specimen. Person: John Judkins VEuPathDB multiplex qPCR threshold cycle for Human orthopneumovirus in nasopharynx or oropharynx Influenza A, 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 Influenza A virus in a nasopharyngeal or oropharyngeal swab specimen. Person: John Judkins VEuPathDB multiplex qPCR threshold cycle for Influenza A virus in nasopharynx or oropharynx Influenza 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 Influenza B virus in a nasopharyngeal or oropharyngeal swab specimen. Person: John Judkins VEuPathDB multiplex qPCR threshold cycle for Influenza B virus in nasopharynx or oropharynx Influenza C, 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 Influenza C virus in a nasopharyngeal or oropharyngeal swab specimen. Person: John Judkins VEuPathDB multiplex qPCR threshold cycle for Influenza C virus in nasopharynx or oropharynx 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 a nasopharyngeal or oropharyngeal swab specimen. Person: John Judkins VEuPathDB multiplex qPCR threshold cycle for Human respirovirus 1 in nasopharynx or oropharynx 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 a nasopharyngeal or oropharyngeal swab specimen. Person: John Judkins VEuPathDB multiplex qPCR threshold cycle for Human orthorubulavirus 2 in nasopharynx or oropharynx 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 a nasopharyngeal or oropharyngeal swab specimen. Person: John Judkins VEuPathDB multiplex qPCR threshold cycle for Human respirovirus 3 in nasopharynx or oropharynx 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 a nasopharyngeal or oropharyngeal swab specimen. Person: John Judkins VEuPathDB multiplex qPCR threshold cycle for Human orthorubulavirus 4 in nasopharynx or oropharynx 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 a nasopharyngeal or oropharyngeal swab specimen. Person: John Judkins VEuPathDB multiplex qPCR threshold cycle for Enterovirus or Parechovirus in nasopharynx or oropharynx Rhinovirus, 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 Rhinovirus in a nasopharyngeal or oropharyngeal swab specimen. Person: John Judkins VEuPathDB multiplex qPCR threshold cycle for Rhinovirus in nasopharynx or oropharynx Adenovirus, by multiplexed qPCR A virus in nasopharyngeal or oropharyngeal swab datum that specifies whether Adenoviridae were detected by multiplex real time polymerase chain reaction assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Adenoviridae in nasopharynx or oropharynx by multiplex real time polymerase chain reaction assay Coronavirus 229, by multiplexed qPCR A virus in nasopharyngeal or oropharyngeal swab datum that specifies whether Human coronavirus 229E was detected by multiplex real time polymerase chain reaction assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Human coronavirus 229E in nasopharynx or oropharynx by multiplex real time polymerase chain reaction assay Coronavirus 43, by multiplexed qPCR A virus in nasopharyngeal or oropharyngeal swab datum that specifies whether Human coronavirus OC43 was detected by multiplex real time polymerase chain reaction assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Human coronavirus OC43 in nasopharynx or oropharynx by multiplex real time polymerase chain reaction assay Coronavirus 63, by multiplexed qPCR A virus in nasopharyngeal or oropharyngeal swab datum that specifies whether Human coronavirus NL63 was detected by multiplex real time polymerase chain reaction assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Human coronavirus NL63 in nasopharynx or oropharynx by multiplex real time polymerase chain reaction assay Coronavirus HKU, by multiplexed qPCR A virus in nasopharyngeal or oropharyngeal swab datum that specifies whether Human coronavirus HKU1 was detected by multiplex real time polymerase chain reaction assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Human coronavirus HKU1 in nasopharynx or oropharynx by multiplex real time polymerase chain reaction assay Cytomegalovirus, by multiplexed qPCR A virus in nasopharyngeal or oropharyngeal swab datum that specifies whether Cytomegalovirus was detected by multiplex real time polymerase chain reaction assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Cytomegalovirus in nasopharynx or oropharynx by multiplex real time polymerase chain reaction assay Human bocavirus, by multiplexed qPCR A virus in nasopharyngeal or oropharyngeal swab datum that specifies whether Human bocavirus was detected by multiplex real time polymerase chain reaction assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Human bocavirus in nasopharynx or oropharynx by multiplex real time polymerase chain reaction assay Human metapneumonoviruses A/B, by multiplexed qPCR A virus in nasopharyngeal or oropharyngeal swab datum that specifies whether Human metapneumovirus was detected by multiplex real time polymerase chain reaction assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Human metapneumovirus in nasopharynx or oropharynx by multiplex real time polymerase chain reaction assay Human respiratory syncytial viruses A/B, by multiplexed qPCR A virus in nasopharyngeal or oropharyngeal swab datum that specifies whether Human orthopneumovirus was detected by multiplex real time polymerase chain reaction assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Human orthopneumovirus in nasopharynx or oropharynx by multiplex real time polymerase chain reaction assay Influenza A, by multiplexed qPCR A virus in nasopharyngeal or oropharyngeal swab datum that specifies whether Influenza A virus was detected by multiplex real time polymerase chain reaction assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Influenza A virus in nasopharynx or oropharynx by multiplex real time polymerase chain reaction assay Influenza B, by multiplexed qPCR A virus in nasopharyngeal or oropharyngeal swab datum that specifies whether Influenza B virus was detected by multiplex real time polymerase chain reaction assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Influenza B virus in nasopharynx or oropharynx by multiplex real time polymerase chain reaction assay Influenza C, by multiplexed qPCR A virus in nasopharyngeal or oropharyngeal swab datum that specifies whether Influenza C virus was detected by multiplex real time polymerase chain reaction assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Influenza C virus in nasopharynx or oropharynx by multiplex real time polymerase chain reaction assay Parainfluenza 1, by multiplexed qPCR A virus in nasopharyngeal or oropharyngeal swab datum that specifies whether Human respirovirus 1 was detected by multiplex real time polymerase chain reaction assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Human respirovirus 1 in nasopharynx or oropharynx by multiplex real time polymerase chain reaction assay Parainfluenza 2, by multiplexed qPCR A virus in nasopharyngeal or oropharyngeal swab datum that specifies whether Human orthorubulavirus 2 was detected by multiplex real time polymerase chain reaction assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Human orthorubulavirus 2 in nasopharynx or oropharynx by multiplex real time polymerase chain reaction assay Parainfluenza 3, by multiplexed qPCR A virus in nasopharyngeal or oropharyngeal swab datum that specifies whether Human respirovirus 3 was detected by multiplex real time polymerase chain reaction assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Human respirovirus 3 in nasopharynx or oropharynx by multiplex real time polymerase chain reaction assay Parainfluenza 4, by multiplexed qPCR A virus in nasopharyngeal or oropharyngeal swab datum that specifies whether Human orthorubulavirus 4 was detected by multiplex real time polymerase chain reaction assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Human orthorubulavirus 4 in nasopharynx or oropharynx by multiplex real time polymerase chain reaction assay Parechovirus/Enterovirus, by multiplexed qPCR A virus in nasopharyngeal or oropharyngeal swab datum that specifies whether Picornaviridae was detected by multiplex real time polymerase chain reaction assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Picornaviridae in nasopharynx or oropharynx by multiplex real time polymerase chain reaction assay Rhinovirus, by multiplexed qPCR A virus in nasopharyngeal or oropharyngeal swab datum that specifies whether Rhinovirus was detected by multiplex real time polymerase chain reaction assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Rhinovirus in nasopharynx or oropharynx by multiplex real time polymerase chain reaction assay Any bacteria, by multiplexed qPCR A bacteria in nasopharyngeal or oropharyngeal swab datum that specifies whether bacteria were detected by multiplex real time polymerase chain reaction assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of bacteria in nasopharynx or oropharynx by multiplex real time polymerase chain reaction assay Haemophilus parahaemolyticus, by multiplexed qPCR A bacteria in nasopharyngeal or oropharyngeal swab datum that specifies whether Haemophilus parahaemolyticus was detected by multiplex real time polymerase chain reaction assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Haemophilus parahaemolyticus in nasopharynx or oropharynx by multiplex real time polymerase chain reaction assay Streptococcus pneumoniae, by bacteriology A bacteria in nasopharyngeal or oropharyngeal swab datum that specifies whether Streptococcus pneumoniae was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Streptococcus pneumoniae in nasopharynx or oropharynx Any virus, by multiplexed qPCR A virus in nasopharyngeal or oropharyngeal swab datum that specifies whether a virus was detected by multiplex real time polymerase chain reaction assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of virus in nasopharynx or oropharynx by multiplex real time polymerase chain reaction assay Measles morbillivirus, by PCR A virus in nasopharyngeal or oropharyngeal swab datum that specifies whether Measles morbillivirus was detected by polymerase chain reaction assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Measles morbillivirus in nasopharynx or oropharynx by polymerase chain reaction assay Any noncontaminant bacteria, by multiplexed qPCR A bacteria in pleural fluid datum that specifies whether bacteria were detected by multiplex real time polymerase chain reaction assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of bacteria in pleural fluid by multiplex real time polymerase chain reaction assay Bordetella pertussis, by multiplexed qPCR A bacteria in pleural fluid datum that specifies whether Bordetella pertussis was detected by multiplex real time polymerase chain reaction assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Bordetella pertussis in pleural fluid by multiplex real time polymerase chain reaction assay Escherichia coli, by bacteriology A bacteria in pleural fluid datum that specifies whether Escherichia coli was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Escherichia coli in pleural fluid Haemophilus influenzae, by bacteriology A bacteria in pleural fluid datum that specifies whether Haemophilus influenzae was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Haemophilus influenzae in pleural fluid Haemophilus influenzae, by multiplexed qPCR A bacteria in pleural fluid datum that specifies whether Haemophilus influenzae was detected by multiplex real time polymerase chain reaction assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Haemophilus influenzae in pleural fluid by multiplex real time polymerase chain reaction assay Haemophilus parahaemolyticus, by multiplexed qPCR A bacteria in pleural fluid datum that specifies whether Haemophilus parahaemolyticus was detected by multiplex real time polymerase chain reaction assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Haemophilus parahaemolyticus in pleural fluid by multiplex real time polymerase chain reaction assay Legionella, by multiplexed qPCR A bacteria in pleural fluid datum that specifies whether Legionella was detected by multiplex real time polymerase chain reaction assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Legionella in pleural fluid by multiplex real time polymerase chain reaction assay Moraxella catarrhalis (Branhamella catarrhalis), by bacteriology A bacteria in pleural fluid datum that specifies whether Moraxella catarrhalis was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Moraxella catarrhalis in pleural fluid Moraxella catarrhalis (Branhamella catarrhalis), by multiplexed qPCR A bacteria in pleural fluid datum that specifies whether Moraxella catarrhalis was detected by multiplex real time polymerase chain reaction assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Moraxella catarrhalis in pleural fluid by multiplex real time polymerase chain reaction assay Mycoplasma pneumoniae, by multiplexed qPCR A bacteria in pleural fluid datum that specifies whether Mycoplasmoides pneumoniae was detected by multiplex real time polymerase chain reaction assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Mycoplasmoides pneumoniae in pleural fluid by multiplex real time polymerase chain reaction assay Salmonella, by multiplexed qPCR A bacteria in pleural fluid datum that specifies whether Salmonella was detected by multiplex real time polymerase chain reaction assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Salmonella in pleural fluid by multiplex real time polymerase chain reaction assay Staphylococcus aureus, by bacteriology A bacteria in pleural fluid datum that specifies whether Staphylococcus aureus was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Staphylococcus aureus in pleural fluid Staphylococcus aureus, by multiplexed qPCR A bacteria in pleural fluid datum that specifies whether Staphylococcus aureus was detected by multiplex real time polymerase chain reaction assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Staphylococcus aureus in pleural fluid by multiplex real time polymerase chain reaction assay Streptococcus group F, by bacteriology A bacteria in pleural fluid datum that specifies whether Beta Streptococcus Group F was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Beta Streptococcus Group F in pleural fluid Streptococcus pneumoniae, by bacteriology A bacteria in pleural fluid datum that specifies whether Streptococcus pneumoniae was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Streptococcus pneumoniae in pleural fluid Streptococcus pneumoniae, by multiplexed qPCR A bacteria in pleural fluid datum that specifies whether Streptococcus pneumoniae was detected by multiplex real time polymerase chain reaction assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Streptococcus pneumoniae in pleural fluid by multiplex real time polymerase chain reaction assay Pneumocystis jiroveci, by multiplexed qPCR A eukaryota in pleural fluid datum that specifies whether Pneumocystis jirovecii was detected by multiplex real time polymerase chain reaction assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Pneumocystis jirovecii in pleural fluid by multiplex real time polymerase chain reaction assay 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 a pleural fluid specimen. Person: John Judkins VEuPathDB multiplex qPCR threshold cycle for Bordetella pertussis in pleural fluid 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 a pleural fluid specimen. Person: John Judkins VEuPathDB multiplex qPCR threshold cycle for Chlamydia pneumoniae in pleural fluid 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 a pleural fluid specimen. Person: John Judkins VEuPathDB multiplex qPCR threshold cycle for Haemophilus influenzae in pleural fluid Legionella, 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 Legionella in a pleural fluid specimen. Person: John Judkins VEuPathDB multiplex qPCR threshold cycle for Legionella in pleural fluid 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 a pleural fluid specimen. Person: John Judkins VEuPathDB multiplex qPCR threshold cycle for Moraxella catarrhalis in pleural fluid 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 a pleural fluid specimen. Person: John Judkins VEuPathDB multiplex qPCR threshold cycle for Mycoplasmoides pneumoniae in pleural fluid Salmonella, 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 Salmonella in a pleural fluid specimen. Person: John Judkins VEuPathDB multiplex qPCR threshold cycle for Salmonella in pleural fluid 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 a pleural fluid specimen. Person: John Judkins VEuPathDB multiplex qPCR threshold cycle for Staphylococcus aureus in pleural fluid 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 a pleural fluid specimen. Person: John Judkins VEuPathDB multiplex qPCR threshold cycle for Streptococcus pneumoniae in pleural fluid 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 a pleural fluid specimen. Person: John Judkins VEuPathDB multiplex qPCR threshold cycle for Pneumocystis jirovecii in pleural fluid Adenovirus, 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 Adenoviridae in a pleural fluid specimen. Person: John Judkins VEuPathDB multiplex qPCR threshold cycle for Adenoviridae in pleural fluid 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 a pleural fluid specimen. Person: John Judkins VEuPathDB multiplex qPCR threshold cycle for Human coronavirus 229E in pleural fluid 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 a pleural fluid specimen. Person: John Judkins VEuPathDB multiplex qPCR threshold cycle for Human coronavirus OC43 in pleural fluid 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 a pleural fluid specimen. Person: John Judkins VEuPathDB multiplex qPCR threshold cycle for Human coronavirus NL63 in pleural fluid 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 a pleural fluid specimen. Person: John Judkins VEuPathDB multiplex qPCR threshold cycle for Human coronavirus HKU1 in pleural fluid 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 a pleural fluid specimen. Person: John Judkins VEuPathDB multiplex qPCR threshold cycle for Cytomegalovirus in pleural fluid 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 a pleural fluid specimen. Person: John Judkins VEuPathDB multiplex qPCR threshold cycle for Human bocavirus in pleural fluid 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 a pleural fluid specimen. Person: John Judkins VEuPathDB multiplex qPCR threshold cycle for Human metapneumovirus in pleural fluid 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 Human orthopneumovirus in a pleural fluid specimen. Person: John Judkins VEuPathDB multiplex qPCR threshold cycle for Human orthopneumovirus in pleural fluid Influenza A, 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 Influenza A virus in a pleural fluid specimen. Person: John Judkins VEuPathDB multiplex qPCR threshold cycle for Influenza A virus in pleural fluid Influenza 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 Influenza B virus in a pleural fluid specimen. Person: John Judkins VEuPathDB multiplex qPCR threshold cycle for Influenza B virus in pleural fluid Influenza C, 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 Influenza C virus in a pleural fluid specimen. Person: John Judkins VEuPathDB multiplex qPCR threshold cycle for Influenza C virus in pleural fluid 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 a pleural fluid specimen. Person: John Judkins VEuPathDB multiplex qPCR threshold cycle for Human respirovirus 1 in pleural fluid 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 a pleural fluid specimen. Person: John Judkins VEuPathDB multiplex qPCR threshold cycle for Human orthorubulavirus 2 in pleural fluid 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 a pleural fluid specimen. Person: John Judkins VEuPathDB multiplex qPCR threshold cycle for Human respirovirus 3 in pleural fluid 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 a pleural fluid specimen. Person: John Judkins VEuPathDB multiplex qPCR threshold cycle for Human orthorubulavirus 4 in pleural fluid 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 Picornaviridae in a pleural fluid specimen. Person: John Judkins VEuPathDB multiplex qPCR threshold cycle for Picornaviridae in pleural fluid Rhinovirus, 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 Rhinovirus in a pleural fluid specimen. Person: John Judkins VEuPathDB multiplex qPCR threshold cycle for Rhinovirus in pleural fluid Adenovirus, by multiplexed qPCR A virus in pleural fluid datum that specifies whether Adenoviridae were detected by multiplex real time polymerase chain reaction assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Adenoviridae in pleural fluid by multiplex real time polymerase chain reaction assay Any virus, by multiplexed qPCR A virus in pleural fluid datum that specifies whether a virus was detected by multiplex real time polymerase chain reaction assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of virus in pleural fluid by multiplex real time polymerase chain reaction assay Chlamydophila pneumoniae, by multiplexed qPCR A virus in pleural fluid datum that specifies whether Chlamydia pneumoniae was detected by multiplex real time polymerase chain reaction assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Chlamydia pneumoniae in pleural fluid by multiplex real time polymerase chain reaction assay Coronavirus 229, by multiplexed qPCR A virus in pleural fluid datum that specifies whether Human coronavirus 229E was detected by multiplex real time polymerase chain reaction assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Human coronavirus 229E in pleural fluid by multiplex real time polymerase chain reaction assay Coronavirus 43, by multiplexed qPCR A virus in pleural fluid datum that specifies whether Human coronavirus OC43 was detected by multiplex real time polymerase chain reaction assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Human coronavirus OC43 in pleural fluid by multiplex real time polymerase chain reaction assay Coronavirus 63, by multiplexed qPCR A virus in pleural fluid datum that specifies whether Human coronavirus NL63 was detected by multiplex real time polymerase chain reaction assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Human coronavirus NL63 in pleural fluid by multiplex real time polymerase chain reaction assay Coronavirus HKU, by multiplexed qPCR A virus in pleural fluid datum that specifies whether Human coronavirus HKU1 was detected by multiplex real time polymerase chain reaction assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Human coronavirus HKU1 in pleural fluid by multiplex real time polymerase chain reaction assay Cytomegalovirus, by multiplexed qPCR A virus in pleural fluid datum that specifies whether Cytomegalovirus was detected by multiplex real time polymerase chain reaction assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Cytomegalovirus in pleural fluid by multiplex real time polymerase chain reaction assay Human bocavirus, by multiplexed qPCR A virus in pleural fluid datum that specifies whether Human bocavirus was detected by multiplex real time polymerase chain reaction assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Human bocavirus in pleural fluid by multiplex real time polymerase chain reaction assay Human metapneumonoviruses A/B, by multiplexed qPCR A virus in pleural fluid datum that specifies whether Human metapneumovirus was detected by multiplex real time polymerase chain reaction assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Human metapneumovirus in pleural fluid by multiplex real time polymerase chain reaction assay Human respiratory syncytial viruses A/B, by multiplexed qPCR A virus in pleural fluid datum that specifies whether Human orthopneumovirus was detected by multiplex real time polymerase chain reaction assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Human orthopneumovirus in pleural fluid by multiplex real time polymerase chain reaction assay Influenza A, by multiplexed qPCR A virus in pleural fluid datum that specifies whether Influenza A virus was detected by multiplex real time polymerase chain reaction assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Influenza A virus in pleural fluid by multiplex real time polymerase chain reaction assay Influenza B, by multiplexed qPCR A virus in pleural fluid datum that specifies whether Influenza B virus was detected by multiplex real time polymerase chain reaction assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Influenza B virus in pleural fluid by multiplex real time polymerase chain reaction assay Influenza C, by multiplexed qPCR A virus in pleural fluid datum that specifies whether Influenza C virus was detected by multiplex real time polymerase chain reaction assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Influenza C virus in pleural fluid by multiplex real time polymerase chain reaction assay Parainfluenza 1, by multiplexed qPCR A virus in pleural fluid datum that specifies whether Human respirovirus 1 was detected by multiplex real time polymerase chain reaction assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Human respirovirus 1 in pleural fluid by multiplex real time polymerase chain reaction assay Parainfluenza 2, by multiplexed qPCR A virus in pleural fluid datum that specifies whether Human orthorubulavirus 2 was detected by multiplex real time polymerase chain reaction assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Human orthorubulavirus 2 in pleural fluid by multiplex real time polymerase chain reaction assay Parainfluenza 3, by multiplexed qPCR A virus in pleural fluid datum that specifies whether Human respirovirus 3 was detected by multiplex real time polymerase chain reaction assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Human respirovirus 3 in pleural fluid by multiplex real time polymerase chain reaction assay Parainfluenza 4, by multiplexed qPCR A virus in pleural fluid datum that specifies whether Human orthorubulavirus 4 was detected by multiplex real time polymerase chain reaction assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Human orthorubulavirus 4 in pleural fluid by multiplex real time polymerase chain reaction assay Parechovirus/Enterovirus, by multiplexed qPCR A virus in pleural fluid datum that specifies whether Picornaviridae was detected by multiplex real time polymerase chain reaction assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Picornaviridae in pleural fluid by multiplex real time polymerase chain reaction assay Rhinovirus, by multiplexed qPCR A virus in pleural fluid datum that specifies whether Rhinovirus was detected by multiplex real time polymerase chain reaction assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB 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. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB 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. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of any pathogen except Legionella or K. pneumoniae in lung by multiplex real time polymerase chain reaction assay Any pathogen except Legionella or K. pneumoniae, by multiplexed qPCR 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. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of any pathogen except Legionella or K. pneumoniae in pleural fluid by multiplex real time polymerase chain reaction assay Any pathogen, by multiplexed qPCR A nasopharyngeal or oropharyngeal swab microbiology datum that specifies whether a pathogen was detected by multiplex real time polymerase chain reaction assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of pathogen in nasopharynx or oropharynx by multiplex real time polymerase chain reaction assay C-reactive protein A blood assay datum of the concentration of C-reactive protein. Person: John Judkins VEuPathDB blood C-reactive protein concentration Bacteria in blood A bacteria in blood datum that specifies whether bacteria were detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of bacteria in blood Acinetobacter in blood A bacteria in blood datum that specifies whether Acinetobacter was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Acinetobacter in blood Candida in blood A eukaryota in blood datum that specifies whether Candida was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Candida in blood Enterobacter in blood A bacteria in blood datum that specifies whether Enterobacter was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Enterobacter in blood Enterococcus in blood A bacteria in blood datum that specifies whether Enterococcus was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Enterococcus in blood Escherichia in blood A bacteria in blood datum that specifies whether Escherichia was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Escherichia in blood Klebsiella in blood A bacteria in blood datum that specifies whether Klebsiella was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Klebsiella in blood Moraxella in blood A bacteria in blood datum that specifies whether Moraxella was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Moraxella in blood Neisseria in blood A bacteria in blood datum that specifies whether Neisseria was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Neisseria in blood Staphylococcus in blood A bacteria in blood datum that specifies whether Staphylococcus was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Staphylococcus in blood Haemophilus in blood A bacteria in blood datum that specifies whether Haemophilus was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Haemophilus in blood Salmonella in blood A bacteria in blood datum that specifies whether Salmonella was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Salmonella in blood Streptococcus in blood A bacteria in blood datum that specifies whether Streptococcus was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Streptococcus in blood Pseudomonas in blood A bacteria in blood datum that specifies whether Pseudomonas was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Pseudomonas in blood Eukaryota in blood A eukaryota in blood datum that specifies whether a eukaryote was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of eukaryote in blood Plasmodium in blood A eukaryota in blood datum that specifies whether Plasmodium was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Plasmodium in blood Salmonella in lung aspirate A bacteria in lung datum that specifies whether Salmonella was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Salmonella in lung Mycoplasma in lung aspirate A bacteria in lung datum that specifies whether Mycoplasmoides was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Mycoplasmoides in lung Chlamydia in lung aspirate A bacteria in lung datum that specifies whether Chlamydia was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Chlamydia in lung Bordetella in lung aspirate A bacteria in lung datum that specifies whether Bordetella was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Bordetella in lung Legionella in lung aspirate A bacteria in lung datum that specifies whether Legionella was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Legionella in lung Pneumocystis in lung aspirate A eukaryota in lung datum that specifies whether Pneumocystis was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Pneumocystis in lung Alphainfluenzavirus in lung aspirate A virus in lung datum that specifies whether Alphainfluenzavirus was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Alphainfluenzavirus in lung Betainfluenzavirus in lung aspirate A virus in lung datum that specifies whether Betainfluenzavirus was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Betainfluenzavirus in lung Bocaparvovirus in lung aspirate A virus in lung datum that specifies whether Bocaparvovirus was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Bocaparvovirus in lung Cytomegalovirus in lung aspirate A virus in lung datum that specifies whether Cytomegalovirus was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Cytomegalovirus in lung Enterovirus in lung aspirate A virus in lung datum that specifies whether Enterovirus was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Enterovirus in lung Gammainfluenzavirus in lung aspirate A virus in lung datum that specifies whether Gammainfluenzavirus was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Gammainfluenzavirus in lung Metapneumovirus in lung aspirate A virus in lung datum that specifies whether Metapneumovirus was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Metapneumovirus in lung Orthopneumovirus in lung aspirate A virus in lung datum that specifies whether Orthopneumovirus was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Orthopneumovirus in lung Respirovirus in lung aspirate A virus in lung datum that specifies whether Respirovirus was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Respirovirus in lung Alphacoronavirus in lung aspirate A virus in lung datum that specifies whether Alphacoronavirus was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Alphacoronavirus in lung Betacoronavirus in lung aspirate A virus in lung datum that specifies whether Betacoronavirus was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Betacoronavirus in lung Pneumonia A diagnosis at patient discharge that is an assertion that a patient has pneumonia. Person: John Judkins VEuPathDB diagnosis of pneumonia at patient discharge Bronchiolitis A diagnosis at patient discharge that is an assertion that a patient has bronchiolitis. Person: John Judkins VEuPathDB diagnosis of bronchiolitis at patient discharge Lower respiratory tract infection A diagnosis at patient discharge that is an assertion that a patient has lower respiratory tract disease. Person: John Judkins VEuPathDB diagnosis of lower respiratory tract disease at patient discharge Afebrile seizure A diagnosis at patient discharge that is an assertion that a patient has seizure. Person: John Judkins VEuPathDB diagnosis of seizure at patient discharge Mucocutaneous candidiasis A diagnosis at patient discharge that is an assertion that a patient has chronic mucocutaneous candidiasis. Person: John Judkins VEuPathDB diagnosis of chronic mucocutaneous candidiasis at patient discharge Anemia A diagnosis at patient discharge that is an assertion that a patient has anemia. Person: John Judkins VEuPathDB diagnosis of anemia at patient discharge Neonatal sepsis A diagnosis at patient discharge that is an assertion that a patient has neonatal sepsis. Person: John Judkins VEuPathDB diagnosis of neonatal sepsis at patient discharge Anaemic heart failure A diagnosis at patient discharge that is an assertion that a patient has anemia and heart failure. Person: John Judkins VEuPathDB diagnosis of anemic heart failure at patient discharge Osteomyelitis A diagnosis at patient discharge that is an assertion that a patient has osteomyelitis. Person: John Judkins VEuPathDB diagnosis of osteomyelitis at patient discharge Asthma A diagnosis at patient discharge that is an assertion that a patient has asthma. Person: John Judkins VEuPathDB diagnosis of asthma at patient discharge Otitis media A diagnosis at patient discharge that is an assertion that a patient has otitis media. Person: John Judkins VEuPathDB diagnosis of otitis media at patient discharge Birth asphyxia A diagnosis at patient discharge that is an assertion that a patient has neonatal asphyxia. Person: John Judkins VEuPathDB diagnosis of neonatal asphyxia at patient discharge Pneumocystis pneumonia A diagnosis at patient discharge that is an assertion that a patient has pneumocystosis. Person: John Judkins VEuPathDB diagnosis of pneumocystosis at patient discharge Cellulitis A diagnosis at patient discharge that is an assertion that a patient has cellulitis. Person: John Judkins VEuPathDB diagnosis of cellulitis at patient discharge Pneumothorax A diagnosis at patient discharge that is an assertion that a patient has pneumothorax. Person: John Judkins VEuPathDB diagnosis of pneumothorax at patient discharge Cerebral palsy A diagnosis at patient discharge that is an assertion that a patient has cerebral palsy. Person: John Judkins VEuPathDB diagnosis of cerebral palsy at patient discharge Congenital heart disease A diagnosis at patient discharge that is an assertion that a patient has congenital heart disease. Person: John Judkins VEuPathDB diagnosis of congenital heart disease at patient discharge Congenital abnormality A diagnosis at patient discharge that is an assertion that a patient has physical disorder. Person: John Judkins VEuPathDB diagnosis of physical disorder at patient discharge Protein malnutrition A diagnosis at patient discharge that is an assertion that a patient has protein-energy malnutrition. Person: John Judkins VEuPathDB diagnosis of protein-energy malnutrition at patient discharge Empyema thoracis A diagnosis at patient discharge that is an assertion that a patient has pleural empyema. Person: John Judkins VEuPathDB diagnosis of pleural empyema at patient discharge Pulmonary tuberculosis A diagnosis at patient discharge that is an assertion that a patient has pulmonary tuberculosis. Person: John Judkins VEuPathDB diagnosis of pulmonary tuberculosis at patient discharge Epilepsy A diagnosis at patient discharge that is an assertion that a patient has epilepsy. Person: John Judkins VEuPathDB diagnosis of epilepsy at patient discharge Septic arthritis A diagnosis at patient discharge that is an assertion that a patient has septic arthritis. Person: John Judkins VEuPathDB diagnosis of septic arthritis at patient discharge Septicemia A diagnosis at patient discharge that is an assertion that a patient has bacterial sepsis. Person: John Judkins VEuPathDB diagnosis of bacterial sepsis at patient discharge Febrile convulsion A diagnosis at patient discharge that is an assertion that a patient has fever-induced seizures. Person: John Judkins VEuPathDB diagnosis of seizure precipitated by febrile infection at patient discharge Sickle cell anemia A diagnosis at patient discharge that is an assertion that a patient has sickle cell anemia. Person: John Judkins VEuPathDB diagnosis of sickle cell anemia at patient discharge Gastroenteritis A diagnosis at patient discharge that is an assertion that a patient has gastroenteritis. Person: John Judkins VEuPathDB diagnosis of gastroenteritis at patient discharge Helminthiasis A diagnosis at patient discharge that is an assertion that a patient has parasitic helminthiasis infectious disease. Person: John Judkins VEuPathDB diagnosis of parasitic helminthiasis infectious disease at patient discharge HIV A diagnosis at patient discharge that is an assertion that a patient has human immunodeficiency virus infectious disease. Person: John Judkins VEuPathDB diagnosis of human immunodeficiency virus infectious disease at patient discharge Urinary tract infection A diagnosis at patient discharge that is an assertion that a patient has urinary system disease. Person: John Judkins VEuPathDB diagnosis of urinary system disease at patient discharge Immunosuppression A diagnosis at patient discharge that is an assertion that a patient has immunosuppression. Person: John Judkins VEuPathDB diagnosis of immunosuppression at patient discharge Upper respiratory tract infection A diagnosis at patient discharge that is an assertion that a patient has upper respiratory tract disease. Person: John Judkins VEuPathDB diagnosis of upper respiratory tract disease at patient discharge Pulmonary tuberculosis A diagnosis at hospital admission that is an assertion that a patient has pulmonary tuberculosis. Person: John Judkins VEuPathDB diagnosis of pulmonary tuberculosis at hospital admission Extrapulmonary tuberculosis A diagnosis at hospital admission that is an assertion that a patient has extrapulmonary tuberculosis. Person: John Judkins VEuPathDB diagnosis of extrapulmonary tuberculosis at hospital admission Severe anemia A diagnosis at hospital admission that is an assertion that a patient has severe anemia. Person: John Judkins VEuPathDB 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. Person: John Judkins VEuPathDB diagnosis of bronchiolitis or respiratory syncytial virus infectious disease at hospital admission Asthma or reactive airway disease A diagnosis at hospital admission that is an assertion that a patient has asthma. Person: John Judkins VEuPathDB diagnosis of asthma at hospital admission Measles A diagnosis at hospital admission that is an assertion that a patient has measles. Person: John Judkins VEuPathDB diagnosis of measles at hospital admission Bronchitis A diagnosis at hospital admission that is an assertion that a patient has bronchitis. Person: John Judkins VEuPathDB diagnosis of bronchitis at hospital admission Malaria A diagnosis at hospital admission that is an assertion that a patient has malaria. Person: John Judkins VEuPathDB diagnosis of malaria at hospital admission Developmental delay or cerebral palsy A diagnosis at hospital admission that is an assertion that a patient has global developmental delay or cerebral palsy . Person: John Judkins VEuPathDB diagnosis of global developmental delay or cerebral palsy at hospital admission Meningitis A diagnosis that is an assertion that a patient has meningitis. Person: John Judkins VEuPathDB diagnosis of meningitis at hospital admission Union council in Bangladesh A fourth-order administrative region of Bangladesh. Person: John Judkins VEuPathDB union council of Bangladesh Community An information content entity about the multiple households that share a location and a common trait such as infrastructure. VEuPathDB 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. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB Bayley scale of infant and toddler development Maternal blood sample A blood specimen collected from a maternal participant under investigation. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/548 ClinEpiDB maternal blood specimen Maternal breast milk sample A milk specimen collected from a maternal participant under investigation. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/548 ClinEpiDB maternal milk specimen Maternal breast milk test A milk assay that has a maternal milk specimen as evaluant. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/548 ClinEpiDB maternal milk assay Maternal blood test A blood assay that has a maternal blood specimen as evaluant. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/548 ClinEpiDB maternal blood assay Saliva sample collection process A collecting specimen from organism that has the objective to obtain a saliva specimen. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB saliva specimen collection process Cytomegalovirus in blood A virus in blood datum that specifies whether Cytomegalovirus was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Cytomegalovirus in blood Virus in blood A virus in blood datum that specifies whether a virus was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB obsolete virus in blood datum true Macrophage count A count of macrophages in a feces specimen. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB number of macrophages in feces Pus cell count A count of dead polymorphonuclear leukocytes in pus in a feces specimen. https://www.biologyonline.com/dictionary/pus-cell number of pus cells in feces Red blood cell count A count of erythrocytes in a feces specimen. Person: John Judkins VEuPathDB number of erythrocytes in feces Ascaris, by microscopy A eukaryota in feces datum that specifies whether Ascaris was detected by microscopy assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Ascaris in feces by microscopy assay Blastocystis hominis, by microscopy A eukaryota in feces datum that specifies whether Blastocystis hominis was detected by microscopy assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB 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. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Entamoeba histolytica or Entamoeba dispar in feces by microscopy assay Escherichia coli, by microscopy A Escherichia coli in feces datum that specifies whether Escherichia coli was detected by microscopy assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Escherichia coli in feces by microscopy assay Giardia, by microscopy A eukaryota in feces datum that specifies whether Giardia was detected by microscopy assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Giardia in feces by microscopy assay Trichomonas hominis, by microscopy A eukaryota in feces datum that specifies whether Pentatrichomonas hominis was detected by microscopy assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Pentatrichomonas hominis in feces by microscopy assay Any pathogen, by microscopy A feces microbiology datum that specifies whether a pathogen was detected by microscopy assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of pathogen in feces by microscopy assay Enrollment location The site of a human subject enrollment. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/520 ClinEpiDB location of human subject enrollment Activin A A blood assay datum of the concentration of activin A. Person: John Judkins VEuPathDB blood activin A concentration Arachidic acid (%) A milk assay datum of the concentration of icosanoic acid. Person: John Judkins VEuPathDB milk arachidic acid concentration Arachidonic acid (%) A milk assay datum of the concentration of arachidonic acid. Person: John Judkins VEuPathDB milk arachidonic acid concentration Behenic acid (%) A milk assay datum of the concentration of docosanoic acid. Person: John Judkins VEuPathDB milk docosanoic acid concentration Capric acid (%) A milk assay datum of the concentration of decanoic acid. Person: John Judkins VEuPathDB milk decanoic acid concentration Dihomo-gamma-linolenic acid (%) A milk assay datum of the concentration of all-cis-icosa-8,11,14-trienoic acid. Person: John Judkins VEuPathDB milk all-cis-icosa-8,11,14-trienoic acid concentration Docosahexaenoic acid (%) A milk assay datum of the concentration of docosahexaenoic acid. Person: John Judkins VEuPathDB milk docosahexaenoic acid concentration Docosapentaenoic acid (5n3) (%) A milk assay datum of the concentration of (7Z,10Z,13Z,16Z,19Z)-docosapentaenoic acid. Person: John Judkins VEuPathDB milk (7Z,10Z,13Z,16Z,19Z)-docosapentaenoic acid concentration Docosapentaenoic acid (5n6) (%) A milk assay datum of the concentration of (4Z,7Z,10Z,13Z,16Z)-docosa-4,7,10,13,16-pentaenoic acid. Person: John Judkins VEuPathDB milk (4Z,7Z,10Z,13Z,16Z)-docosa-4,7,10,13,16-pentaenoic acid concentration Docosatetraenoic acid (%) A milk assay datum of the concentration of docosatetraenoic acid. Person: John Judkins VEuPathDB milk docosatetraenoic acid concentration Eicosadienoic acid (%) A milk assay datum of the concentration of icosadienoic acid. Person: John Judkins VEuPathDB milk icosadienoic acid concentration Eicosapentaenoic acid (%) A milk assay datum of the concentration of icosapentaenoic acid. Person: John Judkins VEuPathDB milk icosapentaenoic acid concentration Eicosenoic acid (%) A milk assay datum of the concentration of icosenoic acid. Person: John Judkins VEuPathDB milk icosenoic acid concentration Elaidic acid (%) A milk assay datum of the concentration of elaidic acid. Person: John Judkins VEuPathDB milk elaidic acid concentration Gamma-linolenic acid (%) A milk assay datum of the concentration of gamma-linolenic acid. Person: John Judkins VEuPathDB milk gamma-linolenic acid concentration Lauric acid (%) A milk assay datum of the concentration of dodecanoic acid. Person: John Judkins VEuPathDB milk dodecanoic acid concentration Lignoceric acid (%) A milk assay datum of the concentration of tetracosanoic acid. Person: John Judkins VEuPathDB milk tetracosanoic acid concentration Linoelaidic acid (%) A milk assay datum of the concentration of linoelaidic acid. Person: John Judkins VEuPathDB milk linoelaidic acid concentration Linoleic acid (%) A milk assay datum of the concentration of linoleic acid. Person: John Judkins VEuPathDB milk linoleic acid concentration Myristic acid (%) A milk assay datum of the concentration of tetradecanoic acid. Person: John Judkins VEuPathDB milk myristic acid concentration Nervonic acid (%) A milk assay datum of the concentration of (15Z)-tetracosenoic acid. Person: John Judkins VEuPathDB milk nervonic acid concentration Oleic acid (%) A milk assay datum of the concentration of oleic acid. Person: John Judkins VEuPathDB milk oleic acid concentration Palmitelaidic acid (%) A milk assay datum of the concentration of palmitelaidic acid. Person: John Judkins VEuPathDB milk palmitelaidic acid concentration Palmitic acid (%) A milk assay datum of the concentration of hexadecanoic acid. Person: John Judkins VEuPathDB milk hexadecanoic acid concentration Palmitoleic acid (%) A milk assay datum of the concentration of palmitoleic acid. Person: John Judkins VEuPathDB milk palmitoleic acid concentration Stearic acid (%) A milk assay datum of the concentration of octadecanoic acid. Person: John Judkins VEuPathDB milk octadecanoic acid concentration Cytomegalovirus, by ELISA A virus in blood datum that specifies whether Cytomegalovirus was detected by enzyme-linked immunosorbent assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Cytomegalovirus in blood by enzyme-linked immunosorbent assay Cytomegalovirus, by qPCR result 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. Person: John Judkins VEuPathDB qRT-PCR threshold cycle for Cytomegalovirus in feces Interferon gamma A blood assay datum of the concentration of interferon gamma. Person: John Judkins VEuPathDB blood interferon gamma concentration Interleukin 10 A blood assay datum of the concentration of interleukin-10. Person: John Judkins VEuPathDB blood interleukin-10 concentration Interleukin 1 beta A blood assay datum of the concentration of interleukin-1 beta. Person: John Judkins VEuPathDB blood interleukin-1 beta concentration Interleukin 4 A blood assay datum of the concentration of interleukin-4. Person: John Judkins VEuPathDB blood interleukin-4 concentration Interleukin 5 A blood assay datum of the concentration of interleukin-5. Person: John Judkins VEuPathDB blood interleukin-5 concentration Interleukin 6 A blood assay datum of the concentration of interleukin-6. Person: John Judkins VEuPathDB blood interleukin-6 concentration Interleukin 7 A blood assay datum of the concentration of interleukin-7. Person: John Judkins VEuPathDB blood interleukin-7 concentration Interleukin 8 A blood assay datum of the concentration of interleukin-8. Person: John Judkins VEuPathDB blood interleukin-8 concentration Tumor necrosis factor alpha A blood assay datum of the concentration of tumor necrosis factor. Person: John Judkins VEuPathDB blood tumor necrosis factor concentration Eotaxin concentration A milk assay datum of the concentration of eotaxin. Person: John Judkins VEuPathDB milk eotaxin concentration Granulocyte-colony stimulating factor A milk assay datum of the concentration of granulocyte colony-stimulating factor. Person: John Judkins VEuPathDB milk granulocyte colony-stimulating factor concentration Granulocyte-macrophage colony stimulating factor A milk assay datum of the concentration of granulocyte-macrophage colony-stimulating factor. Person: John Judkins VEuPathDB milk granulocyte-macrophage colony-stimulating factor concentration Interleukin 12, p70 A milk assay datum of the concentration of interleukin-12 complex. Person: John Judkins VEuPathDB milk interleukin-12 complex concentration Interleukin 13 A milk assay datum of the concentration of interleukin-13. Person: John Judkins VEuPathDB milk interleukin-13 concentration Interleukin 15 A milk assay datum of the concentration of interleukin-15. Person: John Judkins VEuPathDB milk interleukin-15 concentration Interleukin 17A A milk assay datum of the concentration of interleukin-17A. Person: John Judkins VEuPathDB milk interleukin-17A concentration Interleukin 1 receptor agonist A milk assay datum of the concentration of interleukin-1 receptor antagonist protein. Person: John Judkins VEuPathDB milk interleukin-1 receptor antagonist protein concentration Interleukin 2 A milk assay datum of the concentration of interleukin-2. Person: John Judkins VEuPathDB milk interleukin-2 concentration Interleukin 9 A milk assay datum of the concentration of interleukin-9. Person: John Judkins VEuPathDB milk interleukin-9 concentration Interferon gamma-induced protein 10 A milk assay datum of the concentration of chemokine ligand 10. Person: John Judkins VEuPathDB milk chemokine ligand 10 concentration Monocyte chemoattractant protein 1 A milk assay datum of the concentration of C-C motif chemokine 2. Person: John Judkins VEuPathDB milk C-C motif chemokine 2 concentration Macrophage inflammatory protein 1 alpha A milk assay datum of the concentration of C-C motif chemokine 3. Person: John Judkins VEuPathDB milk C-C motif chemokine 3 concentration Platelet derived growth factor A milk assay datum of the concentration of platelet-derived growth factor complex. Person: John Judkins VEuPathDB milk platelet-derived growth factor complex concentration RANTES A milk assay datum of the concentration of C-C motif chemokine 5. Person: John Judkins VEuPathDB milk C-C motif chemokine 5 concentration Epidermal growth factor A milk assay datum of the concentration of pro-epidermal growth factor. Person: John Judkins VEuPathDB milk pro-epidermal growth factor concentration Endotoxin A blood assay datum of the concentration of endotoxin. Person: John Judkins VEuPathDB blood endotoxin concentration Milk fat globule-EGF factor 8 A milk assay datum of the concentration of lactadherin. Person: John Judkins VEuPathDB milk lactadherin concentration Astrovirus, by qPCR A virus in feces datum that specifies whether Astrovirus was detected by real time polymerase chain reaction assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Astrovirus in feces by real time polymerase chain reaction assay Norovirus, by multiplexed qRT-PCR A virus in feces datum that specifies whether Norovirus was detected by multiplex real time reverse-transcription polymerase chain reaction assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Norovirus in feces by multiplex real time reverse-transcription polymerase chain reaction assay Rotavirus, by qPCR A virus in feces datum that specifies whether Rotavirus was detected by real time polymerase chain reaction assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Rotavirus in feces by real time polymerase chain reaction assay Sapovirus, by qPCR A virus in feces datum that specifies whether Sapovirus was detected by real time polymerase chain reaction assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Sapovirus in feces by real time polymerase chain reaction assay Astrovirus, by qPCR result 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. Person: John Judkins VEuPathDB qPCR threshold cycle for Astroviridae in feces Rotavirus, by qPCR result 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. Person: John Judkins VEuPathDB qPCR threshold cycle for Rotavirus in feces Sapovirus, by qPCR result 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. Person: John Judkins VEuPathDB qPCR threshold cycle for Sapovirus in feces Cryptosporidium, by qPCR A eukaryota in feces datum that specifies whether Cryptosporidium was detected by real time polymerase chain reaction assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Cryptosporidium in feces by real time polymerase chain reaction assay Entamoeba histolytica, by qPCR A eukaryota in feces datum that specifies whether Entamoeba histolytica was detected by real time polymerase chain reaction assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Entamoeba histolytica in feces by real time polymerase chain reaction assay Giardia, by qPCR A eukaryota in feces datum that specifies whether Giardia was detected by real time polymerase chain reaction assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Giardia in feces by real time polymerase chain reaction assay Entamoeba histolytica, by qPCR result 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. Person: John Judkins VEuPathDB qPCR threshold cycle for Entamoeba histolytica in feces Giardia, by qPCR result 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. Person: John Judkins VEuPathDB 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. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB 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. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB 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. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB 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. Person: John Judkins VEuPathDB 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. Person: John Judkins VEuPathDB 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. Person: John Judkins VEuPathDB multiplex qRT-PCR threshold cycle for Poliovirus 3 in feces Regenerating family member 1 beta A feces assay datum of the concentration of REG1B. John Judkins ORCID:0000-0001-6595-0902 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3628379/ https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/506 ClinEpiDB Sheena Tomko feces REG1B concentration Enterobacteria phage MS2, 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 Escherichia phage MS2 in a feces specimen. Person: John Judkins VEuPathDB TaqMan threshold cycle for Escherichia phage MS2 in feces Enterovirus, 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 Enterovirus in a feces specimen. Person: John Judkins VEuPathDB TaqMan threshold cycle for Enterovirus in feces Vitamin D A blood assay datum of the concentration of vitamin D. Person: John Judkins VEuPathDB blood vitamin D concentration Granulocyte-colony stimulating factor A blood assay datum of the concentration of granulocyte colony-stimulating factor. Person: John Judkins VEuPathDB blood granulocyte colony-stimulating factor concentration Interferon gamma A milk assay datum of the concentration of interferon gamma. Person: John Judkins VEuPathDB milk interferon gamma concentration Interleukin 10 A milk assay datum of the concentration of interleukin-10. Person: John Judkins VEuPathDB milk interleukin-10 concentration Interleukin 17A A blood assay datum of the concentration of interleukin-17A. Person: John Judkins VEuPathDB blood interleukin-17A concentration Interleukin 1 beta A milk assay datum of the concentration of interleukin-1 beta. Person: John Judkins VEuPathDB milk interleukin-1 beta concentration Interleukin 4 A milk assay datum of the concentration of interleukin-4. Person: John Judkins VEuPathDB milk interleukin-4 concentration Interleukin 5 A milk assay datum of the concentration of interleukin-5. Person: John Judkins VEuPathDB milk interleukin-5 concentration Interleukin 6 A milk assay datum of the concentration of interleukin-6. Person: John Judkins VEuPathDB milk interleukin-6 concentration Interleukin 7 A milk assay datum of the concentration of interleukin-7. Person: John Judkins VEuPathDB milk interleukin-7 concentration Interleukin 8 A milk assay datum of the concentration of interleukin-8. Person: John Judkins VEuPathDB milk interleukin-8 concentration Macrophage inflammatory protein 1 beta A milk assay datum of the concentration of C-C motif chemokine 4. Person: John Judkins VEuPathDB milk C-C motif chemokine 4 concentration Tumor necrosis factor alpha A milk assay datum of the concentration of tumor necrosis factor. Person: John Judkins VEuPathDB milk tumor necrosis factor concentration Alpha-linolenic acid (%) A milk assay datum of the concentration of alpha-linolenic acid. Person: John Judkins VEuPathDB milk alpha-linolenic acid concentration Cryptosporidium, by qPCR result 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. Person: John Judkins VEuPathDB qPCR threshold cycle for Crytptosporidium in feces Interleukin 2 A blood assay datum of the concentration of interleukin-2. Person: John Judkins VEuPathDB blood interleukin-2 concentration A laboratory test that has a feces specimen as specified input. John Judkins VEuPathDB obsolete feces test true Dog count A count of dogs that live with a household. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB number of dogs with household Maternal urine microbiology test An organism detection assay that detects microorganisms in a maternal urine specimen. maternal urine microbiology assay Syphilis, by VDRL A bacteria in blood datum that specifies whether Treponema was detected by venereal disease research laboratory test. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Treponema in blood by venereal disease research laboratory test Assay that subjects a cerebrospinal fluid specimen to a test for microorganisms. John Judkins cerebrospinal fluid microbiology test VEuPathDB obsolete cerebrospinal fluid microbiology assay true A laboratory test that has a cerebrospinal fluid specimen as specified input. John Judkins VEuPathDB obsolete cerebrospinal fluid test true Maternal blood microbiology test An organism microbiology assay that detects microorganisms in a maternal blood specimen. maternal blood microbiology assay Zone in Ethiopia A second-order administrative region of Ethiopia. Person: John Judkins VEuPathDB zone of Ethiopia Kebele (subdistrict) in Ethiopia A fourth-order administrative region of Ethiopia. Person: John Judkins subdistrict of Ethiopia VEuPathDB kebele of Ethiopia Cranial ultrasound date A third-order administrative region of Ethiopia. Person: John Judkins VEuPathDB woreda of Ethiopia Blood smear performed An information content entity that specifies whether a blood smear has been performed. Person: John Judkins indicator of whether blood smear performed Eukaryota in placental blood A eukaryota in placental blood datum that specifies whether a eukaryote was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of eukaryote in placental blood Placental sample collection process A collecting specimen from organism that has the objective to obtain a placental specimen. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB placenta specimen collection process Plasmodium in placental blood A eukaryota in placental blood datum that specifies whether Plasmodium was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Plasmodium in placental blood Plasmodium, by LAMP A eukaryota in placental blood datum that specifies whether Plasmodium was detected by loop-mediated thermal amplification. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Plasmodium in placental blood by loop-mediated thermal amplification Plasmodium, by microscopy A Plasmodium in placental blood by microscopy assay datum that specifies whether Plasmodium was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Plasmodium in placental blood by microscopy assay Treponema in blood A bacteria in blood datum that specifies whether Treponema was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Treponema in blood Child blood test A blood assay that has a offspring blood specimen as evaluant. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/548 ClinEpiDB offspring blood assay Child blood sample A blood specimen collected from an offspring participant under investigation. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/548 ClinEpiDB offspring blood specimen Child blood microbiology test A blood microbiology assay that has a offspring blood specimen as evaluant. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/548 ClinEpiDB offspring blood microbiology assay Plasmodium, by microscopy A eukaryota in umbilical cord blood datum that specifies whether Plasmodium was detected by microscopy assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Plasmodium in umbilical cord blood by microscopy assay Eukaryota in umbilical cord blood A eukaryota in umbilical cord blood datum that specifies whether a eukaryote was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of eukaryote in umbilical cord blood Plasmodium in umbilical cord blood A eukaryota in umbilical cord blood datum that specifies whether Plasmodium was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Plasmodium in umbilical cord blood Plasmodium, by microscopy result 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. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB Plasmodium in umbilical cord blood by microscopy assay datum Plasmodium, by microscopy result 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. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB 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. attractant IRO:0000034 obsolete arthropod attractor role true An infusion material extracted from alfalfa. IRO:0001059 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. BG-lure IRO:0001060 obsolete BG-lure scent dispenser true An infusion material extracted from hay. hay or grass infusion IRO:0000037 hay infusion An information content entity that specifies that no attractant was used in an anthropod trap no attractant used IRO:0000153 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. new jersey trap catch Cire. N. J. agrie. Exp. Stn. 1942 No.421 pp.8 IRO:0000031 obsolete New Jersey light trap true An arthropod trap that is designed to collect gravid female arthropods or their eggs. gravid trap catch IRO:0000030 obsolete gravid trap true 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. EVS light trap EVS trap catch IRO:0000029 VSMO:0001295 obsolete encephalitis virus surveillance trap true A device manufactured by BioGents that is designed to count mosquitoes passing through the device, differentiating the mosquitoes from other arthropods. BG-Counter trap catch IRO:0000143 obsolete BG-Counter true 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. CDC light trap catch IRO:0000163 obsolete Centers for Disease Control and Prevention light trap true 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. BG-Sentinal trap catch IRO:0000028 VSMO:0001906 obsolete BG-Sentinel trap true An arthropod trap consisting of a static physical barrier designed to funnel arthropods in flight into a container. barrier catch IRO:0000017 obsolete barrier trap true 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. OVI light-suction trap IRO:0000154 Parasites Vectors 8, 239 (2015) obsolete Onderstepoort Veterinary Institute light-suction trap true 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. resting box catch IRO:0000021 Proceedings of the Eighty-Second Annual Meeting of the New Jersey Mosquito Control Association, Inc. 1989, pp 53-57. obsolete resting box trap true 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. shannon trap catch IRO:0000191 The American Journal of Tropical Medicine and Hygiene, Volume s1-19, Issue 2, 1 Mar 1939, p. 131 - 140 obsolete Shannon trap true An arthropod trap that is designed to capture arthropods resting on a surface by coating the surface with adhesive. sticky trap catch IRO:0000128 obsolete sticky trap true 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. artificial pit shelter IRO:0000005 obsolete artificial pit shelter true 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. resting bucket catch IRO:0000141 Kreppel et al. Parasites & Vectors (2015) 8:462 obsolete resting bucket true 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. mosquito magnet pro catch IRO:0000022 obsolete Mosquito Magnet trap true An arthropod specimen collection process that involves exposing arthropods to pesticide, then collecting them once they become dead or immobilized. knockdown collection 38th Report East Malling Research Station 1949-50 , 1951, p.148 IRO:0000014 obsolete knockdown arthropod specimen collection process true A gravid trap consisting of an arthropod attractant and adhesive surface. MosquiTRAP catch IRO:0000140 obsolete MosquiTRAP true 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. sticky resting bucket catch IRO:0000142 obsolete sticky resting bucket true A light trap designed to be placed inside a building. indoor light trap catch MIRO:30000009 obsolete light trap for indoor use true A knockdown arthropod specimen collection process in which the pesticide is pyrethrum. pyrethrum spray catch MIRO:30000023 obsolete knockdown arthropod specimen collection by pyrethrum spray true An arthropod trap that uses light as an attractant. light trap catch MIRO:30000065 obsolete light trap true An arthropod specimen collection process meant to collect live specimens. catch of live specimens MIRO:30000045 obsolete live arthropod specimen collection process true An arthropod specimen collection process in which the arthropods are in the larval stage. collection of larvae MIRO:30000022 obsolete larval specimen collection process true An arthropod specimen collection by aspiration that occurs in the daytime. MIRO:30000007 obsolete daytime arthropod specimen collection by aspiration true An arthropod specimen collection by aspiration that occurs while the arthropod is biting a human. man biting catch MIRO:30000017 obsolete human-biting arthropod specimen collection by aspiration true 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. oviposition trap ovitrap catch MIRO:30000016 VSMO:0001501 obsolete ovitrap true An arthropod specimen collection by aspiration that occurs while the arthropod is biting a human inside a building. man biting catch - indoors MIRO:30000019 obsolete human-biting indoor arthropod specimen collection by aspiration true An arthropod specimen collection by aspiration designed to catch specimens that are in the process of biting a human outside a building. man biting catch - outdoors MIRO:30000018 obsolete human-biting outdoor arthropod specimen collection by aspiration true 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. catch by aspiration MIRO:30000043 obsolete arthropod specimen collection by aspiration true An arthropod specimen collection by aspiration that catches specimens resting inside an animal house. animal shed resting catch MIRO:30000027 obsolete arthropod resting in animal house specimen collection by aspiration true An animal-biting arthropod specimen collection by aspiration that occurs while the arthropod is resting outside a building during a period of inactivity. outdoors shelter catch MIRO:30000024 obsolete arthropod resting outdoors specimen collection by aspiration true An arthropod trap that is positioned adjacent to a window of a building and is designed to collect arthropods flying out of the building. outlet window trap catch Bull World Health Organ. 1948; 1(2): 253–296. MIRO:30000020 obsolete outlet window trap true A live arthropod specimen collection process in which the arthropods are in the adult stage. collection of adults MIRO:30000052 obsolete adult arthropod specimen collection process true An arthropod specimen collection by aspiration that occurs while the arthropod is biting an animal. animal biting catch MIRO:30000012 obsolete animal-biting arthropod specimen collection by aspiration true An arthropod resting outdoors specimen collection by aspiration that occurs while the arthropod rests on a processed material such as a wall or furniture. outdoors shelter catch - artificial MIRO:30000026 obsolete arthropod resting outdoors on artificial support specimen collection by aspiration true A light trap designed to be placed outside a building. outdoor light trap catch MIRO:30000010 obsolete light trap for outdoor use true A device designed to catch arthropods. trap catch MIRO:30000011 obsolete arthropod trap true A specimen collection process that has the objective of collecting arthropods as specimens. collection of arthropods field population catch MIRO:30000044 VSMO:0001445 obsolete arthropod specimen collection process true An animal-biting arthropod specimen collection by aspiration that occurs outside a building. animal biting catch - outdoors MIRO:30000014 obsolete animal-biting outdoor arthropod specimen collection by aspiration true An arthropod resting outdoors specimen collection by aspiration that occurs while the arthropod rests on an unprocessed material such as a plant. outdoors shelter catch - natural MIRO:30000025 obsolete arthropod resting outdoors on natural support specimen collection by aspiration true An arthropod specimen collection process that has the objective of collecting mosquitoes from an aquatic environment. aquatic environment catch MIRO:30000048 obsolete aquatic arthropod specimen collection process true A count of the traps deployed in a study design execution. VBcv:0001122 number of traps An arthropod specimen collection process that occurs while the arthropods land on a surface. collection of landing insects VSMO:0001457 For example, while they are landing on a human bait. obsolete landing arthropod specimen collection process true A device that consists of a network of mesh and is designed to capture adult arthropods. VSMO:0001522 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] obsolete hand-held sweep net true An arthropod trap that is designed to trap an arthropod as it emerges from water at the beginning of its adult stage. trap for emerging adult arthropods American Midland Naturalist, Vol. 97, No. 2 (Apr., 1977), pp. 381-389 VSMO:0001352 obsolete trap for emerging adult arthropods true 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. CDC gravid trap J Am Mosq Control Assoc. 1988 Dec;4(4):536-8. VSMO:0001510 obsolete Centers for Disease Control and Prevention gravid trap true 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 VSMO:0001595 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 true 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. collection of larvae from dippers collection of pupae from dippers dipper for immatures MIRO:30000063 MIRO:30000064 VSMO:0001479 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]" obsolete dipper for arthropod immatures true 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 VSMO:0000514 obsolete resting flight-capable arthropod specimen collection process true 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. VSMO:0001649 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] obsolete free-standing window trap true 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 VSMO:0001355 Most commonly used to collect mosquitoes. obsolete device for resting of adult arthropods for collection true 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 true 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. obsolete baited net trap true 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 infusion infused material An arthropod specimen collection process in which the arthropods are in the pupal stage. collection of pupae MIRO:30000050 obsolete pupal specimen collection process true An arthropod trap that is designed to be attractive to an arthropod as a place to rest during a period of inactivity. obsolete resting arthropod trap true A time measurement datum that measures a temporal interval of insecticide exposure. Person: Chris Stoeckert duration of insecticide exposure A light source that provides UV light for use in a distant area using a delivery system. Jie Zheng obsolete UV light source true A light source that provides visible light for use in a distant area using a delivery system. Jie Zheng obsolete visible light source true This species is not in NCBITaxon so is assigned a EUPATH ID. John Judkins ORCID:0000-0001-6595-0902 https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/105 PopBio Psorophora johnstonii This species is not in NCBITaxon so is assigned a EUPATH ID. John Judkins ORCID:0000-0001-6595-0902 https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/105 PopBio Psorophora mathesoni This species is not in NCBITaxon so is assigned a EUPATH ID. John Judkins ORCID:0000-0001-6595-0902 https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/105 PopBio Psorophora mexicana This subspecies is not in NCBITaxon so is assigned a EUPATH ID. John Judkins ORCID:0000-0001-6595-0902 https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/105 PopBio Toxorhynchites rutilus rutilus This taxonomic label is not in NCBITaxon, so this term is assigned a EUPATH ID. John Judkins ORCID:0000-0001-6595-0902 https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/105 PopBio Aedes atlanticus-tormentor morphological group This species is not in NCBITaxon so is assigned a EUPATH ID. John Judkins ORCID:0000-0001-6595-0902 https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/105 PopBio Aedes fijiensis This species is not in NCBITaxon so is assigned a EUPATH ID. John Judkins ORCID:0000-0001-6595-0902 https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/105 PopBio Aedes hodgkini This species is not in NCBITaxon so is assigned a EUPATH ID. John Judkins ORCID:0000-0001-6595-0902 https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/105 PopBio Aedes hokkaidensis This species is not in NCBITaxon so is assigned a EUPATH ID. John Judkins ORCID:0000-0001-6595-0902 https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/105 PopBio Aedes idahoensis obsolete Aedes juppi true Person: John Judkins obsolete Aedes ledgeri true This species is not in NCBITaxon so is assigned a EUPATH ID. John Judkins ORCID:0000-0001-6595-0902 https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/105 PopBio Aedes mathesoni This taxonomic label is not in NCBITaxon, so this term is assigned a EUPATH ID. John Judkins ORCID:0000-0001-6595-0902 VBsp:0000997 https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/105 PopBio Aedes mathesoni complex This species is not in NCBITaxon so is assigned a EUPATH ID. John Judkins ORCID:0000-0001-6595-0902 https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/105 PopBio Aedes subdentatus This species is not in NCBITaxon so is assigned a EUPATH ID. John Judkins ORCID:0000-0001-6595-0902 https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/105 PopBio Aedes tricholabis This subspecies is not in NCBITaxon so is assigned a EUPATH ID. John Judkins ORCID:0000-0001-6595-0902 https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/105 PopBio Aedes vexans arabiensis This taxonomic label is not in NCBITaxon, so this term is assigned a EUPATH ID. John Judkins ORCID:0000-0001-6595-0902 https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/105 PopBio Aedes vexans sensu lato This subspecies is not in NCBITaxon so is assigned a EUPATH ID. John Judkins ORCID:0000-0001-6595-0902 https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/105 PopBio Aedes vexans vexans This species is not in NCBITaxon so is assigned a EUPATH ID. John Judkins ORCID:0000-0001-6595-0902 https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/105 PopBio Aedes washinoi obsolete Anopheles barberi true This taxonomic label is not in NCBITaxon, so this term is assigned a EUPATH ID. Jie Zheng https://orcid.org/0000-0002-2999-0103 John Judkins ORCID:0000-0001-6595-0902 https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/105 PopBio Anopheles culicifacies AD subgroup This species is not in NCBITaxon so is assigned a EUPATH ID. John Judkins ORCID:0000-0001-6595-0902 https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/105 PopBio Anopheles distinctus This species is not in NCBITaxon so is assigned a EUPATH ID. John Judkins ORCID:0000-0001-6595-0902 https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/105 PopBio Anopheles flavicosta Person: John Judkins obsolete Anopheles franciscanus true This species is not in NCBITaxon so is assigned a EUPATH ID. John Judkins ORCID:0000-0001-6595-0902 https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/105 PopBio Anopheles georgianus This species is not in NCBITaxon so is assigned a EUPATH ID. John Judkins ORCID:0000-0001-6595-0902 https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/105 PopBio Anopheles listeri This species is not in NCBITaxon so is assigned a EUPATH ID. John Judkins ORCID:0000-0001-6595-0902 https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/105 PopBio Anopheles natalensis This species is not in NCBITaxon so is assigned a EUPATH ID. John Judkins ORCID:0000-0001-6595-0902 https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/105 PopBio Anopheles perplexens This taxonomic label is not in NCBITaxon, so this term is assigned a EUPATH ID. John Judkins ORCID:0000-0001-6595-0902 https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/105 PopBio Anopheles sinensis sensu lato This species is not in NCBITaxon so is assigned a EUPATH ID. John Judkins ORCID:0000-0001-6595-0902 https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/105 PopBio Anopheles umbrosus Person: John Judkins obsolete Culex aurantapex true This species is not in NCBITaxon so is assigned a EUPATH ID. John Judkins ORCID:0000-0001-6595-0902 https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/105 PopBio Culex chorleyi This species is not in NCBITaxon so is assigned a EUPATH ID. John Judkins ORCID:0000-0001-6595-0902 https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/105 PopBio Culex cinerellus This species is not in NCBITaxon so is assigned a EUPATH ID. John Judkins ORCID:0000-0001-6595-0902 https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/105 PopBio Culex cuyanus obsolete Culex inconspicuosus true This species is not in NCBITaxon so is assigned a EUPATH ID. John Judkins ORCID:0000-0001-6595-0902 https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/105 PopBio Culex lineata This species is not in NCBITaxon so is assigned a EUPATH ID. John Judkins ORCID:0000-0001-6595-0902 https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/105 PopBio Culex peringueyi Person: John Judkins obsolete Culex rubinotus true This species is not in NCBITaxon so is assigned a EUPATH ID. John Judkins ORCID:0000-0001-6595-0902 https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/105 PopBio Culex salisburiensis Person: John Judkins obsolete Culex stigmatosoma true This species is not in NCBITaxon so is assigned a EUPATH ID. John Judkins ORCID:0000-0001-6595-0902 https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/105 PopBio Culex trifoliatus obsolete Mimomyia hispida true Person: John Judkins obsolete Mimomyia mediolineata true Person: John Judkins obsolete Mimomyia mimomyiaformis true This species is not in NCBITaxon so is assigned a EUPATH ID. John Judkins ORCID:0000-0001-6595-0902 https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/105 PopBio Sergentomyia theodori This species is not in NCBITaxon so is assigned a EUPATH ID. John Judkins ORCID:0000-0001-6595-0902 https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/105 PopBio Uranotaenia hopkinsi obsolete Uranotaenia mashonaensis true This species is not in NCBITaxon so is assigned a EUPATH ID. John Judkins ORCID:0000-0001-6595-0902 https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/105 PopBio Wyeomyia haynei A data item that is about resistance to an insecticide. Person: John Judkins obsolete insecticide resistance datum true A scalar measurement datum of the concentration of an insecticide. Person: John Judkins insecticide concentration datum An insecticide concentration datum expressed as a percent. Person: John Judkins VEuPathDB insecticide concentration in percent An insecticide concentration datum that has a parts per notation unit. Person: John Judkins VEuPathDB insecticide concentration in parts per notation unit An insecticide concentration datum that has an area density unit. Person: John Judkins VEuPathDB insecticide concentration in area density unit An insecticide concentration datum that has a mass density unit. Person: John Judkins VEuPathDB 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. Person: John Judkins VEuPathDB 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. Person: John Judkins LC50 VBcv:0000726 lethal insecticide concentration 50 A lethal insecticide concentration 50, expressed as a percent. Person: John Judkins LC50 in percent VEuPathDB lethal insecticide concentration 50 in percent A lethal insecticide concentration 50 that has a parts per notation unit. Person: John Judkins LC50 in parts per million or billion VEuPathDB lethal insecticide concentration 50 in parts per notation unit A lethal insecticide concentration 50 that has an area density unit. Person: John Judkins LC50 in mass per area VEuPathDB lethal insecticide concentration 50 in area density unit A lethal insecticide concentration 50 that has a mass density unit. Person: John Judkins LC50 in mass per volume VEuPathDB 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. Person: John Judkins LC50 in mass per standard assay bottle VEuPathDB 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. Person: John Judkins LC95 VBcv:0000728 lethal insecticide concentration 95 A lethal insecticide concentration 95, expressed as a percent. Person: John Judkins LC95 in percent VEuPathDB lethal insecticide concentration 95 in percent A lethal insecticide concentration 95 that has a parts per notation unit. Person: John Judkins LC95 in parts per million or billion VEuPathDB lethal insecticide concentration 95 in parts per notation unit A lethal insecticide concentration 95 that has an area density unit. Person: John Judkins LC95 in mass per area VEuPathDB lethal insecticide concentration 95 in area density unit A lethal insecticide concentration 95 that has a mass density unit. Person: John Judkins LC95 in mass per volume VEuPathDB 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. Person: John Judkins LC95 in mass per standard assay bottle VEuPathDB 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. Person: John Judkins LC99 VBcv:0000729 lethal insecticide concentration 99 A lethal insecticide concentration 99, expressed as a percent. Person: John Judkins LC99 in percent VEuPathDB lethal insecticide concentration 99 in percent A lethal insecticide concentration 99 that has a parts per notation unit. Person: John Judkins LC99 in parts per million or billion VEuPathDB lethal insecticide concentration 99 in parts per notation unit A lethal insecticide concentration 99 that has an area density unit. Person: John Judkins LC99 in mass per area VEuPathDB lethal insecticide concentration 99 in area density unit A lethal insecticide concentration 99 that has a mass density unit. Person: John Judkins LC99 in mass per volume VEuPathDB 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. Person: John Judkins LC99 in mass per standard assay bottle VEuPathDB 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. Person: John Judkins LC90 VBcv:0000727 lethal insecticide concentration 90 A lethal insecticide concentration 90, expressed as a percent. Person: John Judkins LC90 in percent VEuPathDB 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. Person: John Judkins LT90 VBcv:0000733 https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/77 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. Person: John Judkins LT95 VBcv:0000734 https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/77 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. Person: John Judkins KDT50 PMC2459197 VBcv:0000714 median knockdown time A lethal insecticide concentration 90 that has a parts per notation unit. Person: John Judkins LC90 in parts per million or billion VEuPathDB lethal insecticide concentration 90 in parts per notation unit A lethal insecticide concentration 90 that has an area density unit. Person: John Judkins LC90 in mass per area VEuPathDB lethal insecticide concentration 90 in area density unit A lethal insecticide concentration 90 that has a mass density unit. Person: John Judkins LC90 in mass per volume VEuPathDB 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. Person: John Judkins LC90 in mass per standard assay bottle VEuPathDB 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. Person: John Judkins VEuPathDB 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. Person: John Judkins VEuPathDB 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. Person: John Judkins VEuPathDB population fraction with greater enzymatic activity than 99th percentile of reference population A count of the specimens involved in an assay. Person: John Judkins VEuPathDB 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. VEuPathDB prevalence of Kdr L1014F A data item that is the output of an assay to quantify the frequency of genetic variation resulting in Kdr S989P. VEuPathDB prevalence of Kdr S989P A data item that is the output of an assay to quantify the frequency of genetic variation resulting in Kdr I1011M. VEuPathDB prevalence of Kdr I1011M A data item that is the output of an assay to quantify the frequency of genetic variation resulting in Kdr I1011V. VEuPathDB prevalence of Kdr I1011V A data item that is the output of an assay to quantify the frequency of genetic variation resulting in Kdr L1014S. VEuPathDB prevalence of Kdr L1014S A data item that is the output of an assay to quantify the frequency of genetic variation resulting in Kdr L1014C. VEuPathDB prevalence of Kdr L1014C A data item that is the output of an assay to quantify the frequency of genetic variation resulting in Kdr V1016G. VEuPathDB prevalence of Kdr V1016G A data item that is the output of an assay to quantify the frequency of genetic variation resulting in Kdr V1016I. VEuPathDB prevalence of Kdr V1016I A data item that is the output of an assay to quantify the frequency of genetic variation resulting in Kdr I1532T. VEuPathDB prevalence of Kdr I1532T A data item that is the output of an assay to quantify the frequency of genetic variation resulting in Kdr F1534C. VEuPathDB prevalence of Kdr F1534C A data item that is the output of an assay to quantify the frequency of genetic variation resulting in Kdr F1534L. VEuPathDB prevalence of Kdr F1534L A data item that is the output of an assay to quantify the frequency of genetic variation resulting in Kdr F1534S. VEuPathDB prevalence of Kdr F1534S A data item that is the output of an assay to quantify the frequency of genetic variation resulting in Kdr N1575Y. VEuPathDB prevalence of Kdr N1575Y A data item that is the output of an assay to quantify the frequency of genetic variation resulting in Kdr D1763Y. VEuPathDB prevalence of Kdr D1763Y A data item that is the output of an assay to quantify the frequency of genetic variation resulting in AChE1 G119S. VEuPathDB prevalence of AChE1 G119S A data item that is the output of an assay to quantify the frequency of genetic variation resulting in Gste2 L119F. VEuPathDB prevalence of Gste2 L119F A data item that is the output of an assay to quantify the frequency of genetic variation resulting in Rdl A296G. VEuPathDB prevalence of Rdl A296G A data item that is the output of an assay to quantify the frequency of genetic variation resulting in Rdl A296S. VEuPathDB prevalence of Rdl A296S Number of mosquito collections in a survey dataset. A count of collections of specimens that have only arthropods as their members. Person: John Judkins VEuPathDB 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. VEuPathDB prevalence of wild type Kdr L1014 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. VEuPathDB prevalence of wild type Kdr S989 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. VEuPathDB prevalence of wild type Kdr I1011 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. VEuPathDB prevalence of wild type Kdr V1016 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. VEuPathDB prevalence of wild type Kdr I1532 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. VEuPathDB prevalence of wild type Kdr F1534 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. VEuPathDB prevalence of wild type Kdr N1575 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. VEuPathDB prevalence of wild type Kdr D1763 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. VEuPathDB prevalence of wild type AChE1 G119 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. VEuPathDB prevalence of wild type AChE1 F290 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. VEuPathDB prevalence of wild type AChE1 F331 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. VEuPathDB prevalence of wild type Gste2 I114 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. VEuPathDB prevalence of wild type Gste2 L119 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. VEuPathDB prevalence of wild type Rdl A296 An arthropod specimen collection process in which the arthropods are in the embryo stage. collection of eggs MIRO:30000049 obsolete egg specimen collection process true An arthropod specimen collection process in which the arthropods are in the larval stage and a trap is used to collect the specimens. collection of larvae from traps MIRO:30000062 larval specimen collection process from traps A data item that is the specified output of an organism identification assay. species assay result VBcv:0000961 obsolete organism identification datum true A data item that is about the concentration of an insecticide that kills 100% of a population of insects. Person: John Judkins LC100 VEuPathDB lethal insecticide concentration 100 A lethal insecticide concentration 100, expressed as a percent. Person: John Judkins LC100 in percent VEuPathDB 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. Person: John Judkins VEuPathDB obsolete well net for arthropod immatures true An arthropod specimen collection process that has the objective of collecting gravid female arthropods. Person: John Judkins VEuPathDB obsolete gravid female arthropod specimen collection process true An arthropod specimen collection process that involves a device that produces data specifying the types of arthropod collected. Person: John Judkins VEuPathDB obsolete arthropod collection process with automated identification true An adult arthropod specimen collection process that has the objective of collecting arthropods capable of flight, through the use of a barrier trap. Person: John Judkins VEuPathDB obsolete flying adult arthropod collection process by passive interception true 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. Jie Zheng Bob MacCallum https://en.wikipedia.org/wiki/Geohash https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/122 VectorBase geohash code GEOHASH 1 A geohash code encoding of geospatial location using 1 character. Jie Zheng Bob MacCallum https://en.wikipedia.org/wiki/Geohash https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/122 VectorBase geohash 1 GEOHASH 2 A geohash code encoding of geospatial location using 2 characters. Jie Zheng Bob MacCallum https://en.wikipedia.org/wiki/Geohash https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/122 VectorBase geohash 2 GEOHASH 3 A geohash code encoding of geospatial location using 3 characters. Jie Zheng Bob MacCallum https://en.wikipedia.org/wiki/Geohash https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/122 VectorBase geohash 3 GEOHASH 4 A geohash code encoding of geospatial location using 4 characters. Jie Zheng Bob MacCallum https://en.wikipedia.org/wiki/Geohash https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/122 VectorBase geohash 4 GEOHASH 5 A geohash code encoding of geospatial location using 5 characters. Jie Zheng Bob MacCallum https://en.wikipedia.org/wiki/Geohash https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/122 VectorBase geohash 5 GEOHASH 6 A geohash code encoding of geospatial location using 6 characters. Jie Zheng Bob MacCallum https://en.wikipedia.org/wiki/Geohash https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/122 VectorBase geohash 6 A geohash code encoding of geospatial location using 7 characters. Jie Zheng Bob MacCallum https://en.wikipedia.org/wiki/Geohash https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/122 VectorBase geohash 7 A geohash code encoding of geospatial location using 32 characters. Jie Zheng Bob MacCallum https://en.wikipedia.org/wiki/Geohash https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/122 VectorBase 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. Person: John Judkins VEuPathDB geolocation provenance information Geolocation An objective specification to obtain geolocation data whose value has a particular degree of precision. Person: John Judkins VEuPathDB https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/126 geolocation precision objective specification A geolocation precision objective specification of zero decimal places. Person: John Judkins VEuPathDB https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/126 geolocation precision objective of zero decimal places A geolocation precision objective specification of one decimal place. Person: John Judkins VEuPathDB https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/126 geolocation precision objective of one decimal place A geolocation precision objective specification of two decimal places. Person: John Judkins VEuPathDB https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/126 geolocation precision objective of two decimal places A geolocation precision objective specification of three decimal places. Person: John Judkins VEuPathDB https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/126 geolocation precision objective of three decimal places A geolocation precision objective specification of four decimal places. Person: John Judkins VEuPathDB https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/126 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. https://www.ivcc.com/market-access/actellic-300cs 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 Person: John Judkins VEuPathDB https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/117 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 Person: John Judkins VEuPathDB https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/117 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 Person: John Judkins VEuPathDB https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/117 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 Person: John Judkins VEuPathDB https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/117 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 Person: John Judkins VEuPathDB https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/117 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 Person: John Judkins VEuPathDB https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/117 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 Person: John Judkins VEuPathDB https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/117 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. Person: John Judkins VEuPathDB female insect feeding status A female insect feeding status about a gravid female insect. Person: John Judkins VEuPathDB gravid female insect feeding status A gravid female insect feeding status of having a visible blood meal. Person: John Judkins VEuPathDB fed gravid female insect status A gravid female insect feeding status of not having a visible blood meal. Person: John Judkins VEuPathDB unfed gravid female insect status A female insect feeding status of not having a visible blood meal. Person: John Judkins VEuPathDB unfed female insect status A female insect feeding status of having a visible blood meal. Person: John Judkins VEuPathDB 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. VEuPathDB prevalence of Cyp4J5 L43F 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. John Judkins VEuPathDB https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/303 Jie Zheng John Judkins Sarah Kelly Lurex attractor An arthropod specimen collection process in which tick specimens are collected by the general public i.e., citizen scientists. John Judkins https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0199644#sec020 https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/336 Jie Zheng Sarah Kelly 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. John Judkins VBcv:0001143 https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/323 Bob MacCallum geolocation provision information Geolocation provenance information that specifies that the number of decimal places in the data were truncated. John Judkins VBcv:0001155 https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/323 Bob MacCallum geolocation obfuscation information Geolocation provenance information that specifies that data were calculated by the curator or found using a geolocation lookup service. John Judkins VBcv:0001141 https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/323 Bob MacCallum 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. John Judkins VBcv:0001156 https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/323 Bob MacCallum 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. John Judkins VBcv:0001157 https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/323 Bob MacCallum 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. John Judkins VBcv:0001158 https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/323 Bob MacCallum 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. John Judkins VBcv:0001159 https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/323 Bob MacCallum 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. John Judkins ORCID:0000-0001-6595-0902 inferred essential, putatively lethal FungiDB Achchuthan Shanmugasundram ORCID: 0000-0003-2349-6929 Jie Zheng ORCID:0000-0002-2999-0103 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. VEuPathDB prevalence of wild type Cyp4J5 L43 This species is not in NCBITaxon so is assigned a EUPATH ID. John Judkins ORCID:0000-0001-6595-0902 https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/442 PopBio Sarah Kelly Anopheles nuneztovari sensu lato This species is not in NCBITaxon so is assigned a EUPATH ID. John Judkins ORCID:0000-0001-6595-0902 https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/462 PopBio Sarah Kelly Anaplasma phagocytophilum str. Ap-ha This species is not in NCBITaxon so is assigned a EUPATH ID. John Judkins ORCID:0000-0001-6595-0902 https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/462 PopBio Sarah Kelly Anaplasma phagocytophilum str. Ap-v1 A time measurement datum that specifies the date that starts a process that results in a collection of specimens. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/465 PopBio Bob MacCallum 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. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/465 PopBio Bob MacCallum 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. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/465 PopBio Bob MacCallum indicator of specimen collection date discontinuity An information content entity that is about a population of tick specimens. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/429 PopBio Bob MacCallum Jie Zheng Sarah Kelly information on collected tick population A record of missing knowledge indicating a lack of information on collected tick population. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/429 PopBio Bob MacCallum Jie Zheng Sarah Kelly 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. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/429 PopBio Bob MacCallum Jie Zheng Sarah Kelly 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. John Judkins ORCID:0000-0001-6595-0902 https://www.cdc.gov/ticks/surveillance/TickSurveillanceData.html https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/429 PopBio Bob MacCallum Jie Zheng Sarah Kelly established information on collected tick population This species is not in NCBITaxon so is assigned a EUPATH ID. Jie Zheng https://orcid.org/0000-0002-2999-0103 MIRO:40003423 https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/535 PopBio Bob MacCallum Anopheles pollicaris This species is not in NCBITaxon so is assigned a EUPATH ID. Jie Zheng https://orcid.org/0000-0002-2999-0103 MIRO:40000247 https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/535 PopBio Bob MacCallum Armigeres magnus This species is not in NCBITaxon so is assigned a EUPATH ID. Jie Zheng https://orcid.org/0000-0002-2999-0103 MIRO:40000251 https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/535 PopBio Bob MacCallum Armigeres traubi This species is not in NCBITaxon so is assigned a EUPATH ID. Jie Zheng https://orcid.org/0000-0002-2999-0103 MIRO:40002490 https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/535 PopBio Bob MacCallum Culex alis This species is not in NCBITaxon so is assigned a EUPATH ID. Jie Zheng https://orcid.org/0000-0002-2999-0103 MIRO:40002718 https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/535 PopBio Bob MacCallum Culex whitei This species is not in NCBITaxon so is assigned a EUPATH ID. Jie Zheng https://orcid.org/0000-0002-2999-0103 https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/527 PopBio Bob MacCallum Anopheles culicifacies BCE subgroup This species is not in NCBITaxon so is assigned a EUPATH ID. Jie Zheng https://orcid.org/0000-0002-2999-0103 MIRO:40001012 https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/535 PopBio Bob MacCallum Aedes condolescens This species is not in NCBITaxon so is assigned a EUPATH ID. Jie Zheng https://orcid.org/0000-0002-2999-0103 MIRO:40000104 https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/535 PopBio Bob MacCallum Anopheles grabhamii This species is not in NCBITaxon so is assigned a EUPATH ID. Jie Zheng https://orcid.org/0000-0002-2999-0103 MIRO:40003399 https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/535 PopBio Bob MacCallum Anopheles hodgkini This species is not in NCBITaxon so is assigned a EUPATH ID. Jie Zheng https://orcid.org/0000-0002-2999-0103 MIRO:40000142 https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/535 PopBio Bob MacCallum Anopheles namibiensis A collecting specimen from organism that has the objective to obtain an umbilical cord blood specimen. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB umbilical cord blood specimen collection process Hydroxychloroquine concentration (ug/mL) A blood assay datum of the concentration of hydroxychloroquine. Person: John Judkins VEuPathDB 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. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Severe acute respiratory syndrome coronavirus 2 in nasopharynx or oropharynx by real time reverse-transcription polymerase chain reaction assay District in Uganda A second-order administrative region of Uganda. Person: John Judkins VEuPathDB district of Uganda Region in Uganda A first-order administrative region of Uganda. Person: John Judkins VEuPathDB region of Uganda Schistosoma mansoni, by microscopy A eukaryota in maternal urine datum that specifies whether Schistosoma mansoni was detected by microscopy assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB ClinEpiDB presence of Schistosoma mansoni in maternal urine by microscopy assay Maternal urine test A urine assay that has a maternal urine specimen as evaluant. maternal urine assay Maternal saliva test A saliva assay that evaulates a specimen collected from the biological mother of an infant. John Judkins VEuPathDB maternal saliva assay Schistosoma in maternal urine A eukaryota in maternal urine datum that specifies whether Schistosoma was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/449 ClinEpiDB Sheena Tomko presence of Schistosoma in maternal urine Eukaryota in maternal urine A eukaryota in maternal urine datum that specifies whether a eukaryote was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/450 ClinEpiDB Sheena Tomko presence of eukaryote in maternal urine Ever exclusively breastfed An information on suckling behavior that indicates whether, in the duration between health care encounters, an infant was only fed by suckling. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/452 Sheena Tomko information on whether only fed by suckling Latrine used for storage Information on disposal of human excreta material that specifies whether a latrine was observed by an investigation agent as being used for storage. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/512 Sheena Tomko indicator of latrine used for storage Household minimum dietary diversity A household information that specifies whether the diversity of food consumed by the household meets the minimum standard set by the World Health Organization. John Judkins ORCID:0000-0001-6595-0902 https://inddex.nutrition.tufts.edu/data4diets/indicator/household-dietary-diversity-score-hdds https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/513 Sheena Tomko indicator of whether household met WHO diet minimum dietary diversity Ward in Tanzania A fourth-order administrative region of Tanzania. Person: John Judkins VEuPathDB ward of Tanzania Antibiotic The first mention of an antibiotic that is administered as part of a treatment. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/496 ClinEpiDB Sheena Tomko first antibiotic in treatment Mycobacterium tuberculosis, by PCR A cerebrospinal fluid microbiology datum that specifies whether Mycobacterium tuberculosis was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Mycobacterium tuberculosis in cerebrospinal fluid by polymerase chain reaction assay Histoplasma capsulatum, by PCR A eukaryota in urine datum that specifies whether Histoplasma capsulatum was detected by polymerase chain reaction assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Histoplasma capsulatum in urine by polymerase chain reaction assay Bacteria in cerebrospinal fluid A cerebrospinal fluid microbiology datum that specifies whether bacteria were detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of bacteria in cerebrospinal fluid Bacteria in urine A urine microbiology datum that specifies whether bacteria were detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of bacteria in urine Cryptococcus in blood A eukaryota in blood datum that specifies whether Cryptococcus was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Cryptococcus in blood Cryptococcus in cerebrospinal fluid A cerebrospinal fluid microbiology datum that specifies whether Cryptococcus was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Cryptococcus in cerebrospinal fluid Eukaryota in cerebrospinal fluid A cerebrospinal fluid microbiology datum that specifies whether a eukaryote was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of eukaryote in cerebrospinal fluid Histoplasma in blood A eukaryota in blood datum that specifies whether Histoplasma was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Histoplasma in blood Histoplasma in cerebrospinal fluid A cerebrospinal fluid microbiology datum that specifies whether Histoplasma was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Histoplasma in cerebrospinal fluid Histoplasma in urine A eukaryota in urine datum that specifies whether Histoplasma was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Histoplasma in urine Mycobacterium in blood A bacteria in blood datum that specifies whether Mycobacterium was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Mycobacterium in blood Mycobacterium in cerebrospinal fluid A cerebrospinal fluid microbiology datum that specifies whether Mycobacterium was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB presence of Mycobacterium in cerebrospinal fluid Mycobacterium in urine A urine microbiology datum that specifies whether Mycobacterium was detected. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB 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. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/519 ClinEpiDB Sheena Tomko TaqMan threshold cycle for Shigella flexneri in feces excluding serotype 6 Mother's BMI A body mass index (BMI) calculated from measurements of the biological mother of a child. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/491 ClinEpiDB Sheena Tomko maternal body mass index Steroid end date A treatment information that specifies the date of the last administration of a steroid in the treatment. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/492 ClinEpiDB Sheena Tomko date of end of steroid treatment Zinc administered, caregiver report Treatment information that specifies whether a caregiver of a participant under investigation reported administering zinc to the participant. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/493 ClinEpiDB Sheena Tomko indicator of caregiver reporting zinc administered Antibiotic, 2 The second mention of an antibiotic that is administered as part of a treatment. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/496 ClinEpiDB Sheena Tomko second antibiotic in treatment Antibiotic end date A treatment information that specifies the date of the last administration of the antibiotic that is mentioned first as part of the treatment. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/497 ClinEpiDB Sheena Tomko date of end of first antibiotic treatment Antibiotic 2 end date A treatment information that specifies the date of the last administration of the antibiotic that is mentioned second as part of the treatment. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/498 ClinEpiDB Sheena Tomko date of end of second antibiotic treatment Salbutamol end date A treatment information that specifies the date of the last administration of albuterol in the treatment. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/499 ClinEpiDB Sheena Tomko date of end of albuterol treatment Ranitidine end date A treatment information that specifies the date of the last administration of ranitidine in the treatment. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/500 ClinEpiDB Sheena Tomko date of end of ranitidine treatment Medication, 2 The second mention of a medication that is administered as part of a treatment. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/501 ClinEpiDB Sheena Tomko second medication in treatment Medication, 3 The third mention of a medication that is administered as part of a treatment. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/502 ClinEpiDB Sheena Tomko third medication in treatment Medication, 4 The fourth mention of a medication that is administered as part of a treatment. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/503 ClinEpiDB Sheena Tomko 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. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/507 ClinEpiDB Sheena Tomko maternal feces assay to detect inflammation Bayley scales assessment age 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. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/508 ClinEpiDB Sheena Tomko age of Bayley scale evaluation Food at birth An information content entity that specifies food products, including water, fed to a neonate within approximately an hour after its birth. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/510 ClinEpiDB Sheena Tomko 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. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/519 ClinEpiDB Sheena Tomko TaqMan threshold cycle for Shigella flexneri 6 in feces Maternal enrollment location 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. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/520 ClinEpiDB Sheena Tomko location of maternal human subject enrollment Nebulizer treatment duration A time measurement datum of the duration of a treatment consisting of oral administrations of medication with a nebulizer. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/521 ClinEpiDB Sheena Tomko duration of treatment with nebulizer Breastfeeding initiated An information on suckling behavior that indicates whether it started within a hour after baby delivery. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/451 ClinEpiDB Sheena Tomko indicator of suckling behavior within hour after baby delivery Bag and mask resuscitation performed An information content entity that specifies whether bag valve mask ventilation was performed during a baby delivery. John Judkins ORCID:0000-0001-6595-0902 http://purl.bioontology.org/ontology/SNOMEDCT/425447009 https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/435 ClinEpiDB Sheena Tomko indicator of bag valve mask ventilation performed during baby delivery Observed work characteristics Information that specifies the frequency at which a planned process, in which a birth attendant participates, is observed by an investigation agent. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/437 ClinEpiDB Sheena Tomko information on frequency of observed birth attendant activity Healthcare activities on admission Health care information that is about health care processes that occur during admission for baby delivery and involve the same patient. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/438 ClinEpiDB Sheena Tomko 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. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/439 ClinEpiDB Sheena Tomko information on health care immediately preceding baby delivery Healthcare activities at delivery Health care information that is about health care processes that occur during baby delivery and involve the same patient. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/440 ClinEpiDB Sheena Tomko 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. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/441 ClinEpiDB Sheena Tomko 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 infant formula Liquids for consumption A chemical food component in liquid form. liquid chemical food component Solids for consumption 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) Way to cook food food cooking Continent One of the large, unbroken masses of land into which the Earth's surface is divided. continent Collection site A reference to a place on the Earth, by its name or by its geographical location. geographic location Average mapping coverage Coverage (read depth or depth) is the average number of reads representing a given nucleotide in the reconstructed sequence. read coverage 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. nursing behavior suckling behavior 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. molecular function molecular_function 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. enzyme activity catalytic activity 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 revertase activity RNA-dependent DNA polymerase activity RNA-dependent deoxyribonucleate nucleotidyltransferase activity RNA-directed DNA polymerase, group II intron encoded RNA-directed DNA polymerase, transposon encoded RNA-instructed DNA polymerase activity RT deoxynucleoside-triphosphate:DNA deoxynucleotidyltransferase (RNA-directed) activity reverse transcriptase activity revertase activity RNA-directed DNA polymerase activity Catalysis of the reaction: acetylcholine + H2O = choline + acetate. AcCholE acetyl.beta-methylcholinesterase activity acetylcholine acetylhydrolase activity acetylcholine hydrolase activity acetylthiocholinesterase activity choline esterase I activity true cholinesterase activity acetylcholinesterase 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. RX:glutathione R-transferase activity S-(hydroxyalkyl)glutathione lyase activity glutathione S-alkyl transferase activity glutathione S-alkyltransferase activity glutathione S-aralkyltransferase activity glutathione S-aryltransferase activity glutathione S-transferase activity glutathione conjugation reaction glutathione transferase activity The reproductive process in which the parent is separated from its offspring either by giving birth to live young or by laying eggs. egg laying giving birth parturition 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. breathing respiration 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. biological process physiological process single organism process single-organism process biological_process 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. gene expression The covalent alteration of one or more amino acid residues within a histone protein. histone modification Catalysis of the hydrolysis of any ester bond. esterase activity 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. antibody immunoglobulin complex 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 B lymphocyte receptor complex B-cell receptor complex B-lymphocyte receptor complex BCR complex antibody immunoglobulin complex, membrane bound B cell receptor 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. macromolecular complex macromolecule complex protein complex protein containing complex protein-protein complex protein-containing complex 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. DNA nucleotidyltransferase activity deoxynucleate polymerase activity deoxyribonucleate nucleotidyltransferase activity deoxyribonucleic acid polymerase activity deoxyribonucleic polymerase activity DNA 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. T lymphocyte receptor complex T-cell receptor complex T-lymphocyte receptor complex TCR TCR complex T cell receptor complex 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. antibody immunoglobulin complex, circulating A protein complex that possesses DNA polymerase activity and is involved in template directed synthesis of DNA. DNA polymerase complex A nonsteroidal regulator, composed of two covalently linked inhibin beta-A subunits (sometimes known as activin beta-A or activin/inhibin beta-A). activin A complex 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. IL-12 complex IL12A IL12B p35 p40 interleukin-12 complex Catalysis of the hydrolysis of a carboxylic ester bond. carboxylate esterase activity carboxylic esterase activity hydrolase activity acting on ester bonds carboxylic ester hydrolase activity 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. ferritin complex 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. IgM immunoglobulin complex 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. antibody-mediated neutralization immunoglobulin-mediated neutralization 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). PDGF complex PDGF-AA dimer PDGF-AB dimer PDGF-BB dimer PDGF-CC dimer PDGF-DD dimer platelet-derived growth factor complex Intrauterine contraceptive device 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 Birth rate Any of various rates involving number of births in a population; usually used as shorthand for crude birth rate. birthrate birth rate An abnormality of the urinary system. Urinary tract abnormalities Urinary tract abnormality Urinary tract anomalies Abnormality of the urinary system 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. Renal failure Renal failure in adulthood Renal insufficiency A phenotypic abnormality. Organ abnormality Phenotypic abnormality Genitourinary The presence of any abnormality of the genitourinary system. Abnormality of the GU system Genitourinary abnormality Genitourinary disease Genitourinary dysplasia Genitourinary tract anomalies Genitourinary tract malformation Urogenital abnormalities Urogenital anomalies Abnormality of the genitourinary system Abnormality of the oral cavity, i.e., the opening or hollow part of the mouth. Abnormality of the oral cavity Abnormal oral cavity morphology 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. Hydrocephaly Nonsyndromal hydrocephalus Too much cerebrospinal fluid in the brain Hydrocephalus An abnormality of the face. Abnormal face Abnormality of the countenance Abnormality of the face Abnormality of the physiognomy Abnormality of the visage Anomaly of face Anomaly of the face Disorder of face Disorder of the face Facial abnormality Facial anomaly Abnormality of the face Epistaxis, or nosebleed, refers to a hemorrhage localized in the nose. Bloody nose Frequent nosebleeds Nasal haemorrhage Nasal hemorrhage Nose bleed Nose bleeding Nosebleed Epistaxis Eye Any abnormality of the eye, including location, spacing, and intraocular abnormalities. Abnormal eye Abnormality of the eye Eye disease Abnormality of the eye Sunken eye An eye that is more deeply recessed into the plane of the face than is typical. Deep set eye Deep-set eyes Deeply set eye Enophthalmos Ocular depression Sunken eye Sunken eyes Deeply set eye Abnormal alignment, positioning, or spacing of the teeth, i.e., misaligned teeth. Abnormal dental position Abnormal teeth spacing Abnormality of alignment of teeth Abnormality of position of teeth Abnormality of teeth spacing Crooked teeth Malaligned teeth Malposition of teeth Malpositioned teeth Misalignment of teeth Teeth, malposition Tooth malposition Neurological An abnormality of the nervous system. Abnormality of the nervous system Brain and/or spinal cord issue Neurologic abnormalities Neurological abnormality Abnormality of the nervous system A state of unease characterized by diffuse motor activity or motion, subject to limited control, nonproductive, or disorganized behavior. Fidgetiness Restiveness Restlessness Blood in urine 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). Blood in urine High urine occult blood Hematuria An abnormality of the skin. Abnormality of the skin Dermatopathy Dermopathy Skin abnormality Abnormality of the skin Jaundice Yellow pigmentation of the skin due to bilirubin, which in turn is the result of increased bilirubin concentration in the bloodstream. Icterus Jaundice Yellow skin Yellowing of the skin Jaundice An abnormal accumulation of fluid beneath the skin, or in one or more cavities of the body. Dropsy Fluid retention Hydrops Oedema Water retention Edema Sweating Abnormal excessive perspiration (sweating) despite the lack of appropriate stimuli like hot and humid weather. Diaphoresis Excessive sweating Increased sweating Profuse sweating Sweating Sweating profusely Sweating, increased Hyperhidrosis Paleness Abnormally pale skin. Paleness Skin paleness Pallor 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. Itching Itchy skin Skin itching Pruritus Laminar thickening of skin. Diffusely thickened skin Pachydermia Thick skin Thickened skin Thickened skin An abnormality of the fetus or the birth of the fetus, excluding structural abnormalities. Abnormality of prenatal development or birth Abnormality of prenatal development or birth A state of disinterestedness, listlessness, and indifference, resulting in difficulty performing simple tasks or concentrating. Lethargy Lethargy Coma Complete absence of wakefulness and content of conscience, which manifests itself as a lack of response to any kind of external stimuli. Coma Coma 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. Cognitive delay Delayed cognitive development Delayed development Delayed developmental milestones Delayed intellectual development Delayed milestones Delayed psychomotor development Developmental delay Developmental delay in early childhood Developmental delay, global Developmental retardation Lack of psychomotor development Mental and motor retardation Motor and developmental delay Motormental retardation Psychomotor delay Psychomotor development deficiency Psychomotor development failure Psychomotor developmental delay Retarded development Retarded mental development Retarded psychomotor development Global developmental delay An abnormality of the liver. Abnormal liver Abnormality of the liver Liver abnormality Liver disease Abnormality of the liver Failure to thrive (FTT) refers to a child whose physical growth is substantially below the norm. Faltering weight Poor weight gain Postnatal failure to thrive Undergrowth Weight faltering Failure to thrive Small for gestational age Smaller than normal size according to sex and gestational age related norms, defined as a weight below the 10th percentile for the gestational age. Birth weight less than 10th percentile Low birth weight Small for gestational age Small for gestational age Fetal movement An abnormality of fetal movement. Abnormal intrauterine movements Prenatal movement abnormality Skin An abnormality of the integument, which consists of the skin and the superficial fascia. Abnormality of the integument Abnormal hair An abnormality of the hair. Abnormality of the hair Abnormality of the hair shaft Hair abnormality Abnormal hair morphology A noncongenital process of hair loss, which may progress to partial or complete baldness. Hair loss Alopecia The birth of a baby of less than 37 weeks of gestational age. Premature birth Premature delivery Premature delivery of affected infants Preterm birth Preterm delivery Shortened gestation time Premature birth Any abnormality of the cardiovascular system. Abnormality of the cardiovascular system Cardiovascular abnormality Cardiovascular disease 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. CHF Cardiac failure Cardiac failures Cardiac insufficiency Chronic heart failure Heart failure Congestive heart failure 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. Heart attack MI Myocardial infarction An abnormality of the spleen. Abnormality of the spleen Abnormality of the spleen Splenomegaly Abnormal increased size of the spleen. Increased spleen size Splenomegaly Delivery complications An abnormality of the birth process. Abnormal delivery Delivery complication Abnormal delivery Reduction of total body weight. Loss of weight Weight loss An abnormality of the hematopoietic system. Abnormality of blood and blood-forming tissues Abnormality of the haematopoietic system Abnormality of the hematopoietic system Haematological abnormality Hematologic disease Hematological abnormality Abnormality of blood and blood-forming tissues An abnormality of leukocytes. Abnormality of leukocytes Abnormal leukocyte morphology An abnormal decreased number of leukocytes in the blood. Decreased blood leukocyte number Low white blood cell count Leukopenia Abnormal bleeding An abnormal susceptibility to bleeding, often referred to as a bleeding diathesis. A bleeding diathesis may be related to vascular, platelet and coagulation defects. Bleeding diathesis Bleeding tendency Hemorrhagic diathesis Abnormal bleeding Severe normocytic anemia A kind of anemia in which the volume of the red blood cells is normal. Normocytic anaemia Normocytic anemia Acute kidney injury Sudden loss of renal function, as manifested by decreased urine production, and a rise in serum creatinine or blood urea nitrogen concentration (azotemia). Acute kidney failure Acute renal failure Acute kidney injury Laboratory abnormality Metabolism abnormality Abnormality of metabolism/homeostasis Abnormal acid accumulation or depletion of base. Acidosis Metabolic acidosis 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. Metabolic acidosis Dehydration, caregiver report Dehydration Exsiccosis Dehydration Fever Body temperature elevated above the normal range. Fever Hyperthermia Pyrexia Fever Excessive thirst manifested by excessive fluid intake. Extreme thirst Polydipsia An abnormal increase in the number of leukocytes in the blood. Elevated white blood count High white blood count Increased blood leukocyte number Leukocytosis An abnormality of the viscera of the abdomen. Abnormality of the abdominal organs Gastrointestinal tract defects Abnormality of the abdominal organs Vomiting Forceful ejection of the contents of the stomach through the mouth by means of a series of involuntary spasmic contractions. Emesis Throwing up Vomiting Vomiting Diarrhea Abnormally increased frequency (usually defined as three or more) loose or watery bowel movements a day. Diarrhea Diarrhoea Watery stool Diarrhea Dysphagia Difficulty in swallowing. Deglutition disorder Difficulty swallowing Poor swallowing Swallowing difficulties Swallowing difficulty Dysphagia 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. Nausea and vomiting Nausea and vomiting Nausea A sensation of unease in the stomach together with an urge to vomit. Nausea Nausea Infrequent or difficult evacuation of feces. Constipation Costiveness Dyschezia Constipation Abdominal pain An unpleasant sensation characterized by physical discomfort (such as pricking, throbbing, or aching) and perceived to originate in the abdomen. Abdominal discomfort Abdominal pain Gastro pain Gastrointestinal pain Pain in stomach Stomach pain Upset stomach Abdominal pain Reduced body temperature due to failed thermoregulation. Abnormally low body temperature Hypothermia Hypothermia Respiratory An abnormality of the respiratory system, which include the airways, lungs, and the respiratory muscles. Respiratory abnormality Abnormality of the respiratory system Any structural anomaly of the lung. Abnormality of lung structure Abnormality of the lungs Abnormally shaped lung Lung disease Unusal lung shape Abnormal lung morphology Shortness of breath Difficult or labored breathing. Dyspnea is a subjective feeling only the patient can rate, e.g., on a Borg scale. Abnormal breathing Breathing difficulty Difficult to breathe Difficulty breathing Dyspnoea Panting Shortness of breath Trouble breathing Dyspnea 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. Breathing difficulties Labored breathing Respiratory difficulties Respiratory distress 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. Absence of spontaneous respiration Apneic episodes Apnoea Apnea Hyperlactataemia 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 Increased blood lactate Increased serum lactate Abnormally increased size of the liver. Enlarged liver Hepatomegaly Cephalgia, or pain sensed in various parts of the head, not confined to the area of distribution of any nerve. Headache Headaches Headache An abnormality of the vasculature. Abnormality of blood vessels Abnormality of the vasculature Vascular abnormalities Abnormality of the vasculature An abnormality of the immune system. Abnormality of the immune system Immunological abnormality Abnormality of the immune system Very rapid breathing. Increased respiratory rate or depth of breathing Polypnea Tachypnea Breathing issues An anomaly of the rhythm or depth of breathing. Abnormal pattern of respiration Abnormal respiratory patterns Unusual breathing patterns Abnormal pattern of respiration Abnormal respiration Functional respiratory abnormality Impaired pulmonary function Respiratory problem Abnormal respiratory system physiology Joint pains Joint pain. Arthralgias Arthritic pain Joint pain Joint pains Arthralgia An increased amount of bilirubin in the blood. High blood bilirubin levels Hyperbilirubinemia An abnormality of the composition of urine or the levels of its components. Pee issues Urine issues Abnormality of urine homeostasis Electrolyte disturbances Abnormality of the homeostasis (concentration) of a monoatomic ion. Abnormality of ion homeostasis Electrolyte disorders Electrolyte disturbance Abnormal blood ion concentration Genital ulcers Genital ulcers Abnormal increased size of the viscera of the abdomen. Visceromegaly Muscle aches Pain in muscle. Muscle ache Muscle pain Myalgias Myalgia An unpleasant sensation characterized by physical discomfort (such as pricking, throbbing, or aching) localized to the back. Back pain Back pain Lower back pain An unpleasant sensation characterized by physical discomfort (such as pricking, throbbing, or aching) localized to the lower back. Lower back pain Low back pain Hemoglobinuria The presence of free hemoglobin in the urine. Haemoglobin in urine Hemoglobin in urine Hemoglobinuria Neonatal death Death within the first 28 days of life. Neonatal lethal Neonatal death Stillbirth Death of the fetus in utero after at least 22 weeks of gestation. Fetal death Fetal demise Foetal death Late fetal death Stillbirth Stillborn Stillbirth Abnormally low body weight. Decreased body weight Decreased weight Low body weight Low weight Weight less than 3rd percentile Decreased body weight An abnormality of temperature homeostasis. Abnormality of temperature regulation Body temperature changes Poor temperature regulation Abnormality of temperature regulation Altered consciousness Disturbances of consciousness Lowered consciousness Reduced consciousness/confusion Reduced consciousness/confusion A deficiency in the intake of energy and nutrients. Malnutrition Malnutrition A reduced desire to eat. Decreased appetite Loss of appetite No appetite Poor appetite Poor appetite Spontaneous abortion 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. Early fetal demise Spontaneous abortion Miscarriage Loss of consciousness Loss of consciousness Passing out Loss of consciousness Excessive wrinkled skin Excessive wrinkled skin A tumor (abnormal growth of tissue) of the skin. Dermatological tumors Dermatological tumours Neoplasia of the skin Skin cancer Skin cancer (non-melanoma) Skin tumors Skin tumours Tumor of the skin Tumour of the skin Neoplasm of the skin Stridor Stridor is a high pitched sound resulting from turbulent air flow in the upper airway. Noisy breathing Stridor An abnormal accumulation of excess fluid in the lower extremity resulting in swelling of the feet and extending upward to the lower leg. Dependant edema Dependant oedema Edema of the lower limbs Fluid accumulation in lower limbs Leg edema Leg oedema Lower leg swelling Oedema of the lower limbs Pedal oedema Peripheral edema of lower extremity Peripheral oedema of lower extremity Pedal edema Redness of the skin, caused by hyperemia of the capillaries in the lower layers of the skin. Redness of skin or mucous membrane Erythema A functional abnormality of the immune system. Abnormality of immune system physiology Gastrointestinal An abnormality of the gastrointestinal tract. Abnormality of the GI tract Abnormality of the gastrointestinal tract Digestive system disease Gastrointestinal disease 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. Internal bleeding Internal haemorrhage Internal hemorrhage An abnormality of the regulation of body fluids. Abnormality of fluid regulation Fluid imbalance Abnormality of fluid regulation Any morphological abnormality of the skin. Abnormal skin morphology Abnormal skin structure Abnormality of skin morphology Any abnormality of the physiological function of the skin. Abnormality of skin physiology Abnormality of skin physiology 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 Dermatitis Inflammatory abnormality of the skin Inflammatory skin disease Skin inflammation Inflammatory abnormality of the skin Skin vascular malformation Vascular abnormalities restricted to skin Vascular skin abnormality Abnormality of the urinary system physiology An abnormality of the skin that is not localized to any one particular region. Generalised abnormality of skin Generalized abnormality of skin Generalized abnormality of skin Cognitive, psychiatric or memory anomaly. Abnormality of higher mental function A subjective manifestation of disease localized to the abdomen. Abdominal symptom Increased size of the parotid gland. Hyperplasia of parotid gland Hypertrophy of parotid gland Increased size of parotid gland Enlargement of parotid gland A type of abdominal pain that comes and goes in waves, most often starting and ending suddenly and being of severe intensity. Abdominal colic Number of leukocytes per volume of blood beyond normal limits. Abnormal white blood cell count Abnormal leukocyte count Impaired ability to eat related to problems gathering food and getting ready to suck, chew, or swallow it. Feeding difficulties Feeding problems Poor feeding Feeding difficulties Renal impairment An abnormal functionality of the kidney. Abnormal kidney function Abnormal renal function Abnormality of renal physiology Kidney function issue Renal functional abnormality Abnormal renal physiology An anomaly in the processes involved in the maintenance of an internal equilibrium. Abnormal homeostasis Aches or pains An unpleasant sensory and emotional experience associated with actual or potential tissue damage, or described in terms of such damage. Pain Pain A functional anomaly of the nervous system. Abnormality of nervous system physiology Abnormal nervous system physiology Abnormal functionality of the gastrointestinal tract. Functional abnormality of the GI tract GI dysfunction Functional abnormality of the gastrointestinal tract A sudden, audible expulsion of air from the lungs through a partially closed glottis, preceded by inhalation. Cough Coughing Cough Respiratory failure in the newborn. Asphyxia neonatorum Neonatal asphyxia 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 Ear pain 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). Ear pain Otalgia Pain in the ear Ear pain Wheezing or whistling A high-pitched whistling sound associated with labored breathing. Wheezing Wheezing An anomalous (adventitious) sound produced by the breathing process. Abnormal lung auscultation finding Abnormal breath sound Nasal flaring Widening of the nostrils upon inhalation as a manifestation of respiratory distress. Nasal flaring Chest indrawing 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. Chest retractions Intercostal retractions Shock The state in which profound and widespread reduction of effective tissue perfusion leads first to reversible, and then if prolonged, to irreversible cellular injury. Shock Runny nose Increased discharge of mucus from the nose. Nasal Discharge Runny Nose Rhinorrhea 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). Flaky paint skin appearance Flaky paint dermatosis An abnormal level of an analyte measured in the blood. Abnormal circulating metabolite concentration Clinical status Health status of a family member with respect to the disease being investigated in a proband. Health status 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. Fever induced seizure Seizure precipitated by febrile infection Bipedal edema A palpable swelling in both feet and ankles caused by palpable swelling caused by an increase in interstitial fluid volume (excess fulid). Bipedal oedema Bipedal edema Barking cough A cough with a characteristic sound that has been compared to a seal's bark. Seal-like barking cough Barking cough Relative coldness of a body part to palpitation, often acccompanied by feelings of coldness. Cold skin temperature Cool skin Cool skin temperature Coolness to palpation Coldness Death of a fetus in the uterus. Death before birth Intrauterine death Prenatal death Systemic inflammatory response to infection in newborn babies. Neonatal sepsis 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. Intrapulmonary haemorrhage Intrapulmonary hemorrhage Pulmonary haemorrhage Pulmonary hemorrhage Pain in head and neck region Dysuria Painful or difficult urination. Dull burning sensation with urination Painful or difficult urination Dysuria Pulmonary edema Fluid accumulation in the lungs. Excess fluid in lungs Lung edema Lung oedema Pulmonary oedema Wet lung Pulmonary edema Preeclampsia Pregnancy-induced hypertension in association with significant amounts of protein in the urine. Pre-eclampsia Preeclampsia Chest pain An unpleasant sensation characterized by physical discomfort (such as pricking, throbbing, or aching) localized to the chest. Chest discomfort Chest pain Thoracic pain Chest pain 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. Lymphatic disease Abnormality of the lymphatic system Systemic inflammatory response to infection. Infection in blood stream Sepsis An acute hypersensitivity reaction due to exposure to a previously encountered antigen. Anaphylaxis Anaphylactic shock Eye pain An unpleasant sensation characterized by physical discomfort (such as pricking, throbbing, or aching) localized to the eye. Eye pain Ocular pain A small elevation of the skin containing cloudy or purulent material usually consisting of necrotic inflammatory cells. Pimple Pustula Pustular lesion Pustules Skin pustule Skin pustules Pustule 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. Warts Verrucae Reduced ability to control, or a failure to resist a temptation, urge, or impulse. Impaired self-restraint Impulse control disorders Reduced impulse control 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: Alan Ruttenberg PERSON: Melanie Courtot measurement unit label 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: Alan Ruttenberg PERSON: Barry Smith PERSON: Bjoern Peters PERSON: Jennifer Fostel goal specification OBI Plan and Planned Process/Roles Branch OBI_0000217 objective specification Pour the contents of flask 1 into flask 2 A directive information entity that describes an action the bearer will take. Alan Ruttenberg 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 http://www.golovchenko.org/cgi-bin/wnsearch?q=label#4n 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. datum label 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: Alan Ruttenberg PERSON: Chris Stoeckert PERSON: Jonathan Rees data data item 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 PERSON: Jonathan Rees based on Oxford English Dictionary symbol 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. PERSON: Chris Stoeckert OBI_0000142 information content entity 1 1 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. PERSON: Alan Ruttenberg PERSON: Melanie Courtot 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 PERSON: Alan Ruttenberg PERSON: Bjoern Peters 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 OBI_0000270 adapted from discussion on OBI list (Matthew Pocock, Christian Cocos, Alan Ruttenberg) algorithm curation status specification The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value. Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting) PERSON:Bill Bug GROUP:OBI:<http://purl.obolibrary.org/obo/obi> OBI_0000266 curation status specification 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 OBI_0000042 group:OBI data set 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. person:Alan Ruttenberg person:Allyson person:Chris Stoeckert OBI_0000030 group:OBI image data about an ontology part Data about an ontology part is a data item about a part of an ontology, for example a term Person:Alan Ruttenberg data about an ontology part 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 Alan Ruttenberg Clint Dowland OBI Plan and Planned Process branch OBI_0000344 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 plan specification https://github.com/information-artifact-ontology/IAO/issues/231#issuecomment-1010455131 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? person:Chris Stoeckert OBI_0000305 group:OBI measurement datum 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. PERSON: Alan Ruttenberg PERSON: Melanie Courtot obsolescence reason specification 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 textual entity document A journal article, patent application, laboratory notebook, or a book A collection of information content entities intended to be understood together as a whole PERSON: Lawrence Hunter document publication journal article, newspaper story, book, etc. A document that is the output of a publishing process. PERSON: Chris Stoeckert PERSON: Jie Zheng PERSON: Lawrence Hunter published document Revisit the term in Octorber 2020. Improve the defintion. publication 1 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 Alan Ruttenberg AR notes: We need to discuss whether it should include site. cartesian spatial coordinate datum http://groups.google.com/group/bfo-discuss/browse_thread/thread/9d04e717e39fb617 1 A cartesion spatial coordinate datum that uses one value to specify a position along a one dimensional spatial region Alan Ruttenberg one dimensional cartesian spatial coordinate datum A scalar measurement datum that is the result of measurement of length quality Alan Ruttenberg 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. Alan Ruttenberg Barry Smith, Werner Ceusters denotator type Weight A scalar measurement datum that is the result of measurement of mass quality 2009/09/28 Alan Ruttenberg. Fucoidan-use-case Person:Alan Ruttenberg mass measurement datum A scalar measurement datum that is the result of measuring a temporal interval 2009/09/28 Alan Ruttenberg. Fucoidan-use-case Person:Alan Ruttenberg 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:Alan Ruttenberg Person:Chris Stoeckart email address 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 https://en.wikipedia.org/wiki/Publishing VEuPathDB publishing process A document that is in preparation for submission to be published. PERSON: Jie Zheng EFO_0001795 in preparation VEuPathDB 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:Alan Ruttenberg Person:Bjoern Peters Person:Melanie Courtot assigning a CRID 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: Alan Ruttenberg PERSON: Bill Hogan PERSON: Bjoern Peters PERSON: Melanie Courtot CRID symbol Original proposal from Bjoern, discussions at IAO calls centrally registered identifier symbol 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. 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. PERSON: Alan Ruttenberg PERSON: Bill Hogan PERSON: Bjoern Peters PERSON: Melanie Courtot CRID Original proposal from Bjoern, discussions at IAO calls 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 PERSON: Alan Ruttenberg PERSON: Bill Hogan PERSON: Bjoern Peters PERSON: Melanie Courtot CRID registry Original proposal from Bjoern, discussions at IAO calls https://github.com/information-artifact-ontology/IAO/issues/237 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. Justin Whorton Mathias Brochhausen proper name https://github.com/information-artifact-ontology/IAO/issues/237 Mathias Brochhausen 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) identifier A planned process that provides a reference to an individual entity shared by a group of subscribers to refer to that individual entity. Justin Whorton Mathias Brochhausen dubbing process naming https://github.com/information-artifact-ontology/IAO/issues/237 Mathias Brochhausen 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. Alan Ruttenberg Justin Whorton Mathias Brochhausen code map code system codeset coding system controlled vocabulary https://github.com/information-artifact-ontology/IAO/issues/237 Alan Ruttenberg Clint Dowland Matt Diller Sarah Bost William R. Hogan 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. ontology module 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. base ontology module 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 editors 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 main release ontology 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. bridge ontology 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 import ontology module 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 subset ontology module 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. curation subset ontology module 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 exclusion subset ontology module external import ontology module An imported ontology module that is derived from an external ontology. Derivation methods include the OWLAPI SLME approach. external import external import ontology module species subset ontology module A subset ontology that is crafted to either include or exclude a taxonomic grouping of species. taxon subset species subset ontology module 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. reasoned ontology module 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 generated ontology module template generated ontology module An ontology module that is automatically generated from a template specification and fillers for slots in that template. template generated ontology module taxonomic bridge ontology module taxonomic bridge ontology module ontology module subsetted by expressivity 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 obo basic subset ontology module ontology module subsetted by OWL profile ontology module subsetted by OWL profile EL++ ontology module 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 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 Hysterectomy The surgical removal (cutting out) of part or all of uterus. uterus surgical removal hysterectomy 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. OxRes oxidized residue A protein modification that by reaction of iodoacetamide effectively replaces a residue alpha-amino- or alpha-imino-hydrogen with a carboxamidomethyl group. (carbamoylmethyl)amino Carbamidomethyl Iodoacetamide derivative iodoacetamide derivatized amino-terminal residue Culex pseudovishnui Culex vishnui rat rats Rattus Mus norvegicus Norway rat brown rat rat rats Rattus norvegicus Mus rattus Rattus rattoides Rattus wroughtoni black rat house rat roof rat Rattus rattus Hymenolepis nana Rodentolepis nana Vira Viridae viruses Viruses woodland malaria mosquito Anopheles punctipennis Cytomegalovirus Mansonia bonneae mammalian hepatitis B-type viruses Orthohepadnavirus HBV Human hepatitis B virus hepatitis B virus (HBV) hepatitis B virus HBV hepatitis B virus, HBV human hepatitis B virus HBV Hepatitis B virus Aedes hendersoni Ochlerotatus henderson Ochlerotatus hendersoni Adenovirus Adenoviridae Aedini Anopheles jeyporensis Anopheles jeyporiensis Balantidium cf. coli Balantioides cf. coli Common tern Flussseeschwalbe Sterna hirundo Culex atratus Culex abominator Culex cedecei Culex iolambdis Culex mulrennani Culex peccator Cervus timorensis Javan rusa Sunda sambar Rusa timorensis Pipra striata Pardalotus striatus Iodamoeba Rotaviruses Rotavirus Anopheles lesteri Alphaviridae arboviruses group A Alphavirus Eastern equine encephalomyelitis virus eastern equine encephalomyelitis EEE eastern equine encephalomyelitis virus EEEV Eastern equine encephalitis virus Western equine encephalomyelitis virus Western equine encephalitis virus Flavivirus (arbovirus group B) Flaviviridae arboviruses group B Flavivirus Ardea virescens green heron Butorides virescens Entamoeba coli Endolimax nana St. Louis encephalitis virus Saint Louis encephalitis virus WNV West Nile virus Anas columbianus Olor columbianus tundra swan whistling swan Cygnus columbianus Hepatitis C virus group Hepatitis C viruses Hepatitis C-like viruses Hepacivirus HCV Hepatitis C virus hepatitis C virus HCV human hepatitis C virus human hepatitis C virus HCV human hepatitis virus C HCV post-transfusion hepatitis non A non B virus Hepacivirus C Human coronavirus 229E Coronavirus 229E HCoV-229E Human coronavirus (STRAIN 229E) Human coronavirus serogroup 229E Human coronavirus strain 229E Human coronavirus 229E negative-sense genome single-stranded RNA viruses Mononegavirales Paramyxoviridae Anopheles fluviatilis Strix otus long-eared owl Asio otus Fringilla noctis lesser Antillean bullfinch Loxigilla noctis Fringilla bicolor Tiaris bicolor black-faced grassquit Melanospiza bicolor Human parainfluenza virus 3 HPIV-3 HPIV3 Human parainfluenza 3 virus Human parainfluenza virus 3 Human parainfluenza virus type 3 Parainfluenza virus type 3 human parainfluenza virus human parainfluenza virus 3 HPIV3 human parainfluenza virus type 3 PIV3 parainfluenza virus type 3 PIV-3 Human respirovirus 3 fluviatilis species complex Anopheles fluviatilis S Anopheles fluviatilis T Anopheles minimus Cell-associated subacute sclerosing panencephalitis Measles virus Subacute sclerosing panencephalitis virus measles virus MV rougeole virus rubeola virus subacute sclerose panencephalitis virus subacute sclerosing panencephalitis virus, SSPEV Measles morbillivirus Pneumovirinae Pneumoviridae HRSV Human respiratory syncytial virus human RSV Human orthopneumovirus Aedes (Ochlerotatus) diantaeus Aedes diantaeus Ochlerotatus diantaeus Orthomyxoviridae FLUAV Human Influenza A Virus Influenza virus type A influenza A virus Influenza A virus Anopheles pretoriensis Anopheles rufipes Anopheles theileri typhus group FLUBV Influenza virus type B Influenza B virus FLUCV Influenza C viruses Influenza virus type C Influenza C virus eared dove Zenaida auriculata Bunyavirus la crosse La Crosse virus Lentivirinae Lentivirus AIDS virus HIV HIV-1 HIV1 Human immunodeficiency virus type 1 LAV-1 human immunodeficiency virus 1 HIV-1 human immunodeficiency virus HIV-1 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 human immunodeficiency virus-1 HIV-1 Human immunodeficiency virus 1 bony vertebrates Euteleostomi Adenophorea Chromadorea Protomacleaya Aedes theobaldi Ochlerotatus theobaldi Caliciviridae Norwalk calicivirus Norwalk virus NV Norwalk virus Anopheles neomaculipalpus Bacteriophage MS2 Enterobacteria phage MS2 Enterobacterio phage MS2 phage MS2 xLevivirus subgroup I Escherichia phage MS2 Picornavirus Picornaviridae Enterovirus Enteroviruses Enterovirus Aedes atlanticus Ochlerotatus atlanticus Aedes increpitus Ochlerotatus increpitus Aedes niphadopsis Ochlerotatus niphadopsis Aedes sierrensis Ochlerotatus sierrensis Aedes spencerii Ochlerotatus spencerii Aedes thelcter Ochlerotatus thelcter Aedes thibaulti Ochlerotatus thibaulti Aedes tortilis Ochlerotatus tortilis Psorophora longipalpus Psorophora pygmaea Psorophora signipennis Aedes zoosophus Ochlerotatus zoosophus Culex bahamensis Culiseta particeps Psorophora discolor Aedes mitchellae Ochlerotatus mitchellae Aedes schizopinax Ochlerotatus schizopinax Ecdysozoa Lophotrochozoa HPV-1 Human poliovirus 1 Human poliovirus type 1 PV1 Polio virus 1 Poliovirus type 1 poliovirus type 1 PV1 Poliovirus 1 Poliovirus type 1 (strain Sabin) human poliovirus strain Sabin 1 Human poliovirus 1 strain Sabin HPV-2 Human Poliovirus type 2 Human poliovirus 2 Poliovirus type 2 Poliovirus 2 HPV-3 Human poliovirus 3 Human poliovirus type 3 Polio virus 3 Poliovirus serotype 3 Poliovirus type 3 Poliovirus 3 Anopheles claviger Aedes cantans Ochlerotatus cantans Aedes caspius Ochlerotatus caspius Aedes cataphylla Ochlerotatus cataphylla Aedes cinereus Aedes detritus Ochlerotatus detritus Aedes (Finlaya) geniculatus Ochlerotatus (Finlaya) geniculatus Ochlerotatus geniculatus Aedes geniculatus Aedes pullatus Ochlerotatus pullatus Aedes rusticus Ochlerotatus rusticus Aedes sticticus Ochlerotatus sticticus Dendroica striata black-poll warbler blackpoll warbler Setophaga striata Aedes vexans nipponii "Alphaproteobacteriota" Whitman et al. 2018 Alphaproteobacteriota Proteobacteria Proteobacteriota proteobacteria purple photosynthetic bacteria and relatives Pseudomonadota Human calicivirus genogroup 1 Norovirus genogroup 1 Norovirus genogroup I Norwalk-like virus genogroup 1 Norovirus GI Norovirus genogroup 2 Norovirus genogroup II Norwalk-like virus genogroup 2 Norwalk-like viruses genogroup 2 human calicivirus genogroup 2 Norovirus GII Proteobacteria gamma subdivision Purple bacteria, gamma subdivision g-proteobacteria gamma proteobacteria gamma subdivision gamma subgroup Gammaproteobacteria Anopheles pampanai "Firmicutes" corrig. Gibbons and Murray 1978 (Approved Lists 1980) Bacillaeota Bacillota corrig. Gibbons and Murray 2021 Bacillus/Clostridium group Clostridium group firmicutes Firmicuteota Firmicutes Low G+C firmicutes clostridial firmicutes firmicutes low G+C Gram-positive bacteria low GC Gram+ Bacillota Coquillettidia crassipes Coquillettidia (Coquillettidia) richiardii Culex richiardii Mansonia richiardii Coquillettidia richiardii Aedes khazani Phagomyia khazani Armigeres flavus Phagomyia Armigeres Armigeres <genus> Culex subalbatus Armigeres subalbatus Dengue virus Larus atricilla Laughing gull Leucophaeus atricilla ring-bill gull ring-billed gull Larus delawarensis HPIV-1 HPIV1 Human parainfluenza 1 virus Human parainfluenza virus 1 Human parainfluenza virus type 1 Parainfluenza virus type 1 human parainfluenza virus human parainfluenza virus type 1 HPIV-1 human parainfluenza virus type 1 hPIV1 Human respirovirus 1 Staphylococcus Aurococcus Staphylococcus Vibrio cholerae serogroup O1 Vibrio cholerae O1 Micrococcus aureus Micrococcus pyogenes Staphlococcus pyogenes citreus Staphylococcus aureus subsp. anaerobius Staphylococcus pyogenes aureus Staphylococcus aureus Respiratory syncytial virus RSV respiratory syncytial virus RS respiratory syncytial virus RS virus respiratory syncytial virus RSV Respiratory syncytial virus Albococcus epidermidis Micrococcus epidermidis Staphylococcus epidermidis albus Staphylococcus epidermidis Anopheles nitidus Aedes fulvus Ochlerotatus fulvus Shigella flexneri serotype 2b Shigella flexneri 2b Juppius Aedes juppi Ochlerotatus juppi Aedes caballus Ochlerotatus caballus Anopheles argyropus Blastocystis Blastocystis hominis Anopheles vinckei Streptococcus HAdV-F Human adenovirus F Human mastadenovirus F Streptococcus pneumoniae Diplococcus pneumoniae Micrococcus pneumoniae Streptococcus pneumoniae Streptococcus pyogenes Micrococcus scarlatinae Streptococcus erysipelatos Streptococcus hemolyticus Streptococcus scarlatinae Streptococcus pyogenes Melopsittacus unduratus Psittacus undulatus budgerigar Melopsittacus undulatus Streptococcus group G Streptococcus sp. (group G) Streptococcus sp. group G group G streptococcus Streptococcus sp. 'group G' Phlebotomus Phlebotomus <genus> Phlebotomus (Larroussius) perniciosus Phlebotomus perniciosus Rhodnius Rhodnius prolixus Phlebotomus similis Citrobacter freundii complex Enterococcus Enterococcus proteiformis Enterocoque Micrococcus ovalis Micrococcus zymogenes Streptococcus faecalis Streptococcus glycerinaceus Streptococcus liquefaciens Enterococcus faecalis Streptococcus faecium Enterococcus faecium Pseudomonadaceae spirochetes Spirochaetales Protoculex Aedes tormentor Ochlerotatus tormentor Bacillus/Staphylococcus group Caryophanales Bacillales Anopheles pseudowillmori Anopheles hyrcanus Anopheles dravidicus Anopheles crawfordi Enterovirus EV-C Human enterovirus C Poliovirus Enterovirus C Parechovirus Borrelia burgdorferi Lyme disease spirochete Borreliella burgdorferi Anopheles coustani Anopheles mattogrossensis Orthopodomyia Orthopodomyia alba Uranotaenia Uranotaenia <genus> Uranotaenia sapphirina Aedeomyia Giardia duodenalis assemblage B Giardia lamblia (assemblage B) Giardia intestinalis assemblage B Aedes (Finlaya) japonicus Ochlerotatus japonicus Aedes japonicus Aedes (Finlaya) japonicus japonicus Ochlerotatus japonicus japonicus Aedes japonicus japonicus Phlebotomus (Larroussius) galilaeus Phlebotomus perfiliewi galilaeus Phlebotomus galilaeus Aedes aegypti queenslandensis Aedes aegypti aegypti Aedes malayensis Norwalk-like viruses Norovirus Bacillus cereus var. thuringiensis Bacillus thuringiensis Berliner 1915 (Approved Lists 1980) Bacillus thuringiensis Anopheles sawadwongporni Anopheles vagus Anopheles willmori Bacillus thuringiensis (SUBSP. ISRAELENSIS) Bacillus thuringiensis israelensis Bacillus thuringiensis subsp. israelensis Bacillus thuringiensis var. israelensis Bacillus thuringiensis serovar israelensis Boreotheria Boreoeutheria Culex stigmatosoma Mansonia Mansonia <mosquitos,genus> Aedes Aedes <subgenus> Bacillus difficilis Clostridium difficile Peptoclostridium difficile Clostridioides difficile Anopheles maculipalpis Bocavirus Bocaparvovirus Bacillus tetani Clostridium tetani Anopheles dissidens Anopheles saeungae Anopheles wejchoochotei Anopheles gambiae M Anopheles coluzzii Anopheles demeilloni Anopheles hancocki Anopheles marshallii Aedes (Finlaya) pseudotaeniatus Aedes pseudotaeniatus Collessius (Alloeomyia) pseudotaeniatus Culex pseudotaeniatus Ochlerotatus pseudotaeniatus Collessius pseudotaeniatus Aedes (Finlaya) cogilli Aedes cogilli Ochlerotatus cogilli Phagomyia cogilli Culiseta fumipennis Psittaculidae Aedes (Ochlerotatus) zammitii Aedes zammitii Ochlerotatus zammitii Acartomyia zammitii Trichoglossus haematodus moluccanus rainbow lorikeet Trichoglossus moluccanus Galloanseri ducks, geese, chickens, fowl, quail, currasows and allies Galloanserae Uranotaenia balfouri "Spironema" Vuillemin 1905 Microspironema Treponema Anopheles maculipennis sensu lato BTLHVDV-2014 American black scoter Melanitta nigra americana Oidemia Americana Oidemia americana Oidemia nigra americana black scoter Melanitta americana Culex incidens Culiseta incidens Anopheles pulcherrimus Columba oenas Treponema pallidum pallidum syphilis treponeme Treponema pallidum subsp. pallidum Shigella flexneri 4c Human metapneumovirus HMPV Human metapneumovirus Metapneumovirus Anopheles leesoni Anopheles parensis Culex annulirostris Culex sitiens Culex (Culex) palpalis Taylor Culex palpalis Borreliaceae Borrelia mayonii Candidatus Borrelia mayonii Borreliella mayonii Culex rubinotus Aedeomyia africana Turicella Corynebacterium Aedes epactius Ochlerotatus epactius Wyeomyia pitcher-plant mosquito Wyeomyia smithii Culiseta Culiseta (Culiseta) impatiens Culiseta impatiens Passeroidea Mycobacteriaceae Mycobacterium Lehmann and Neumann 1896 (Approved Lists 1980) Mycobacterium Aedes aegypti formosus Culicoides pulicaris Culicoides impunctatus Bacillus tuberculosis Bacterium tuberculosis Mycobacterium tuberculosis typus humanus Mycobacterium tuberculosis var. hominis Mycobacterium tuberculosis variant tuberculosis Mycobacterium tuberculosis Terrabacteria group Aedeomyia (Lepiothauma) furfurea Aedeomyia furfurea Coquillettidia chrysosoma Aedes (Aedimorphus) hirsutus Aedes hirsutus Culex (Culex) duttoni Culex duttoni Culex (Culex) simpsoni Culex simpsoni Culex (Culex) thalassius Culex thalassius Culex (Culex) vansomereni Culex vansomereni Mimomyia (Mimomyia) splendens Mimomyia splendens Motacilla flava Dobrotworskyius Aedeomyia venustipes Coquillettidia linealis Culiseta inconspicua Culex globocoxitus Dobrotworskyius alboannulatus Finlaya alboannulatus Ochlerotatus alboannulatus Aedes alboannulatus Dobrotworskyius rubrithorax Ochlerotatus rubrithorax Aedes rubrithorax Macleaya macmillani Ochlerotatus macmillani Aedes macmillani Macleaya tremula Ochlerotatus tremulus Aedes tremulus Macleaya wattensis Ochlerotatus wattensis Aedes wattensis Ochlerotatus mallochi Aedes mallochi Aedes sagax Ochlerotatus sagax Aedes vittiger Ochlerotatus vittiger Tripteroides atripes Tripteroides tasmaniensis Polylepidomyia Culex cylindricus Trichomonadidae Nocardia Micropolyspora Nocardia Rotavirus G Anopheles peryassui ardensis group Anopheles nili mosquito Anopheles moucheti Clostridiales Eubacteriales Orthopneumovirus Lactobacillales Respirovirus Clostridioides Aedes (Howardina) bahamensis Ochlerotatus (Howardina) bahamensis Ochlerotatus bahamensis Aedes bahamensis Aedes polynesiensis Yersiniaceae Anopheles incertae sedis Anopheles atropos Anopheles punctimacula Uranotaenia lowii Ochlerotatus Ochlerotatus <genus> Meliphagides Meliphagoidea Anopheles amharicus Anopheles quadriannulatus sp. B Anopheles quadriannulatus B Shigella flexneri X variant Campylobacter Campylobacter hyoilei Vibrio coli Campylobacter coli Anopheles maculatus sensu lato 4821 Anopheles minimus sensu lato 1775 Anopheles barbirostris sensu lato 245 Campylobacter fetus subsp. jejuni Vibrio hepaticus Vibrio jejuni Campylobacter jejuni Influenzavirus A Alphainfluenzavirus Influenzavirus B Betainfluenzavirus Influenzavirus C Gammainfluenzavirus sundaicus species complex Anopheles epiroticus Monera Procaryotae Prokaryota Prokaryotae bacteria eubacteria prokaryote prokaryotes Bacteria Shigella flexneri 5b Mansonia indiana Neobalantidium Balantioides Anopheles peditaeniatus Anopheles messeae x Anopheles daciae Aedes fulvus pallens Ochlerotatus fulvus pallens Psorophora horrida Catageiomyia Aedes dupreei Culex dupreei Coquillett, 1904 Ochlerotatus dupreei Aedes fowleri Aedes sudanensis Anatinae Anserinae Diplomonadida group Fornicata Anopheles gambiae x Anopheles coluzzii Anopheles coluzzii x Anopheles gambiae Helicobacter Anopheles nigerrimus Campylobacter pylori Campylobacter pylori subsp. pylori Campylobacter pyloridis Helicobacter nemestrinae Helicobacter pylori Filterable agent of primary atypical pneumonia Schizoplasma pneumoniae Mycoplasmoides pneumoniae Sylvioidea Campylobacterales Human rotavirus G12 Rotavirus G12 Archaebacteria Mendosicutes Metabacteria Monera Procaryotae Prokaryota Prokaryotae archaea prokaryote prokaryotes Archaea Anopheles culicifacies species D Anopheles culicifacies D Anopheles culicifacies E Anopheles pharoensis Achromobacter Achromobacter Anopheles mascarensis Anopheles intermedius Anopheles intermedius Shingarev, 1928 Anopheles plumbeus Aedes canadensis Ochlerotatus canadensis Aedes trivittatus Ochlerotatus trivittatus Aedes stimulans Ochlerotatus stimulans Aedes grossbecki Ochlerotatus grossbecki Aedes intrudens Ochlerotatus intrudens Sergentomyia Sergentomyia <subgenus> Newell's shearwater Puffinus auricularis newelli Puffinus puffinus newelli Puffinus newelli crucians species complex Culex molestus Culex pipiens f. molestus Culex pipiens molestus Cryptosporidium hominis Shewanella putrefaciens Alteromonas putrefaciens Pseudomonas putrefaciens Shewanella putrefaciens American herring gull Larus argentatus smithsonianus Larus smithsonianus Psorophora varipes Negative-strand RNA viruses Negarnaviricota Polyploviricotina Coronavirus Orthocoronavirinae Embecovirus Anopheles pullus Chryseobacterium indologenes Chryseobacterium indologenes (Yabuuchi et al. 1983) Vandamme et al. 1994 Flavobacterium indologenes Chryseobacterium indologenes Mansoniini RNA viruses RNA viruses and viroids Riboviria Orthoparamyxovirinae Rubulavirinae Orthorubulavirus HPIV-2 HPIV2 Human parainfluenza 2 virus Human parainfluenza virus 2 Human parainfluenza virus type 2 Human rubulavirus 2 PIV-2 Parainfluenza virus type 2 human parainfluenza virus Human orthorubulavirus 2 HPIV type 4 HPIV4 Human parainfluenza virus 4 Human parainfluenza virus type 4 Human rubulavirus 4 Parainfluenza virus type 4 human parainfluenza virus Human orthorubulavirus 4 Culex aurantapex Mimomyia mimomyiaformis Mimomyia mediolineata Ancylostomatoidea Culex (Culex) australicus Culex australicus unclassified Streptococcus Metamonada Anopheles dthali Anopheles superpictus Phlebotomus mascittii Human rotavirus G10 Rotavirus G10 Mansonia dyari Anthochaera Merops carunculata Anthochaera carunculata Merops chrysopterus Anthochaera chrysoptera Certhia novaeHollandiae New Holland honeyeater Phylidonyris novaehollandiae VNI subdivision Cryptococcus neoformans var. grubii VNI Psittacus elegans crimson rosella Platycercus elegans 2019-nCoV COVID-19 virus HCoV-19 Human coronavirus 2019 SARS-2 SARS-CoV-2 SARS-CoV2 SARS2 Severe acute respiratory syndrome coronavirus 2 SAR supergroup Sar Poliovirus type 3 Sabin vaccine strain Human poliovirus 3 strain Sabin American harrier Circus cyaneus hudsonius Falco hudsonius Circus hudsonius Orthornavirae Kitrinoviricota Pisuviricota Pisoniviricetes Revtraviricetes Anopheles sergenti Anopheles sergentii Anopheles donaldi Rotavirus P4 Rotavirus A P4 Rotavirus P8 Rotavirus A P8 Eucarya Eucaryotae Eukarya Eukaryotae eucaryotes eukaryotes Eukaryota Aedes ledgeri Aedes (Finlaya) poicilius Aedes poicilius Human coronavirus NL63 Coronavirus NL63 HCoV-NL63 Human coronavirus NL Human coronavirus NL63 Anopheles franciscanus Acinetobacter lwoffi Acinetobacter genomosp. 9 Acinetobacter genomospecies 9 Acinetobacter mesopotamicus Moraxella lwoffi Acinetobacter lwoffii Enterobacter sakazakii yellow -pigmented Enterobacter cloacae Cronobacter sakazakii Proteobacteria beta subdivision Purple bacteria, beta subdivision b-proteobacteria beta proteobacteria beta subdivision beta subgroup Betaproteobacteria Anolis Carolina anole green anole Anolis carolinensis Culex (Melanoconion) spissipes Culex spissipes Culex opisthopus Culex taeniopus Pseudomonas "Chlorobacterium" Guillebeau 1890, nom. rejic. Opin. 6 (not "Chlorobacterium" Lauterborn 1916) Liquidomonas Loefflerella RNA similarity group I Pseudomonas Aedes (Finlaya) atropalpus Aedes (Georgecraigius) atropalpus Aedes (Ochlerotatus) atropalpus Georgecraigius atropalpus Ochlerotatus atropalpus rock-pool mosquito Aedes atropalpus common pintail northern pintail pintail Anas acuta Colymbus marmoratus Brachyramphus marmoratus Bacillus aeruginosus Bacillus pyocyaneus Bacterium aeruginosum Bacterium pyocyaneum Micrococcus pyocyaneus Pseudomonas polycolor Pseudomonas pyocyanea probable synonym or variety: "Pseudomonas polycolor" Clara 1930 Pseudomonas aeruginosa Group A rotaviruses Rotavirus group A group A rotavirus Rotavirus A Bacillus cholerae-suis Salmonella cholerae-suis Salmonella choleraesuis Salmonella enterica ser. choleraesuis Salmonella enterica Culicoides obsoletus Culicoides scoticus Culicoides dewulfi Human coronavirus HKU1 CoV-HKU1 HCoV-HKU1 Human CoV/HKU1 Human coronavirus HKU1 Phlebotomus (Phlebotomus) papatasi Phlebotomus papatasii Phlebotomus papatasi Ancylostoma Anopheles barberi Aedes inconspicuosus Culex inconspicuosus Hispidimyia hispida Mimomyia hispida Burkholderia cepacia genomovar I Pseudomonas cepacia Pseudomonas kingii Pseudomonas multivorans Burkholderia cepacia Shigella flexneri 7a Bacillus fluorescens Bacillus fluorescens liquefaciens Bacterium fluorescen Liquidomonas fluorescens Pseudomonas fluorescens California black legged tick western blacklegged tick Ixodes pacificus Mycoplasmoides Culex decens Anopheles koliensis Anopheles merus Nyssorhynchus nuneztovari Anopheles nuneztovari Anopheles punctulatus Anopheles mysorensis Anopheles stephensi mysorensis Anopheles stephensi var. mysorensis Asian malaria mosquito Neocellia intermedia Neocellia intermedia Rothwell, 1907 Anopheles stephensi Anopheles notanandai Pseudomonas putida Arthrobacter siderocapsulatus Bacillus fluorescens putidus Bacillus putidus Pseudomonas arvilla Pseudomonas convexa Pseudomonas eisenbergii Pseudomonas incognita Pseudomonas ovalis Pseudomonas rugosa Pseudomonas striata Pseudomonas putida Fischreiher grey heron Ardea cinerea owls Strigiformes Strigidae Aedeomyia catasticta Aedes fumidus Anopheles jamesi Anopheles jamesii Anopheles pallidus Culex (Lutzia) fuscana Culex (Lutzia) fuscanus Culex fuscanus Lutzia (Metalutzia) fuscana Lutzia fuscanus Lutzia fuscana Culex gelidus Lophoceraomyia Culex infantulus Culex nigropunctatus Culex rubithoracis Ficalbiini Ficalbia minima Mansonia annulifera Mansonioides Mansonia Mansonia <mosquitos,subgenus> Mansonia uniformis Mimomyia Mimomyia <genus> Mimomyia Mimomyia <subgenus> Mimomyia chamberlaini Aedes sollicitans Ochlerotatus (Ochlerotatus) sollicitans eastern salt marsh mosquito eastern saltmarsh mosquito Ochlerotatus sollicitans Enterocytozoon bieneusi Laurasiatheria Euarchontoglires Rodents and rabbits Glires Anthropoidea Simiiformes "Pseudomonas stanieri" Mandel 1966 Achromobacter sewerinii Achromobacter stutzeri Bacillus denitrificans II Bacillus nitrogenes Bacillus stutzeri Pseudomonas perfectomarina Pseudomonas perfectomarina (ex ZoBell and Upham 1944) Baumann et al. 1983 Pseudomonas stutzeri (Lehmann and Neumann 1896) Sijderius 1946 (Approved Lists 1980) Stutzerimonas perfectomarina Stutzerimonas stutzeri Coronavirus OC43 HCoV-OC43 Human coronavirus (strain OC43) Human coronavirus strain OC43 Human coronavirus OC43 Aedes pseudoscutellaris Culex brevipalpis Heizmannia Heizmannia <genus> Heizmannia discrepans Verrallina Verrallina <genus> Neomacleaya indicus Verrallina indica Fredwardsius vittatus Aedes vittatus Armigeres Armigeres <subgenus> Leicesteria Anopheles philippinensis Myzomyia rossi var. indefinitus Anopheles indefinitus Pseudomonas RNA homology group II Burkholderia Kingella tetrapods Tetrapoda amniotes Amniota Theria Theria <mammals> Pseudoficalbia Uranotaenia recondita Uranotaenia Uranotaenia <subgenus> Orthopodomyia anopheloides Uranotaenia atra Malaya genurostris Uranotaenia bicolor Anopheles splendidus Heizmannia chandi Anopheles aitkenii Tripteroides aranoides Culex minor Diapsida diapsids Sauria Leucophaeus Aedes (Ochlerotatus) communis Aedes communis Culex communis Ochlerotatus (Ochlerotatus) communis Ochlerotatus communis Aedes abserratus Ochlerotatus abserratus Aedes aurifer Ochlerotatus aurifer Aedes cantator Ochlerotatus cantator Aedes excrucians Ochlerotatus excrucians Aedes taeniorhynchus Culex taeniorhynchus Ochlerotatus taeniorhynchus Culex cilliata Psorophora ciliata Culiseta morsitans Culiseta minnesotae Culiseta melanura Coquillettidia Coquillettidia perturbans Megarhinus septentrionalis Toxorhynchites rutilus septentrionalis Human bocavirus Entamoebida Entamoebidae Fungi/Metazoa group opisthokonts Opisthokonta Culiseta annulata Bilateria Ancylostomatidae Protostomia Neoptera Phlebotomus (Larroussius) tobbi Phlebotomus tobbi carnivores Carnivora alveolates Alveolata Cricetidae Muroidea Neotominae Streptococcus sp. (group C) Streptococcus sp. group C group C streptococcus Streptococcus sp. 'group C' Rickettsieae Anopheles paludis Anopheles (Anopheles) tenebrosus Anopheles coustani tenebrosus Anopheles tenebrosus Anopheles (Anopheles) ziemanni Anopheles coustani ziemanni Anopheles ziemanni Culex fuscocephala Aedes malayi Culex malayi Culex hutchinsoni Culiciomyia minutissimus Culex minutissimus Culex pallidothorax Rhinoskusea Aedes wardi Ochlerotatus wardi Taeniorhynchus whitmorei Culex whitmorei Macleaya Macleaya <mosquitos> Acarus cajennensis Cayenne tick Amblyomma cajennense Gulf Coast tick Amblyomma maculatum Anocentor Dermacentor Dermacentor andersoni American dog tick Dermacentor variabilis Rhipicephalus Rhipicephalus <genus> Ixodes sanguineus Rhipicephalus rutilus brown dog tick Rhipicephalus sanguineus Anopheles melas Anopheles quadriannulatus Anopheles sundaicus Human rotavirus 4 Human rotavirus G4 Human rotavirus serotype 4 Human rotavirus serotype G4 Human serotype G4 rotavirus Rotavirus serotype G4 Rotavirus G4 Enterobacter cloacae complex Pecora Mus tanezumi Oriental house rat Rattus brunneusculus Tanezumi rat Rattus tanezumi Anopheles benarrochi B Trichuris human whipworm Trichuris trichiura Motacillidae malaria parasite P. ovale Plasmodium ovale Culex pluvialis Influenza A 2009 H1N1 swine influenza virus Streptococcus sp. (group A) group A streptococci group A streptococcus Streptococcus sp. 'group A' Mycobacteroides abscessus "Mycobacterium abcessus" Moore and Frerichs 1953 "Mycobacterium chelonei" (sic) Bergey et al. 1923 Mycobacterium abscessus Mycobacterium chelonae subsp. abscessus Mycobacterium chelonei subsp. abscessus Mycobacteroides abscessus marsh rice rat Oryzomys palustris Chikungunya virus Nyctea scandiaca Snowy owl Strix scandiaca Bubo scandiacus Streptococcus pneumoniae str. D39 Streptococcus pneumoniae strain D39 Streptococcus pneumoniae D39 Shigella flexneri 1a Culicoides (Avaritia) chiopterus Culicoides chiopterus unclassified Rotavirus A Anopheles annulipes Aedes iyengari Aedes lugubris Verrallina lugubris Aedes portonovoensis Ochlerotatus portonovoensis Feliformia Caniformia Anopheles (Cellia) rampae Anopheles cf. maculatus 'form K' Anopheles maculatus group species K Anopheles sp. 'maculatus group K' Anopheles rampae Culex pipiens f. pipiens Culex pipiens pipiens Culex restuans Culex salinarius Medicago sativa subsp. sativa alfalfa lucerne Medicago sativa Brown anole Norops sagrei Anolis sagrei Astroviridae Rubulavirus Thraupini tanagers Thraupidae Sigmodontinae Stenotrophomonas Stenotrophomonas Pseudomonas beteli Pseudomonas maltiphilia Pseudomonas maltophilia Stenotrophomonas africana Xanthomonas maltiphilia Xanthomonas maltophilia Stenotrophomonas maltophilia Anopheles (Cellia) leucosphyrus Anopheles leucosphyrus dirus species complex Myzomyia longipalpis Anopheles longipalpis Cronobacter Anopheles atroparvus Anopheles labranchiae Anopheles maculipennis Anopheles messeae Shigella flexneri serotype 1b Shigella flexneri 1b Plasmodium Plasmodium (Plasmodium) biting midges no-see-ums Ceratopogonidae Culicoides punkies Culicoides <genus> Culicoides punctatus Culicoidea Chironomoidea Rhodnius robustus complex Rhodnius robustus I Rhodnius robustus II Rhodnius robustus III Rhodnius robustus IV Culex univittatus Pneumocystis jirovecii Culex mimeticus Hematozoa Vivier 1982 Aconoidasida Eimeriorina eastern woodrat Neotoma floridana Hesperomys gossypinus cotton mouse Peromyscus gossypinus Sigmodon hispiedis hispid cotton rat Sigmodon hispidus Culex erraticus Culex erythrothorax Culex nigripalpus Culex (Melanoconion) pilosus Culex pilosus Culex territans Culex (Lutzia) tigripes Culex tigripes Lutzia (Metalutzia) tigripes Lutzia tigripes Culex (Culex) torrentium Culex torrentium Shigella flexneri 3a Shigella flexneri 5a Shigella flexneri 6 Shigella flexneri Y Human rotavirus (serotype G / strain 116E) Human rotavirus 9 Human rotavirus A G9 Human rotavirus G9 Human rotavirus serotype 9 Rotavirus G9 Rhipicephalinae Anopheles aquasalis Shigella flexneri serotype 2a Shigella flexneri 2a Barn swallow Rauchschwalbe Hirundo rustica American malaria mosquito Anopheles paulistensis Nyssorhynchus darlingi Anopheles darlingi Nyssorhynchus konderi Anopheles konderi Nyssorhynchus oswaldoi Anopheles oswaldoi Shigella flexneri 3b Culicomorpha Anophelinae Culicinae Gracula melanocephala noisy miner Manorina melanocephala Cyclospora Anopheles Anopheles <subgenus> Anopheles Anopheles <series> maculipennis group maculipennis subgroup Sarcobium Legionella punctipennis group freeborni species complex maculipennis species complex Cellia Neocellia Neomyzomyia Pyretophorus leucosphyrus subgroup punctulatus species complex gambiae species complex Nyssorhynchus albimanus section argyritarsis section oswaldoi series oswaldoi group oswaldoi subgroup Chilomastix Aedes ochraceus Lasioconops poicilipes Culex poicilipes Dikarya Eurotiomycetidae Anopheles campestris Anthus pratensis Vibrio cholerae serogroup O139 Vibrio cholerae O139 Toxorhynchites Aedes punctor Ochlerotatus punctor Picornavirales Entamoeba dispar Acinetobacteraceae Branhamaceae Moraxellaceae Acinetobacter Acinetobacter Anopheles pseudopunctipennis Acinetobacter genomosp. 2 Acinetobacter genomospecies 2 Bacterium anitratum Acinetobacter baumannii Acinetobacter genomosp. 1 Acinetobacter genomospecies 1 Micrococcus calcoaceticus Moraxella calcoacetica Neisseria winogradskyi Acinetobacter calcoaceticus Chilomastix mesnili Borrelia miyamotoi Diplobacillus Moraxella Fungal organism Mycota fungi Fungi Pneumocystis Bacillus duplex non liquefaciens Moraxella (subgen. Moraxella Lwoff 1939) nonliquefaciens (Scarlett 1916) Bovre 1984 Moraxella nonliquefaciens Pseudomonas luteola Chryseomonas luteola Chryseomonas polytricha group Ve-1 Pseudomonas luteola Branhamella catarrhalis Mikrokkokus catarrhalis Moraxella (subgen. Branhamella Catlin 1970) catarrhalis (Frosch and Kolle 1896) Bovre 1984 Moraxella catarrhalis Vitreoscillaceae Neisseriaceae Lichenostomus penicillatus Meliphaga penicillata White-plumed honeyeater Ptilotula penicillata "Merismopedia" Zopf 1885 Gonococcus Neisseria Isospora belli Cystoisospora belli trumperter swan Cygnus buccinator Herpestes auropunctata Herpestes auropunctatus small Indian mongoose Urva auropunctata Neisseria meningitidis Diplokokkus intracellularis meningitidis Micrococcus intracellularis Micrococcus meningitidis Micrococcus meningitidis cerebrospinalis Neisseria weichselbaumii Neisseria meningitidis Uranotaenia mashonaensis Anopheles (Cellia) baimaii Anopheles dirus D Anopheles baimaii Fringilla domestica Haussperling House sparrow Passer domesticus ascomycete fungi ascomycetes sac fungi Ascomycota Endomycetales budding yeasts Saccharomycetales Norovirus genogroup GII.4 Norovirus GII.4 'Candida glycerinogenes' Candida acidothermophilum Candida krusei Issatchenkia orientalis Saccharomyces krusei Pichia kudriavzevii crucians subgroup Anopheles bradleyi Anopheles earlei Anopheles walkeri Aedes (Neomelaniconion) mcintoshi Aedes mcintoshi Aedes (Aedimorphus) cumminsii Aedes cumminsii Histoplasma Ajellomyces capsulatus (Kwon-Chung) McGinnis & Katz, 1979 Cryptococcus capsulatus Emmonsiella capsulata Histoplasma capsulatum Lepus palustris marsh rabbit Sylvilagus palustris Alcaligenaceae Aspergillus Aspergillus parasiticus Tyto alba guttata Aedes (Finlaya) notoscriptus Aedes (Rampamyia) notoscriptus Ochlerotatus notoscriptus Rampamyia notoscriptus Aedes notoscriptus Ancylostoma duodenale human pinworm Enterobius vermicularis Necator New World hookworm Necator americanus Anopheles (Cellia) pseudojamesi Anopheles ramsayi Anopheles pseudojamesi Bordetella Culex pipiens complex Bacterium tussis-convulsivae Haemophilus pertussis Hemophilus pertussis Microbe de la coqueluche Bordetella pertussis Cryptococcus Filobasidiella Cryptococcus <basidiomycete fungi> Culex (Culex) coronator Culex coronator Deinocerites cancer Culex Culex <subgenus> Culiciomyia Eumelanomyia Lutzia Lutzia <mosquitos> Maillotia Melanoconion Aedimorphus Stegomyia Finlaya Mucidus Neomelaniconion Ochlerotatus Ochlerotatus <subgenus> Sabethini Culicini Megarhinus rutilus Toxorhinchites rutilus Toxorhynchites rutilus Tripteroides Tripteroides <genus> triannulatus group Enterobacteraceae enterobacteria gamma-3 proteobacteria Enterobacteriaceae "Salmonella paratyphi-A" (Brion and Kaiser 1902) Castellani and Chalmers 1919 Bacterium paratyphi Bacterium paratyphi typhus A Salmonella choleraesuis choleraesuis (serotype paratyphi A) Salmonella choleraesuis subsp. choleraesuis serovar Paratyphi A Salmonella paratyphi Salmonella paratyphi A Salmonella paratyphi-a Salmonella enterica subsp. enterica serovar Paratyphi A Citrobacter Levinea Citrobacter Culex modestus Citrobacter freundii Bacterium freundii Citrobacter ballerupensis Escherichia freundii Salmonella ballerup Salmonella hormaechei the Ballerup group of bacteria the Bethesda group of bacteria Citrobacter freundii Enterobacter "Aerobacter" Hormaeche and Edwards 1958 Cloaca Enterobacter Torulopsis Candida Candida albicans Candida albicans var. stellatoidea Candida stellatoidea Dematium albicans Endomyces albicans Monilia albicans Monilia stellatoidea Myceloblastanon albicans Mycotorula albicans Oidium albicans Parasaccharomyces albicans Procandida albicans Procandida stellatoidea Saccharomyces albicans Syringospora albicans Candida albicans Aerobacter aerogenes Enterobacter aerogenes Klebsiella mobilis Klebsiella aerogenes Aerobacter cloacae Bacillus cloacae Bacterium cloacae Cloaca cloacae Enterobacter cloacae Toxostoma Carbo auritus double-crested cormorant Phalacrocorax auritus Escherichia Culex theileri Escherichia coli Bacillus coli Bacterium coli Bacterium coli commune E. coli Enterococcus coli Escherichia/Shigella coli Escherichia coli Anser sandvicensis Branta sandvicensis Culex nebulosus Human rotavirus P6 Isospora Mucidus alternans Ochlerotatus alternans Aedes alternans Klebsiella Calymmatobacterium Donovania Hyalococcus Klebsiella Klebsiella oxytoca Bacillus oxytocus perniciosus Klebsiella oxytoca Trichomonas Pentatrichomonas hominis Klebsiella pneumoniae 'Klebsiella aerogenes' (Kruse) Taylor et al. 1956 Bacillus pneumoniae Bacterium pneumoniae crouposae Hyalococcus pneumoniae Klebsiella pneumoniae aerogenes Klebsiella pneumoniae Giardia Centropus Giardia duodenalis Giardia lamblia Lamblia intestinalis Giardia intestinalis Entamoeba Entamoeba histolytica Anopheles barbirostris subgroup clade III Citrobacter genomospecies 6 Citrobacter braakii apicomplexans Apicomplexa Eimeriids Eimeriidae Cryptosporidium Cryptosporidium parvum Plasmodium Toxostoma rufum albitarsis series albitarsis group Nyssorhynchus albitarsis Anopheles albitarsis Nyssorhynchus braziliensis Anopheles braziliensis Nyssorhynchus deaneorum Anopheles deaneorum Nyssorhynchus marajoara Anopheles marajoara Laticorn Arribalzagia Myzorhynchus Nyssorhynchus triannulatus Anopheles triannulatus Avaritia Culicoides Culicoides <subgenus> Liquidobacterium Proteus Proteus <enterobacteria> Plasmodium (Laverania) falciparum malaria parasite P. falciparum Plasmodium falciparum Proteus mirabilis Ardea caledonica Nycticorax caledonicus Haemamoeba vivax Haemamoeba vivax Grassi and Feletti, 1890 malaria parasite P. vivax Plasmodium vivax Plasmodium malariae Aedes (Finlaya) koreicus Aedes (Hulecoeteomyia) koreicus Ochlerotatus koreicus Aedes koreicus Theileria microti Babesia microti Septata intestinalis Encephalitozoon intestinalis Salmonella Aedes mascarensis leucosphyrus species complex Anopheles (Cellia) balabacensis Anopheles balabacensis barbirostris group barbirostris subgroup coustani group hyrcanus group lesteri subgroup umbrosus group Anopheles bancroftii Myzomyia funestus group minimus group Anopheles flavirostris Anopheles karwari Anopheles kochi Anopheles longirostris Anopheles subpictus Anopheles tessellatus annularis group Anopheles annularis group Anopheles annularis Anopheles farauti 2 Anopheles farauti No.2 Anopheles hinesorum Anopheles farauti 4 Anopheles farauti No.4 Anopheles farauti No. 4 Salmonella cholerae-suis subsp. cholerae-suis Salmonella choleraesuis subsp. choleraesuis Salmonella enterica I Salmonella enterica subsp. I Salmonella enterica subsp. Subsp. I Salmonella enterica subsp. Subsp. Ixxx Salmonella enterica subsp. enterica Larroussius Paraphlebotomus Sergentomyia Sergentomyia <genus> Sergentomyia minuta Phlebotomus (Larroussius) perfiliewi Phlebotomus perfiliewi Chryseobacterium Planobacterium Chryseobacterium Dermacentor occidentalis Apansporoblastina Serratia Serratia Serratia <enterobacteria> Serratia liquefaciens Aerobacter liquefaciens Serratia liquefaciens Serratia marcescens Bacillus marcescens Serratia marcescens subsp. marcescens Serratia marcescens subsp. sakuensis Serratia marcescens flatworm flatworms Platyhelminthes CDC Enteric Group 17 Enterobacter muelleri Enterobacter asburiae Schistosoma Schistosoma mansoni Schistosoma haematobium Shigella Cyclophyllidea Taenia Shigella boydii Hymenolepididae rat tapeworm Hymenolepis diminuta Bacillus dysenteriae Bacillus dysentericus Bacillus shigae Eberthella dysenteriae Escherichia/Shigella dysenteriae Shigella shigae Shigella dysenteriae Escherichia flexneri Escherichia/Shigella flexneri Shigella paradysenteriae Shigella flexneri Nemata nematode nematodes roundworm roundworms Nematoda African malaria mosquito Anopheles funestus Anopheles vaneedeni Rhabditida Bacterium sonnei Shigella sonnei Strongyloides Strongyloides stercoralis Ascaris common roundworm Ascaris lumbricoides Spirurida Spirurina Yersinia Yersinia <enterobacteria> Bacterium enterocoliticum Yersinia enterocolitica Anopheles culicifacies species A Anopheles culicifacies A Anopheles culicifacies species B Anopheles culicifacies B Anopheles culicifacies species C Anopheles culicifacies C culicifacies species complex Aeromonas ZIKV Zika virus Aeromonas dourgesi Aeromonas hydrophila (Chester 1901) Stanier 1943 (Approved Lists 1980) Aeromonas liquefaciens Bacillus hydrophilus fuscus Bacterium hydrophilum Proteus hydrophilus Proteus ichthyosmius Pseudomonas hydrophila Aeromonas hydrophila Aedes camptorhynchus Ochlerotatus (Ochlerotatus) camptorhynchus Ochlerotatus camptorhynchus Norovirus genogroup GI.1 Norovirus GI.1 Borrelia burgdorferi group Borrelia burgdorferi sensu lato Lyme Disease Borrelia Borreliella Australorbis glabratus Planorbis glabratus bloodfluke planorb Biomphalaria glabrata Coquillettidia metallica Beneckea Listonella Microspira Pacinia Vibrio Aedes flavescens Ochlerotatus flavescens Aedes dorsalis Ochlerotatus dorsalis Orthopodomyia signifera arthropods Arthropoda Bacillo virgola del Koch Bacillus cholerae Bacillus cholerae-asiaticae Kommabacillus Liquidivibrio cholerae Microspira comma Pacinia cholerae-asiaticae Spirillum cholerae Spirillum cholerae-asiaticae Vibrio albensis Vibrio cholera Vibrio cholerae biovar albensis Vibrio cholerae bv. albensis Vibrio cholerae-asiaticae Vibrio comma Vibrio cholerae Mansonia fuscopennata Coquillettidia fuscopennata Coquillettidia maculipennis Mansonia africana Oculeomyia Culex annulioris Beneckea parahaemolytica Oceanomonas parahaemolytica Pasteurella parahaemolytica Vibrio parahaemolyticus Streptococcus anginosus group 'Vibrio eltor' Vibrio cholerae O1 biovar eltor Vibrio cholerae biovar El Tor Vibrio cholerae biovar eltor Vibrio eltor Vibrio cholerae O1 biovar El Tor Aedes metallicus Anopheles farauti sensu stricto Anopheles farauti Franklin's gull Larus franklini Larus franklinii Larus pipixcan Leucopheus pipixcan Leucophaeus pipixcan hard ticks hardbacked ticks scale ticks Ixodidae Coronavirus Coronavirus group 1 Group 1 species Alphacoronavirus Coronavirus Coronavirus group 2 Group 2 species Betacoronavirus Aponomma Amblyomma Haemalastor americanus Lone Star tick Amblyomma americanum Ixodes Ixodes dammini black-legged tick blacklegged tick deer tick shoulder tick Ixodes scapularis Aedes w-albus Culex ethiopicus Culex bitaeniorhynchus C 27 Group Fergusonia Pleisomonas Plesiomonas Aeromonas shigelloides Fergusonia shigelloides Pleisomonas shigelloides Plesiomonas shigelloides corrig. (Bader 1954) Habs and Schubert 1962 (Approved Lists 1980) Plesiomonas shigelloides Anopheles rivulorum Culiseta inornata Culex declarator Human rotavirus G8 Human rotavirus serotype G8 Rotavirus G8 Pasteurellaceae Nematocera nonbiting midges Chironomidae mosquitos Culicidae Aedes Aedes <genus> Balantidium coli Neobalantidium coli Paramecium coli Balantioides coli Aedes (Stegomyia) aegypti Stegomyia aegypti yellow fever mosquito Aedes aegypti Asian tiger mosquito Stegomyia albopicta forest day mosquito Aedes albopictus Aedes simpsoni Aedes triseriatus Ochlerotatus triseriatus Culex vexans Aedes vexans Anopheles Anopheles <genus> African malaria mosquito Anopheles gambiae S Anopheles gambiae sensu stricto Anopheles gambiae saccharomyceta common malaria mosquito Anopheles quadrimaculatus Anopheles albimanus Anopheles (Cellia) dirus Anopheles dirus sensu stricto Anopheles dirus western malaria mosquito Anopheles freeborni Anopheles hermsi Anopheles arabiensis Culex Culex <genus> Culex agilis Culex autogenicus Culex azoriensis Culex bicolor Culex bifurcatus Culex calcitrans Culex calloti Culex comitatus Culex consobrinus Culex dipseticus Culex disjunctus Culex doliorum Culex domesticus Culex erectus Culex fasciatus Culex haematophagus Culex longefurcatus Culex luteus Culex marginalis Culex melanorhinus Culex meridionalis Culex osakaensis Culex pallipes Culex phytophagus Culex quasimodestus Culex rufinus Culex rufus Culex sternopunctatus Culex thoracicus Culex torridus Culex trifurcatus Culex unistriatus Culex varioannulatus common house mosquito northern house mosquito Culex pipiens Culex fatigans Culex pipiens fatigans Culex pipiens quinquefasciatus southern house mosquito Culex quinquefasciatus Culex tarsalis Culex tritaeniorhynchus Psorophora Psorophora ferox black flies blackflies Simuliidae sand flies sandflies Phlebotominae Lutzomyia Lutzomyia <genus> Lutzomyia longipalpis Human rotavirus 1 Human rotavirus G1 Human rotavirus serotype 1 Human rotavirus serotype G1 Human rotavirus subtype G1 Rotavirus serotype G1 human serotype G1 rotavirus Rotavirus G1 Haemophilus Haemophilus Anopheles sacharovi Bacillus X Haemophilus haemolyticus Haemophilus influenzae Bacterium influenzae Coccobacillus pfeifferi Haemophilus meningitidis Influenza-bacillus Mycobacterium influenzae Haemophilus influenzae Haemophilus parainfluenzae Human rotavirus 2 Human rotavirus G2 Human rotavirus serotype 2 Human rotavirus serotype G2 Rotavirus G2 Human rotavirus 3 Human rotavirus G3 Human rotavirus serotype 3 Human rotavirus serotype G3 Rotavirus G3 Haemophilus aphrophilus Haemophilus paraphrophilus Aggregatibacter aphrophilus Haemophilus parahaemolyticus Aedes fitchii Ochlerotatus fitchii Aedes implicatus Ochlerotatus implicatus Aedes provocans Ochlerotatus provocans Aedes riparius Ochlerotatus riparius maculatus group maculatus species complex Anopheles maculatus group Anopheles maculatus nivipes species complex Anopheles (Anopheles) sinensis Anopheles sinensis Armigeres kesseli American widgeon American wigeon Anas americana Mareca americana alpha-1 proteobacteria rickettsias Rickettsiales Ochlerotatus incertae sedis Aedes melanimon Ochlerotatus melanimon Aedes nigromaculis Ochlerotatus nigromaculis Aedes squamiger Ochlerotatus squamiger Lutra canadensis Northern American river otter river otter Lontra canadensis Vertebrata vertebrates Vertebrata <vertebrates> Rickettsia akamushi Rickettsia orientalis Rickettsia tsutsugamushi Theileria tsutsugamushi Orientia tsutsugamushi 'Streptococcus viridans' Streptococcus viridans Burkholderia/Oxalobacter/Ralstonia group Burkholderiales "Prowazekia" Coles 1953 Bedsonia Chlamydophila Miyagawanella Rakeia Rickettsiaformis Chlamydia Capsularis Ristella Bacteroides Bacillus fragilis Bacteroides inaequalis Bacteroides incommunis Bacteroides uncatus Fusiformis fragilis Pseudobacterium fragilis Pseudobacterium inaequalis Pseudobacterium incommunis Pseudobacterium uncatum Ristella fragilis Ristella incommunis Ristella uncata Sphaerophorus inaequalis Sphaerophorus intermedius Bacteroides fragilis Salientia anurans frogs frogs & toads frogs and toads Anura Chlamydophila pneumoniae Chlamydia pneumoniae Calamita cinereus Hyla cinerea green tree frog Dryophytes cinereus Corynebacteriales Corynebacteriales Goodfellow and Jones 2015 Corynebacterineae Mycobacteriales Janke 1924 (Approved Lists 1980) Mycobacteriales Lacertilia iguanian lizards Iguania Common green iguana Lacerta igvana common iguana Iguana iguana Aedes bancroftianus Ochlerotatus bancroftianus Achromobacter xylosoxidans Achromobacter xilosoxidans Achromobacter xylosoxidans subsp. xylosoxidans Achromobacter xylosoxydans Alcaligenes denitrificans subsp. xylosoxydans Alcaligenes xylosoxidans Alcaligenes xylosoxidans subsp. xylosoxidans Alcaligenes xylosoxydans Achromobacter xylosoxidans Wyeomyia vanduzeei Wyeomyia mitchellii Phlebotomus (Larroussius) neglectus Phlebotomus neglectus Paraphlebotomus sergenti Phlebotomus (Paraphlebotomus) sergenti Phlebotomus sergenti Sergentomyia dentata Culex neavei Aedes annulipes Ochlerotatus annulipes Culiseta ochroptera Anopheles crucians Mansonia titillans Psorophora columbiae Psorophora confinnis Psorophora cyanescens Psorophora howardii Neomelaniconion lineatopenne Aedes lineatopennis Bananaquit Certhia flaveola Coereba flaveola Culex thriambus avian birds Aves Burkholderia cepacia complex Burkholderia multivorans Burkholderia cepacia genomovar II Burkholderia multivorans Eurasian skylark Alauda arvensis Neognathae waterfowl Anatidae Branta Anas canadensis Anser canadensis Canada goose Branta canadensis swans Cygnus Anas olor mute swan Cygnus olor herons Ardeidae night herons Nycticorax Ardea nycticorax black-crowned night-heron Nycticorax nycticorax shorebirds and others Charadriiformes gull gulls Laridae Larus great black-backed gull Larus marinus pigeons Columbidae Columba Columba domestica Columba livia domestica carrier pigeon domestic pigeon rock dove rock pigeon Columba livia Columba palumbus landfowls Galliformes turkeys Phasianidae Francolinus Gallus domesticus Gallus gallus domesticus Phasianus gallus bantam chicken chickens Gallus gallus Bacillus typhi Bacterium (subgen. Eberthella) typhi Salmonella choleraesuis serovar Typhi Salmonella choleraesuis typhi Salmonella enterica ser. typhi Salmonella enterica serotype Typhi Salmonella enterica serovar Typhi Salmonella typhi Salmonella enterica subsp. enterica serovar Typhi Aedes campestris Ochlerotatus campestris Acinetobacter calcoaceticus/baumannii complex Bacillus/Lactobacillus/Streptococcus group Firmibacteria Bacilli Anopheles (Celia) squamosus Anopheles squamosus Culex (Culex) antennatus Culex antennatus song birds Passeriformes Australian magpie Cracticus tibicen Gymnorhina tibicen Enterobacteriaceae and related endosymbionts Enterobacteriaceae group Enterobacteriales gamma-3 proteobacteria Enterobacterales honeyeaters Meliphagidae Cetartiodactyla even-toed ungulates whales, hippos, ruminants, pigs, camels etc. Artiodactyla Amsel Eurasian blackbird blackbird Turdus merula Ibis, herons and pelicans Pelecaniformes parrots and others Psittaciformes Marsupialia marsupials Metatheria American opossums opossums Didelphidae Didelphis brush-tailed possums Trichosurus Placentalia eutherian mammals placental mammals placentals Eutheria nine-banded armadillo Dasypus novemcinctus Anopheles aconitus Anopheles varuna minimus species complex Giardia duodenalis assemblage A Giardia lamblia (assemblage A) Giardia intestinalis assemblage A Culex perexiguus Phlebotomus (Adlerius) simici Phlebotomus simici Phlebotomus (Paraphlebotomus) alexandri Phlebotomus alexandri Sergentomyia fallax New World monkeys monkey monkeys Platyrrhini Anaplasma phagocytophila Cytoecetes bovis Cytoecetes phagocytophila Ehrlichia equi Ehrlichia phagocytophila (Foggie 1949) Philip 1962 (Approved Lists 1980) Ehrlichia sp. 'HGE agent' HGE agent Rickettsia phagocytophila ovis agent of human granulocytic ehrlichiosis human granulocytic Ehrlichia Anaplasma phagocytophilum Sapporo-like viruses Sapovirus Burkholderia cenocepacia Burkholderia cepacia genomovar III Burkholderia cenocepacia human Homo sapiens dog, coyote, wolf, fox Canidae Canis canis Canis domesticus Canis familiaris dog dogs Canis lupus familiaris Canis vulpes red fox silver fox Vulpes vulpes Ursus lotor northern raccoon raccoon Procyon lotor cat family Felidae Felis domesticus Felis silvestris catus cat cats domestic cat Felis catus "Bacteroidota" Whitman et al. 2018 BCF group Bacteroides-Cytophaga-Flexibacter group Bacteroidetes CFB group CFB group bacteria Cytophaga-Flexibacter-Bacteroides phylum Sphingobacteria Bacteroidota Equus przewalskii f. caballus Equus przewalskii forma caballus domestic horse equine horse Equus caballus Aedes infirmatus Ochlerotatus infirmatus boars pigs Suidae Shigella dysenteriae 1 Shigella flexneri 4a deer Cervidae Cervus alces Eurasian elk elk european elk, moose Alces alces white-tailed deer Odocoileus virginianus Odocoileinae Bovidae Loxia cardinalis northern cardinal Cardinalis cardinalis Poliovirus type 2 Sabin vaccine strain Human poliovirus 2 strain Sabin Bos bovis Bos primigenius taurus bovine cattle cow dairy cow domestic cattle domestic cow ox oxen Bos taurus Capra aegagrus hircus domestic goat goat goats Capra hircus Ovis ammon aries Ovis orientalis aries Ovis ovis domestic sheep lambs sheep wild sheep Ovis aries Oryx Caprinae rabbits and hares Leporidae European hare Lepus capensis europaeus Lepus europaeus European rabbit Japanese white rabbit Lepus cuniculus domestic rabbit rabbit rabbits Oryctolagus cuniculus Sylvilagus Toxostoma cf. curvirostre PS-1 Toxostoma curvirostre PS-1 Toxostoma curvirostre Lepus sylvaticus floridanus eastern cottontail Sylvilagus floridanus rodent rodents Rodentia 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. ABO Hemolytic Disease of Newborn ABO Hemolytic Disease of the Newborn ABO Isoimmunization Hemolytic Disease due to ABO Isoimmunization ABO Hemolytic Disease of the Newborn Mixed Commensal Flora The presence of more than one fungal and/or bacterial organism in a culture. MIXED FLORA Mixed Flora Mixed Flora Elective abortions count A measurement of the total number of induced abortions experienced by a female subject. INABORTN Number of Induced Abortions Number of Induced Abortions Spontaneous abortions count 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. Number of Spontaneous Abortions SPABORTN Number of Spontaneous Abortions Any rod-shaped, Gram-negative, non-spore forming, motile or non-motile bacteria which can ferment lactose with the production of acid and gas. COLIFORM BACTERIA Coliform Bacteria Coliform Bacteria Gestational age at delivery The gestational age of the subject at birth. GSTABRTH Gestational Age at Birth weeks gestation at birth weeks_gestation_at_birth Gestational Age at Birth Edinburgh postnatal depression scale A 10-item, self-rating questionnaire designed to screen postpartum women for indications of depression. EPDS Edinburgh Postnatal Depression Scale Edinburgh Postnatal Depression Scale (EPDS) Edinburgh Postnatal Depression Scale Fundal height A measurement of the distance between the pubic symphysis and the top of the palpable uterus. FUNDHT Fundal Height Fundal Height Diagnostic imaging Any method that uses a visual display of structural or functional patterns of organs or tissues for diagnostic evaluation. Diagnostic Imaging Medical Imaging Diagnostic Imaging Severe Acute Respiratory Infection (SARI) A respiratory infectious disorder that leads to an acute illness that requires medical attention. SARI Severe Acute Respiratory Infection Severe Acute Respiratory Infection Reference A note acknowledging a source of information or quoting a passage. Bibliographic Reference Reference bibliographicDesignation Reference 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) IV Fluid Intravenous Fluid IV Fluid Protocol deviations 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) DVTERM Deviation PROTOCOL DEVIATION Protocol Deviation protocol deviation Protocol Deviation A subtype of Staphylococcus characterized by an inability to produce free plasma coagulase. CNS COAGULASE NEGATIVE STAPHYLOCOCCUS Coagulase-Negative Staphylococcus Coagulase-Negative Staphylococcus Bed time Beginning hour of sleep. At Bedtime Bedtime HS Hour Of Sleep QHS hora somni Hour Of Sleep Trimester A period of three months; especially one of the three three-month periods into which human pregnancy is divided. Trimester Trimester 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. Rhinovirus Rhinovirus Child 1 birth complications The development of a problematic medical situation that occurs concurrently with the birth of a neonate. Birth Complication Birth Complication Visit number The numerical identifier of the visit. Visit Number visit number visit_number Visit Number Given birth year The year in which a person was born. BRTHYR BRTHYY Birth Year year of birth year_of_birth Birth Year 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. THICK SMEAR Thick Smear Technique Thick Smear Technique 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. THIN SMEAR Thin Smear Technique Thin Smear Technique 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. Alpha-Hemolytic Streptococcus STREPTOCOCCUS ALPHA-HEMOLYTIC Alpha-Hemolytic Streptococcus 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. Beta-Hemolytic Streptococcus STREPTOCOCCUS BETA-HEMOLYTIC Beta-Hemolytic Streptococcus A non-taxonomic grouping of beta hemolytic species within the Streptococcus genus that are assigned to the F group. BETA STREPTOCOCCUS, GROUP F Beta Streptococcus Group F Beta Streptococcus Group F Pregnancy outcome Findings observed at the end of a pregnancy. PRGOUT Pregnancy Outcome pregnancy outcome pregnancy_outcome Pregnancy Outcome Fetal heart tones The sounds of the fetal heart. Fetal Heart Tone Fetal Heart Tone Abdominal pain/contractions A tightening of the involuntary smooth muscles of the uterus. Uterine Contraction Uterine Contraction Vaginal bleeding Hemorrhage from the vagina that may range from light spotting to heavy flow during pregnancy. Vaginal Bleeding during Pregnancy Vaginal Bleeding during Pregnancy Adverse events 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. AE adverse reaction adverse event A surgery where incisions are made through a woman's abdomen and uterus to deliver her baby. cesarean section caesarean section Cohort 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. Yongqun He WEB: http://www.uptodate.com/contents/glossary-of-common-biostatistical-and-epidemiological-terms cohort study design Randomized controlled/clinical trial A study design in which patients are randomly assigned to two or more interventions. Yongqun He WEB: http://www.uptodate.com/contents/glossary-of-common-biostatistical-and-epidemiological-terms randomized controlled trial design 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 Person: Jie Zheng summing data transformation http://dictionary.reference.com/browse/summing PRISM 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. Tracker:https://github.com/obcs/obcs/issues/7 Person: Jie Zheng Jie Zheng PRISM sum value A material entity that is bearer of a medication role. Person: Chris Stoeckert, Jie Zheng Penn Group medication material Buffy coat sample 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. Person: Jie Zheng, Chris Stoeckert http://en.wikipedia.org/wiki/Buffy_coat buffy coat specimen Blood sample volume 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 OBIB NCI BBRB blood specimen volume 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). Alice Nzinga cross sectional study design planned process 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. Bjoern Peters branch derived 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) planned process 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 biological feature identification objective reference substance role 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 reference substance OBI reference substance role chromatography column 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. Frank Gibson http://en.wikipedia.org/wiki/Column_chromatography open tracker https://sourceforge.net/tracker/index.php?func=detail&aid=2881353&group_id=177891&atid=886178 chromatography column 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. PERSON: Alan Ruttenberg processed material chromatography device A device that facilitates the separation of mixtures. The function of a chromatography device involves passing a mixture dissolved in a "mobile phase" through a stationary phase, which separates the analyte to be measured from other molecules in the mixture and allows it to be isolated. Frank Gibson chromatography instrument http://en.wikipedia.org/wiki/Chromatography open tracker https://sourceforge.net/tracker/index.php?func=detail&aid=2881353&group_id=177891&atid=886178 chromatography device mass spectrometer 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 Frank Gibson http://en.wikipedia.org/wiki/Mass_spectrometry mass spectrometer Investigation type investigation Lung cancer investigation using expression profiling, a stem cell transplant investigation, biobanking is not an investigation, though it may be part of an investigation a planned process that consists of parts: planning, study design execution, documentation and which produce conclusion(s). Bjoern Peters OBI branch derived Could add specific objective specification Following OBI call November 2012,26th: it was decided there was no need for adding "achieves objective of drawing conclusion" as existing relations were providing equivalent ability. this note closes the issue and validates the class definition to be part of the OBI core editor = PRS study investigation 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") GROUP: Role Branch OBI Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term. evaluant role Laboratory test 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. PlanAndPlannedProcess Branch measuring scientific observation OBI branch derived study assay any method assay sample preparation for assay A sample_preparation_for_assay is a protocol_application including material_enrollments and biomaterial_transformations. definition_source: OBI. PlanAndPlannedProcess Branch study OBI branch derived sample preparation for assay culture medium A growth medium or culture medium is a substance in which microorganisms or cells can grow. Wikipedia, growth medium, Feb 29, 2008 a processed material that provides the needed nourishment for microorganisms or cells grown in vitro. changed from a role to a processed material based on on Aug 22, 2011 dev call. Details see the tracker item: http://sourceforge.net/tracker/?func=detail&aid=3325270&group_id=177891&atid=886178 Modification made by JZ. Person: Jennifer Fostel, Jie Zheng OBI culture medium reagent role 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 reagent 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 material processing A cell lysis, production of a cloning vector, creating a buffer. A planned process which results in physical changes in a specified input material PERSON: Bjoern Peters PERSON: Frank Gibson PERSON: Jennifer Fostel PERSON: Melanie Courtot PERSON: Philippe Rocca Serra material transformation OBI branch derived 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 OBI 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 principal investigator role a responsible party role played by a person responsible for the overall conduct of a study Person: Jennifer Fostel principal investigator 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 specimen 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. GROUP: Role Branch OBI specimen role Experimental intervention design 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. Philppe Rocca-Serra OBI branch derived intervention design filter paper A device manufacture with the intent to provide a porous unsized paper used for filtering. Frank Gibson sep:00107 filter paper study group role 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 Jennifer Fostel study group population 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 population imaging assay An assay that produces a picture of an entity. PlanAndPlannedProcess Branch OBI branch derived imaging assay 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 OBI chromatin immunoprecipitation investigation agent role The person perform microarray experiments and submit microarray results (including raw data, processed data) with experiment description to ArrayExpress. A role borne by an entity and that is realized in a process that is part of an investigation in which an objective is achieved. These processes include, among others: planning, overseeing, funding, reviewing. Implementing a study means carrying out or performing the study and providing reagents or other materials used in the study and other tasks without which the study would not happen. Philly2013: Historically, this role would have been borne only by humans or organizations. However, we now also want to enable representing investigations run by robot scientists such as ADAM (King et al, Science, 2009) GROUP: Role Branch investigator OBI Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term. study person role 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) investigation agent role reference subject role 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 Jennifer Fostel reference participant OBI 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 PlanAndPlannedProcess Branch OBI branch derived enzymatic cleavage 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. PERSON: Alan Ruttenberg PERSON: Bjoern Peters PERSON: Philippe Rocca-Serra PERSON: Susanna Sansone GROUP: OBI organization DNA extraction A DNA extraction is a nucleic acid extraction where the desired output material is DNA. PlanAndPlannedProcess Branch OBI branch derived DNA extraction 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. Jennifer Fostel organism feature identification objective 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. PlanAndPlannedProcess Branch OBI branch derived + wikipedia (http://en.wikipedia.org/wiki/Protocol_%28natural_sciences%29) study protocol protocol adding a material entity into a target 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. BP branch derived adding a material entity into a target analyte role 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. GROUP: Role Branch OBI Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term. 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 PERSON: Philippe Rocca-Serra eluted material OBI Bionaterial eluate material to be added role 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). Role Branch OBI 9 March 09 from discussion with PA branch material to be added role interpreting data 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 PERSON: Bjoern Peters PERSON: Jennifer Fostel Bjoern Peters drawing a conclusion based on data planning 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'. Bjoern Peters Bjoern Peters Plans and Planned Processes Branch planning mass analyzer The mass analyzer of the Voyager-DE(tm) STR Biospectrometry Workstation A Mass analyzer is a device that separates ions according to their mass-to-charge ratio. All mass spectrometers are based on dynamics of charged particles in electric and magnetic fields in vacuum where the two laws of Lorentz force law and Newton's second law of motion apply. Frank Gibson PERSON: Daniel Schober http://en.wikipedia.org/wiki/Mass_spectrometry#Mass_analyzer mass analyzer ion source 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))). Frank Gibson http://en.wikipedia.org/wiki/Mass_spectrometry#Ion_source ion source ion detector The ion detector of the Voyager-DE(tm) STR Biospectrometry Workstation An ion detector is a device that measures and records the charge induced or current produced when an ion passes by or hits a surface. Example: In a scanning instrument the signal produced in the detector during the course of the scan versus where the instrument is in the scan (at what m/Q) will produce a mass spectrum, a record of ions as a function of m/Q. Frank Gibson http://en.wikipedia.org/wiki/Mass_spectrometry#Detector ion detector light emission function A light emission function is an excitation function to excite a material to a specific excitation state that it emits light. Bill Bug Daniel Schober Frank Gibson Melanie Courtot light emission function 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. Bill Bug Daniel Schober Frank Gibson Melanie Courtot magnify function contain function A syringe, a beaker A contain function is a function to constrain a material entities location in space Bill Bug Daniel Schober Frank Gibson Melanie Courtot contain function heat function A heat function is a function that increases the internal kinetic energy of a material Bill Bug Daniel Schober Frank Gibson Melanie Courtot heat function 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. Bill Bug Daniel Schober Frank Gibson Melanie Courtot material separation function 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. Bill Bug Daniel Schober Frank Gibson Melanie Courtot synthesizing function 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 Frank Gibson filter function 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. Daniel Schober Frank Gibson Melanie Courtot power supply electricity supply function ionization function The ion source in amass spectrometer 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. Bill Bug Daniel Schober Frank Gibson Melanie Courtot http://en.wikipedia.org/wiki/Ionization ionization function 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. Daniel Schober Frank Gibson Melanie Courtot cool function image acquisition function An image acquisition function is a function to acquire an image of a material Frank Gibson image acquisition function solid support function 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 Daniel Schober Frank Gibson Melanie Courtot 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. Bill Bug Daniel Schober Frank Gibson Melanie Courtot environment control function primer role 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. GROUP: OBI BIomaterial Branch GROUP: OBI BIomaterial Branch PCR product nucleic acid template role 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 polymerase chain reaction 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. OBI Plan PCR adapted from wikipedai polymerase chain reaction reverse transcriptase enzyme and has_function some GO:0003964 (RNA-directed DNA polymerase activity) person:Melanie Courtot group:OBI reverse transcriptase 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 PERSON: Philippe Rocca-Serra extracted material GROUP: OBI Biomatrial Branch extract 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. Elisabetta Manduchi James Malone PERSON: Elisabetta Manduchi averaging objective 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. person: Melanie Courtot GROUP:OBI enzyme 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 PERSON: Jie Zheng PERSON: Philippe Rocca-Serra GROUP: OBI Biomaterial Branch polyacrylamide gel adding material objective 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 BP adding material objective genotyping assay 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. Philippe Rocca-Serra SNP analysis genotype profiling OBI Biomaterial genotyping assay analyte measurement objective 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 PERSON: Bjoern Peters PPPB branch 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 PERSON: Philippe Rocca-Serra GROUP: OBI Biomaterial Branch agarose gel analyte assay example of usage: In lab test for blood glucose, the test is the assay, the blood bears evaluant_role and glucose bears the analyte role. The evaluant is considered an input to the assay and the information entity that records the measurement of glucose concentration the output An assay with the objective to capture information about the presence, concentration, or amount of an analyte in an evaluant. Alan Ruttenberg Bjoern Peters Helen Parkinson Philippe Rocca-Serra Alan Ruttenberg Bjoern Peters Helen Parkinson OBI Planned process branch Philippe Rocca-Serra analyte assay target of material addition role 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. GROUP: Role Branch OBI 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. PERSON: Daniel Schober PERSON: Helen Parkinson PERSON: Melanie Courtot PERSON:Frank Gibson measure function material transformation objective 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. PERSON: Bjoern Peters PERSON: Frank Gibson PERSON: Jennifer Fostel PERSON: Melanie Courtot PERSON: Philippe Rocca-Serra artifact creation objective GROUP: OBI PlanAndPlannedProcess Branch material transformation objective manufacturing 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. PERSON: Bjoern Peters PERSON: Frank Gibson PERSON: Jennifer Fostel PERSON: Melanie Courtot PERSON: Philippe Rocca-Serra GROUP: OBI PlanAndPlannedProcess Branch manufacturing manufacturing objective is the objective to manufacture a material of a certain function (device) PERSON: Bjoern Peters PERSON: Frank Gibson PERSON: Jennifer Fostel PERSON: Melanie Courtot PERSON: Philippe Rocca-Serra GROUP: OBI PlanAndPlannedProcess Branch manufacturing objective mass spectrometry assay 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. Philippe Rocca-Serra Philippe Rocca-Serra mass spectrometry assay study design execution 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. branch derived 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. study design execution 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 Philippe Rocca-Serra RT-PCR reverse transcription polymerase chain reaction reverse transcribed polymerase chain reaction manufacturer role 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. GROUP: Role Branch OBI manufacturer role scattered molecular aggregate 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 PERSON: Alan Ruttenberg 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 chromatography consumable A chromatography consumable is a consumable that is used in a chromatography experiment. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01115 chromatography device chromatography consumable DNA sequencing assay Illumina (Solexa) sequencing is an example of DNA sequencing A sequencing assay which determines information on the sequence of a DNA molecule. Philippe Rocca-Serra nucleotide sequencing url:https://en.wikipedia.org/wiki/DNA_sequencing DNA sequencing assay material separation objective 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. PPPB branch PPPB branch material separation objective Urine sample urine specimen 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? urine specimen material combination 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. bp bp material combination Blood sample blood specimen blood drawn from a human for glucose assay a material entity derived from a portion of blood collected from an organism Bjoern Peters Bjoern Peters blood specimen Sample collection process specimen collection process 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. Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation. Philly2013: A specimen collection can have as part a material entity acquisition, such as ordering from a bank. The distinction is that specimen collection necessarily involves the creation of a specimen role. However ordering cell lines cells from ATCC for use in an investigation is NOT a specimen collection, because the cell lines already have a specimen role. Philly2013: The specimen_role for the specimen is created during the specimen collection process. label changed to 'specimen collection process' on 10/27/2014, details see tracker: http://sourceforge.net/p/obi/obi-terms/716/ Bjoern Peters specimen collection 5/31/2012: This process is not necessarily an acquisition, as specimens may be collected from materials already in posession 6/9/09: used at workshop specimen collection process enzyme-linked immunosorbent assay 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. IEDB ELISA IEDB enzyme-linked immunosorbent assay sample from organism a material obtained from an organism in order to be a representative of the whole 5/29: This is a helper class for now 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. sample from organism center value A data item that is produced as the output of a center calculation data transformation and represents the center value of the input data. PERSON: James Malone PERSON: Monnie McGee median center value portioning objective 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. portioning objective average value A data item that is produced as the output of an averaging data transformation and represents the average value of the input data. PERSON: James Malone PERSON: Monnie McGee arithmetic mean average value whole organism preparation 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. whole organism preparation 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 separation into different composition objective specimen collection objective 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. Bjoern Peters Bjoern Peters specimen collection objective creating a mixture of molecules in solution The production of PBS is a process with the objective to prepare a liquid solution of one or more chemicals at desired concentrations. Bjoern Peters PERSON: Helen Parkinson creating a mixture of molecules in solution immunoprecipitation 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 Philippe Rocca-Serra OBI plan and planned process branch immunoprecipitation host role 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 GROUP: Role Branch 30 Mar09 submitted by vaccine community OBI http://en.wikipedia.org/wiki/Host_(biology) host role restriction enzyme The enzyme EcoR1 cuts DNA at the canonical cleavage site CAATTG an enzyme that has a specific target cleavage sites within nucleic acids Kevin Clancy, Bjoern Peters 5/22 Need to explore if there are GO / other classes exist that capture this. We need it now for cloning experiments restriction enzyme material sample role 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. material sample role independent variable specification 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 PERSON: Alan Ruttenberg PERSON: Bjoern Peters PERSON: Chris Stoeckert experimental factor independent variable 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 factor study design independent variable material maintenance objective An objective specification maintains some or all of the qualities of a material over time. PERSON: Bjoern Peters PERSON: Bjoern Peters material maintenance objective amplified DNA Amplied DNA created by PCR DNA that has been produced in an enzymatic amplification process PERSON: Alan Ruttenberg Alan Ruttenberg amplified DNA informed consent 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. Person:Alan Ruttenberg http://clinicaltrials.gov/ct2/info/glossary#informed 2009/09/28 Alan Ruttenberg. Fucoidan-use-case informed consent process primary structure of DNA macromolecule a quality of a DNA molecule that inheres in its bearer due to the order of its DNA nucleotide residues. placeholder for SO BP et al primary structure of DNA macromolecule measurement device A ruler, a microarray scanner, a Geiger counter. A device in which a measure function inheres. GROUP:OBI Philly workshop OBI measurement device manufacturer A person or organization that has a manufacturer role manufacturer material maintenance a process with that achieves the objective to maintain some or all of the characteristics of an input material over time material maintenance record of missing knowledge 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. Bjoern Peters record of missing knowledge complementary nucleotide probe role 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 PERSON:Bjoern Peters complementary nucleotide probe role record of unknown sex 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. Bjoern Peters record of unknown sex 96-well neutralization assay A serum neutralization of viral infectivity assay which is performed in a 96-well plate. Bjoern Peters Melanie Courtot microneutralization assay 96-well neutralization assay 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. Bjoern Peters Melanie Courtot influenza neutralization assay url:http://www.virology.ws/2009/05/28/influenza-microneutralization-assay/ serum neutralization of viral infectivity assay pre-mortem specimen material obtained through a liver biopsy from a human patient a specimen that was taken from a live organism Bjoern Peters MO_705 premortem pre-mortem specimen RNA extract an extract which is the output of an extraction process in which RNA molecules are isolated from a specimen. PERSON: Chris Stoeckert PERSON: Jie Zheng Group: UPenn Group RNA extract 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. Bjoern Peters Melanie Courtot Q-PCR kinetic polymerase chain reaction qPCR quantitative real time polymerase chain reaction url:http://en.wikipedia.org/wiki/Real-time_polymerase_chain_reaction real time polymerase chain reaction assay sequence feature annotation Information about a sequence region Bjoern Peters Bjoern Peters place holder for sequence ontology term sequence feature annotation 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. Bjoern Peters Melanie Courtot RRT-PCR RT-rt PCR qRT-PCR real time reverse-transcription polymerase chain reaction assay cytometric bead array 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. IEDB Luminex assay IEDB cytometric bead array assay infectious agent is a material entity bearing the disposition to infect an organism IEDB IEDB infectious agent study intervention the part of the execution of an intervention design study which is varied between two or more subjects in the study PERSON: Bjoern Peters GROUP: OBI study intervention material separation device flow cytometer A device with a separation function realized in a planed process material separation device categorical measurement datum A measurement datum that is reported on a categorical scale. Bjoern Peters nominal mesurement datum Bjoern Peters categorical measurement datum service consumer role 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 Person:Helen Parkinson OBI service consumer role service provider role Jackson Lab provides experimental animals, EBI provides training on databases, a core facility provides access to a DNA sequencer. is a role which inheres in a person or organization and is realized in in a planned process which provides access to training, materials or execution of protocols for an organization or person PERSON:Helen Parkinson service provider role compound treatment design 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. PERSON: Bjoern Peters MO_555 compound_treatment_design compound treatment design processed specimen 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. Bjoern Peters Bjoern Peters A tissue sample that has been sliced and stained for a histology study. processed specimen container 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?) PERSON: Bjoern Peters container device 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. PERSON: Helen Parkinson instrument OBI development call 2012-12-17. device sequence data 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. Person:Chris Stoeckert GROUP: OBI sequence data administration of material to specimen Staining cells in a tissue slice with a dye. The directed combination of a material entity with a specimen. Bjoern Peters Bjoern Peters administration of material to specimen image acquisition 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. PERSON: Jie Zheng image acquisition image creation nucleic acid extract An extract that is the output of an extraction process in which nucleic acid molecules are isolated from a specimen. PERSON: Jie Zheng UPenn Group nucleic acid extract DNA extract The output of an extraction process in which DNA molecules are purified in order to exclude DNA from organellas. Person: Jie Zheng Group: UPenn group DNA extract electrophoresis system A device that moves charged particles through a medium by using an electric field induced by electrodes. PERSON: Erik Segerdell http://en.wikipedia.org/wiki/Category:Electrophoresis electrophoresis system nucleic acid sequencer An device that is used to determine the order of nucleotides in nucleic acid sequences. PERSON: Erik Segerdell PERSON: Erik Segerdell nucleic acid sequencer gel electrophoresis system An electrophoresis system in which an electric field is applied to a gel matrix PERSON: Erik Segerdell https://en.wikipedia.org/wiki/Gel_electrophoresis gel electrophoresis system protein sequencer An device that is used to determine the order of amino acids in protein sequences. PERSON: Erik Segerdell PERSON: Erik Segerdell protein sequencer Host ID individual organism identifier a CRID symbol used to distinguish one individual organism from another. PERSON: Chris Stoeckert, Jie Zheng MO_169 Individual individual organism identifier 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 MO_178 Age 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 measurement datum Age 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. PERSON:Chris Stoeckert, Jie Zheng MO_710 birth age since birth measurement datum 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. Chris Stoeckert Jie Zheng Penn Group reverse transcription polymerase chain reaction assay half life datum (t 1/2) The time it takes for 50% of a class of stochastic processes to occur. Bjoern Peters t 1/2 Bjoern Peters half life datum (t 1/2) service 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. Carlo; Matt OBI workshop San Diego 2011 service 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. PERSON: Chris Stoeckert, Jie Zheng WEB: wikipedia http://en.wikipedia.org/wiki/Cultivar http://en.wikipedia.org/wiki/Ecotype http://en.wikipedia.org/wiki/Strain_%28biology%29 selective organism creation objective 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 cultivar ecotype strain MO_9 StrainOrLine, MO_71 Ecotype, MO_124 Cultivar selectively maintained organism SNP microarray A DNA microarray used to detect polymorphisms in DNA samples Person: Helen Parkinson EFO_0002703 SNP array SNP microarray ChIP-chip by SNP array assay A ChIP-ChIP assay in which immunoprecipitated chromatin is run on a SNP array to detect polymorphism specific DNA elements in the isolated chromatin ArrayExpress production team EFO:0002764 ChIP-chip by SNP array assay 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 Group: OBI group genetic population background information 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 epigenetic modification identification objective genotyping by high throughput sequencing assay A genotyping assay that uses a high througput sequencer James Malone EFO:0002771 genotyping by high throughput sequencing assay genotyping by array assay A genotyping assay that uses an array ArrayExpress production team EFO:0002767 genotyping by array assay 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 Group: OBI group Group: OBI group genotype information species comparison design A study design that assays differences between distinct species. Person: Chris Stoeckert, Jie Zheng MO_675 species_design species comparison design 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. discussed on San Diego OBI workshop, March 2011 Person: Chris Stoeckert, Jie Zheng MO_58 Allele allele information 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. discussed on San Diego OBI workshop, March 2011 Person: Chris Stoeckert, Jie Zheng MO_605 genotype wild type allele information 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. Person: Chris Stoeckert, Jie Zheng MO_933 binding_site_identification_design protein and DNA interaction identification objective genetic characteristics information a data item that is about genetic material including polymorphisms, disease alleles, and haplotypes. Person: Chris Stoeckert, Jie Zheng 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) genetic characteristics information genotyping design A study design that classifies an individual or group of individuals on the basis of alleles, haplotypes, SNPs. Person: Chris Stoeckert, Jie Zheng MO_560 genotyping_design genotyping design strain comparison design A study design that assays differences between multiple strains, cultivars, serovars, isolates, lines from organisms of a single species. Person: Chris Stoeckert, Jie Zheng MO_462 strain_or_line_design strain comparison design 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 MO_612 cell cell specimen 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). PERSON: Chris Stoeckert, Jie Zheng tissue specimen MO_954 organism_part specimen from organism 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. PERSON: Chris Stoeckert, Jie Zheng MO_997 linear_amplification linear amplification fluorescence detection assay 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. IEDB IEDB fluorescence detection assay sampling time measurement datum sampling time measurement datum A time measurement datum when an observation is made or a sample is taken from a material as measured from some reference point. Person: Chris Stoeckert time point MO_738 timepoint sampling time measurement datum 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. Person: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Assembly Algorithm NIAID GSCID-BRC sequence assembly algorithm material service 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. PERSON: Carlo Torniai PERSON: Matthew Brush PERSON: Carlo Torniai material service rate measurement datum 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 PERSON: Bjoern Peters, Randi Vita IEDB rate measurement datum material storage service 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. PERSON: Carlo Torniai PERSON: Matthew Brush PERSON: Matthew Brush material storage service DNA sequence data The part of a FASTA file that contains the letters ACTGGGAA A sequence data item that is about the primary structure of DNA OBI call; Bjoern Peters OBI call; Melanie Courtout 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. DNA sequence data GenBank ID A CRID symbol uniquely indentifies the submitted GeneBank sequence record. Person: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group GenBank Record ID NIAID GSCID-BRC GenBank ID investigation description A textual entity that describes an investigation. Person: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group study description project description NIAID GSCID-BRC investigation description Sample ID specimen identifier A CRID symbol denotes a specimen and used to distinguish one specimen from another in an investigation. Person: Chris Stoeckert, Jie Zheng specimen ID NIAID GSCID-BRC metadata working group Specimen ID NIAID GSCID-BRC specimen identifier 1 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/ Person: Chris Stoeckert, Jie Zheng PMID PubMed Identifier Website: http://en.wikipedia.org/wiki/Wikipedia:PMID Publication Citation NIAID GSCID-BRC PubMed ID 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. Person: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Depth of Coverage - Average NIAID GSCID-BRC average depth of sequence coverage Sample collection date specimen collection time measurement datum A time measurement datum that is the measure of the time when the specimens are collected. Person: Chris Stoeckert, Jie Zheng collection date NIAID GSCID-BRC metadata working group Specimen Collection Date NIAID GSCID-BRC specimen collection time measurement datum Latitude latitude coordinate measurement datum A measurement datum that is the measure of the latitude coordinate of a site. Person: Chris Stoeckert, Jie Zheng latitude NIAID GSCID-BRC metadata working group Specimen Collection Location - Latitude NIAID GSCID-BRC latitude coordinate measurement datum Collection site longitude longitude coordinate measurement datum A measurement datum that is the measure of the longitude coordinate of a site. Person: Chris Stoeckert, Jie Zheng longitude NIAID GSCID-BRC metadata working group Specimen Collection Location - Longitude NIAID GSCID-BRC longitude coordinate measurement datum Project name investigation title A textual entity that denotes an investigation. Person:Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group study title project title NIAID GSCID-BRC investigation title organism identification objective A biological feature identification objective to identify the organism species in a specimen. Person: Chris Stoeckert, Jie Zheng Penn Group organism species detection objective Organism identification assay organism species detection assay An organism detection assay that identifies the organism species in a specimen. Chris Stoeckert Jie Zheng organism identification assay NIAID GSCID-BRC metadata working group organism species detection assay 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. Person: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Annotation Algorithm NIAID GSCID-BRC sequence annotation algorithm 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. Person: Chris Stoeckert, Jie Zheng BRC Website: http://en.wikipedia.org/wiki/Bioinformatics_Resource_Centers NIAID GSCID-BRC Bioinformatics Resource Center 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. Person: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Website: http://en.wikipedia.org/wiki/Country Specimen Collection Location - Country NIAID GSCID-BRC country name Study identifier investigation identifier A CRID symbol used to identify an investigation. Person: Chris Stoeckert, Jie Zhneg NIAID GSCID-BRC metadata working group project ID NIAID GSCID-BRC investigation identifier grant identifier A CRID symbol used to identify a grant. Person: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group grant ID NIAID GSCID-BRC grant identifier 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 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 grant 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 Person: Chris Stoeckert NIAID GSCID-BRC contact representative role specimen collector role An Investigation agent role borne by a person or organization which is realized in a specimen collection process. Person: Jie Zheng, Chris Stoeckert Penn Group NIAID GSCID-BRC specimen collector role assay array 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 Penn Group assay array cell culture A material entity comprised of cultured cells and the media in which they are being propagated or stored. PERSON:Matthew Brush 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. cell culture organization of specimen provider principal investigator An organization that is the affiliation of the principal investigator providing the specimens for the investigation PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Sample Provider PI's Institution NIAID GSCID-BRC organization of specimen provider principal investigator 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 PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Bioinformatics Resource Center Contact's Institution NIAID GSCID-BRC organization of Bioinformatics Resource Center contact person 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. PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Target Material NIAID GSCID-BRC target material in specimen specification Bioinformatics Resource Center contact person A person who is the contact representative of a Bioinformatics Resource Center PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Bioinformatics Resource Center Contact Name NIAID GSCID-BRC Bioinformatics Resource Center contact person 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. PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Sample Scope NIAID GSCID-BRC specimen-based scope of investigation specification specimen repository organization An organization that provides a service to store and distribute specimens PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Specimen Repository NIAID GSCID-BRC specimen repository organization email address of Bioinformatics Resource Center contact person An email address of the person who is contact representative of a Bioinformatics Resource Center PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Bioinformatics Resource Center Contact's email NIAID GSCID-BRC email address of Bioinformatics Resource Center contact person sequencing facility contact person A person who is the contact representative at the sequencing facility PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Sequencing Facility Contact Name NIAID GSCID-BRC sequencing facility contact person specimen provider principal investigator A person who is a principal investigator and provides the specimen PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Sample Provider Principal Investigator (PI) Name NIAID GSCID-BRC specimen provider principal investigator email address of specimen collector An email address of the person collecting the specimen PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Specimen Collector's email NIAID GSCID-BRC email address of specimen collector Sequencing center sequencing facility organization An organization that provides sequence determination service PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Sequencing Facility NIAID GSCID-BRC sequencing facility organization 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. PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Project Objectives NIAID GSCID-BRC specification of data to be generated in an investigation organization of specimen collector An organization that is the affiliation of the person collecting the specimen PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Specimen Collector's Institution NIAID GSCID-BRC organization of specimen collector email address of sequencing facility contact person An email address of the contact representative at the sequencing facility PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Sequencing Facility Contact's email NIAID GSCID-BRC email address of sequencing facility contact person Sample collector specimen collector A person who collects the specimen PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Specimen Collector Name NIAID GSCID-BRC 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. PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Project Method NIAID GSCID-BRC investigation assay specification organization of sequencing facility contact person An organization that is the affiliation of the contact representative at the sequencing facility PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Sequencing Facility Contact's Institution NIAID GSCID-BRC organization of sequencing facility contact person comment on investigation comment on investigation A textual entity that is about any of the aspects of an investigation worth noting PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Comments NIAID GSCID-BRC comment on investigation 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. PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Target Capture NIAID GSCID-BRC target capture specification specimen identifier assigned by specimen repository A specimen identifier which is assigned by a specimen repository PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Specimen Repository Sample ID NIAID GSCID-BRC specimen identifier assigned by specimen repository Alternative sample ID specimen identifier assigned by sequencing facility A specimen identifier which is assigned by a sequencing facility PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Sample ID - Sequencing Facility NIAID GSCID-BRC specimen identifier assigned by sequencing facility sample preparation for sequencing assay A sample preparation for assay that preparation of nucleic acids for a sequencing assay PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Nucleic Acid Preparation Method NIAID GSCID-BRC sample preparation for sequencing assay email address of specimen provider principal investigator An email address of the principal investigator providing the specimens for the investigation PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Sample Provider PI's email NIAID GSCID-BRC email address of specimen provider principal investigator 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. Person: Jie Zheng Adpated from 'DNA sequencing service' NIAID GSCID-BRC sequencing service conclusion based on data 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. Group:2013 Philly Workshop group Group:2013 Philly Workshop group conclusion based on data cell freezing medium 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. PERSON: Matthew Brush cell freezing medium categorical value specification A value specification that is specifies one category out of a fixed number of nominal categories PERSON:Bjoern Peters categorical value specification 1 1 scalar value specification A value specification that consists of two parts: a numeral and a unit label PERSON:Bjoern Peters scalar value specification value specification 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. PERSON:Bjoern Peters value specification grant agency An organization that provides funding support for projects such as investigations. PERSON: Jie Zheng, Chris Stoeckert funding organization NIAID GSCID-BRC metadata working group NIAID GSCID-BRC grant agency '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. PERSON: Jie Zheng, Chris Stoeckert NIAID GSCID-BRC metadata working group NIAID GSCID-BRC sequence annotation sequence annotation provider A person or organization reporting the feature annotation results from the analysis of a macromolecular sequence. PERSON: Jie Zheng, Chris Stoeckert NIAID GSCID-BRC metadata working group annotation provider NIAID GSCID-BRC sequence annotation provider sequence assembly name A textual entity that is used to denote a sequence assembly. PERSON: Jie Zheng, Chris Stoeckert NIAID GSCID-BRC metadata working group assembly name NIAID GSCID-BRC sequence assembly name 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. PERSON: Jie Zheng, Chris Stoeckert NIAID GSCID-BRC metadata working group NIAID GSCID-BRC sequence annotation reporting role taxonomic diversity assessment by targeted gene survey PMID:20679230 PMID:25367129 An assay that dteremines taxonomic and community diversity information by sequencing specific genomic regions used as marker of identity or diversity. Philippe Rocca-Serra environmental gene survey targeted gene survey targeted gene survey DNA barcoding OBI taxonomic diversity assessment by targeted gene survey 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 biodiversity assessment objective microarray assay 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. IEDB IEDB microarray assay Illumina HiSeq 2000 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 HiSeq 2000 http://res.illumina.com/documents/products/datasheets/datasheet_hiseq_systems.pdf Illumina HiSeq 2000 collection of specimens Blood cells collected from multiple donors over the course of a study. A material entity that has two or more specimens as its parts. Details see tracker: https://sourceforge.net/p/obi/obi-terms/778/ Person: Chris Stoeckert, Jie Zheng OBIB, OBI Biobank collection of specimens physical store a freezer. a humidity controlled box. A container with an environmental control function. For details see tracker item: http://sourceforge.net/p/obi/obi-terms/793/ Chris Stoeckert Duke Biobank, OBIB physical store 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/ OBI developers DOI https://en.wikipedia.org/wiki/Digital_object_identifier https://www.doi.org/ digital object identifier microscopy assay 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. ImmPort PMID:21685355 microscopy assay temperature value specification A value specification that specifies the temperature of some thing. Chris Stoeckert OBI temperature value specification temperature measurement assay An assay to determine the temperature of an evaluant. Bjoern Peters Chris Stoeckert OBI temperature measurement assay antigen specific antibodies assay 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. Bjoern Peters Chris Stoeckert James Overton Randi Vita OBI https://github.com/obi-ontology/obi/issues/825 NCI BBRB antigen specific antibodies assay 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. Bjoern Peters Chris Stoeckert James Overton Randi Vita VDRL test OBI https://github.com/obi-ontology/obi/issues/825 NCI BBRB venereal disease research laboratory test HBV surface antigen assay An analyte assay that is meant to detect hepatitis B virus (HBV) surface antigens. Bjoern Peters Chris Stoeckert James Overton Randi Vita HBsAg assay OBI https://github.com/obi-ontology/obi/issues/825 NCI BBRB HBV surface antigen assay 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. Person: Alan Ruttenberg, Jie Zheng https://en.wiktionary.org/wiki/measurand https://github.com/obi-ontology/obi/issues/778 measurand role Population included defined population inclusion criterion 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. Chris Stoeckert, Mathias Brochhausen MIABIS 2.0 https://github.com/obi-ontology/obi/issues/920 MIABIS 2.0 defined population inclusion criterion differential medium assay An organism detection assay that uses a differential medium to achieve its objective. John Judkins EuPathDB, https://www.uwyo.edu/molb2210_lab/info/biochemical_tests.htm differential medium assay medication time value specification A scalar value specification that specifies the point in time that a human participant under investigation self-administers a medication material John Judkins medication timepoint OBI VEuPathDB medication time value specification medication dose value specification A scalar value specification that specifies the value of the quantity of a material entity administered to an organism as a treatment John Judkins medication dose OBI VEuPathDB medication dose value specification 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 OBI case role in case-control study 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. John Judkins, Bjoern Peters OBI control role in case-control study cerebrospinal fluid specimen A specimen that is derived from cerbrospinal fluid. Chris Stoeckert Chris Stoeckert, Penn Medicine Biobank cerebrospinal fluid specimen Stool sample feces specimen A specimen that is derived from feces. Chris Stoeckert stool specimen Chris Stoeckert, Penn Medicine Biobank feces specimen Gastric fluid sample digestive system fluid or secretion specimen A specimen that is derived from digestive system fluid or secretion. Chris Stoeckert gastric fluid specimen Chris Stoeckert, Penn Medicine Biobank digestive system fluid or secretion specimen Milk sample milk specimen A specimen that is derived from milk. Chris Stoeckert Chris Stoeckert, Penn Medicine Biobank milk specimen Saliva sample saliva specimen A specimen that is derived from saliva. Chris Stoeckert Chris Stoeckert, Penn Medicine Biobank saliva specimen sputum specimen A specimen that is derived from sputum. Chris Stoeckert Chris Stoeckert, Penn Medicine Biobank sputum specimen bone marrow specimen A specimen that is derived from bone marrow. Chris Stoeckert Chris Stoeckert, Penn Medicine Biobank bone marrow specimen Pleural fluid sample pleural fluid specimen A specimen that is derived from pleural fluid. Chris Stoeckert Chris Stoeckert, Penn Medicine Biobank pleural fluid specimen lung specimen A specimen that is derived from lung. Chris Stoeckert Chris Stoeckert, NCI BBRB lung specimen swab specimen A specimen that is stored on a swab as the output of a collecting specimen with swab process. Chris Stoeckert OBIB/OBI https://github.com/obi-ontology/obi/issues/910 OBIB swab specimen collecting specimen with swab 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). Chris Stoeckert OBIB https://github.com/obi-ontology/obi/issues/910 OBIB collecting specimen with swab Nasopharyngeal swab sample nasopharyngeal swab specimen A specimen that is collected with a swab from the surface of a nasopharynx. Chris Stoeckert Chris Stoeckert, OBIB nasopharyngeal swab specimen Oropharyngeal swab sample oropharyngeal swab specimen A specimen that is collected with a swab from the surface of a oropharynx. Chris Stoeckert Chris Stoeckert, OBIB oropharyngeal swab specimen whole metagenome sequencing assay 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.). Rebecca Jackson WMS Bjoern Peters Michelle Giglio https://github.com/obi-ontology/obi/issues/1056 whole metagenome sequencing assay Case-control case-control study design 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. John Judkins, Bjoern Peters Wikipedia, OBI case-control study design Giemsa stain assay 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. Chris Stoeckert Jie Zheng https://github.com/obi-ontology/obi/issues/1093 VEuPathDB Giemsa stain assay 1 individual organism specimen A specimen composed of an individual organism to be studied in an investigation. Person: Jie Zheng EFO_0000542 individual https://github.com/obi-ontology/obi/issues/1092 individual organism specimen Blood microbiology test blood microbiology assay An organism detection assay that detects microorganisms in a blood specimen. John Judkins https://github.com/obi-ontology/obi/issues/1064 blood microbiology assay biopsy Biopsy of a potentially cancerous mole. 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. Damion Dooley Nicole Vasilevsky https://en.wikipedia.org/wiki/Biopsy biopsy bone marrow biopsy 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. Nicole Vasilevsky http://www.webmd.com/cancer/bone-marrow-aspiration-and-biopsy bone marrow biopsy Case series case series study design PMID: 22213493 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. http://orcid.org/0000-0002-8844-9165 https://www.ncbi.nlm.nih.gov/pubmed/22213493 case series design glass bottle A container with a narrow neck that is made of glass. VEuPathDB VEuPathDB https://github.com/obi-ontology/obi/issues/1117 VEuPathDB glass bottle glass bottle coated with insecticides A glass bottle that coated with material designed to control insects. VEuPathDB VEuPathDB https://github.com/obi-ontology/obi/issues/1117 VEuPathDB glass bottle coated with insecticides nested polymerase chain reaction 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. Jie Zheng nested PCR nested-PCR https://en.wikipedia.org/wiki/Nested_polymerase_chain_reaction https://github.com/obi-ontology/obi/issues/1117 VEuPathDB nested polymerase chain reaction counter current immunoelectrophoresis 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. Jie Zheng http://www.ispybio.com/search/protocols/ie%20protocol2.pdf https://github.com/obi-ontology/obi/issues/1117 VEuPathDB counter current immunoelectrophoresis ligase detection reaction 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. Jie Zheng LDR MIRO:20000103 https://github.com/obi-ontology/obi/issues/1117 VEuPathDB ligase detection reaction loop-mediated isothermal amplification 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. Jie Zheng LAMP https://en.wikipedia.org/wiki/Loop-mediated_isothermal_amplification https://github.com/obi-ontology/obi/issues/1117 VEuPathDB loop-mediated isothermal amplification detection of pathogenic organisms objective An organism feature identification objective that aims to detect whether an organism contains pathogenic organisms. Jie Zheng VEuPathDB https://github.com/obi-ontology/obi/issues/1117 VEuPathDB detection of pathogenic organisms objective insecticide resistance detection objective An organism feature identification objective that aims to detect insecticide resistance of an insect. Jie Zheng VEuPathDB https://github.com/obi-ontology/obi/issues/1117 VEuPathDB insecticide resistance detection objective arthropod meal of blood specimen 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. Chris Stoeckert Jie Zheng blood meal VEuPathDB https://github.com/obi-ontology/obi/issues/1117 VEuPathDB arthropod meal of blood specimen polymerase chain reaction assay An assay that uses polymerase chain reaction technique to amplify DNA. VEuPathDB VEuPathDB https://github.com/obi-ontology/obi/issues/1117 VEuPathDB polymerase chain reaction assay 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. VEuPathDB RFLP restriction fragment length polymorphism restriction fragment length polymorphism analysis https://en.wikipedia.org/wiki/Restriction_fragment_length_polymorphism https://github.com/obi-ontology/obi/issues/1117 VEuPathDB restriction fragment length polymorphism assay DNA fingerprinting assay An assay to identify a specific individual organism from a DNA specimen by looking at unique patterns in their DNA. VEuPathDB DNA finger printing DNA fingerprint DNA fingerprinting DNA profiling VEuPathDB https://github.com/obi-ontology/obi/issues/1117 VEuPathDB DNA fingerprinting assay insecticide resistance assay An assay that aims to detect the presence and/or frequency of resistance to insecticides in an organism or organism population. VEuPathDB resistance identification/monitoring MIRO:20000001 https://github.com/obi-ontology/obi/issues/1117 VEuPathDB insecticide resistance assay 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. VEuPathDB monitoring known mutations MIRO:20000096 https://github.com/obi-ontology/obi/issues/1117 VEuPathDB insecticide resistance by monitoring known mutations assay 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. VEuPathDB metabolic resistance assay MIRO:20000003 https://github.com/obi-ontology/obi/issues/1117 VEuPathDB insecticide resistance by detecting enzyme activity assay insecticide resistance bioassay An insecticide resistance assay that is typically conducted to measure the effects of a substance on a living organism. VEuPathDB bioassay MIRO:20000058 https://github.com/obi-ontology/obi/issues/1117 VEuPathDB insecticide resistance bioassay insecticide resistance by detecting alpha esterase activity assay An insecticide resistance by detecting enzyme activity assay that measures activity of alpha esterase. VEuPathDB alpha esterase activity assay IRO:0000149 https://github.com/obi-ontology/obi/issues/1117 VEuPathDB insecticide resistance by detecting alpha esterase activity assay insecticide resistance by detecting beta esterase activity assay An insecticide resistance by detecting enzyme activity assay that measures activity of beta esterase. VEuPathDB beta esterase activity assay IRO:0000150 https://github.com/obi-ontology/obi/issues/1117 VEuPathDB insecticide resistance by detecting beta esterase activity assay insecticide resistance by detecting acetylcholinesterase activity assay An insecticide resistance by detecting enzyme activity assay that measures activity of acetylcholinesterase. VEuPathDB AChE activity assay AChE assay acetylcholinesterase assay MIRO:20000010 MIRO:20000084 MIRO:20000086 https://github.com/obi-ontology/obi/issues/1117 VEuPathDB insecticide resistance by detecting acetylcholinesterase activity assay 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). VEuPathDB GST related assay MIRO:20000083 https://github.com/obi-ontology/obi/issues/1117 VEuPathDB insecticide resistance by detecting glutathione S-transferase activity assay 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. VEuPathDB pNPA assay MIRO:20000019 https://github.com/obi-ontology/obi/issues/1117 VEuPathDB insecticide resistance by detecting carboxylic ester hydrolase activity assay insecticide resistance by detecting mixed-function oxidase assay An insecticide resistance by detecting enzyme activity assay that measures whether mixed-function oxidase activity present. VEuPathDB mixed-function oxidase assay MIRO:20000062 https://github.com/obi-ontology/obi/issues/1117 VEuPathDB insecticide resistance by detecting mixed-function oxidase assay direct insecticide resistance bioassay An insecticide resistance bioassay without the use of any synergist. VEuPathDB direct bioassay MIRO:20000044 https://github.com/obi-ontology/obi/issues/1117 VEuPathDB direct insecticide resistance bioassay topical application insecticide resistance bioassay An insecticide resistance bioassay by adding insecticide directly to the thorax of the insect. VEuPathDB topical application assay IRO:0000155 https://github.com/obi-ontology/obi/issues/1117 VEuPathDB topical application insecticide resistance bioassay direct insecticide resistance diagnostic assay A direct insecticide resistance assay that at preset insecticide dosage scoring mortality to determine resistance of a population. VEuPathDB diagnostic test MIRO:20000075 https://github.com/obi-ontology/obi/issues/1117 VEuPathDB direct insecticide resistance diagnostic assay 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. VEuPathDB dose response test MIRO:20000076 https://github.com/obi-ontology/obi/issues/1117 VEuPathDB insecticide resistance dose response assay insecticide resistance time response assay A direct insecticide resistance assay to determine resistance as a consequence of the time of exposure to insecticide. VEuPathDB time response test MIRO:20000013 https://github.com/obi-ontology/obi/issues/1117 VEuPathDB insecticide resistance time response assay 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. VEuPathDB CDC bottle bioassay MIRO:20000009 https://github.com/obi-ontology/obi/issues/1117 VEuPathDB Centre for Disease Control and Prevention bottle bioassay WHO cone kit diagnostic assay A direct insecticide resistance diagnostic assay uses WHO cone kit. VEuPathDB cone DT MIRO:20000039 https://github.com/obi-ontology/obi/issues/1117 VEuPathDB WHO cone kit diagnostic assay WHO paper kit diagnostic assay A direct insecticide resistance diagnostic assay uses WHO paper kit. VEuPathDB WHO paper kit DT MIRO:20000041 https://github.com/obi-ontology/obi/issues/1117 VEuPathDB WHO paper kit diagnostic assay WHO larvicide diagnostic assay A direct insecticide resistance diagnostic assay tests survival of larvae in a medium supplemented with insecticide. VEuPathDB WHO larvicide DT MIRO:20000049 https://github.com/obi-ontology/obi/issues/1117 VEuPathDB WHO larvicide diagnostic assay insecticide resistance dose response by bottle assay An insecticide resistance dose response assay that performs in a glass bottle coated with insecticides. VEuPathDB bottle bioassay DR test MIRO:20000011 https://github.com/obi-ontology/obi/issues/1117 VEuPathDB insecticide resistance dose response by bottle assay 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. VEuPathDB WHO larvicide DR test MIRO:20000050 https://github.com/obi-ontology/obi/issues/1117 VEuPathDB insecticide resistance dose response by survival of larvae assay insecticide resistance dose response by WHO paper kit assay An insecticide resistance dose response assay using WHO paper kit. VEuPathDB WHO paper kit DR test MIRO:20000048 https://github.com/obi-ontology/obi/issues/1117 VEuPathDB insecticide resistance dose response by WHO paper kit assay 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. VEuPathDB bottle bioassay TR test MIRO:20000030 https://github.com/obi-ontology/obi/issues/1117 VEuPathDB insecticide resistance time response by bottle assay 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. VEuPathDB WHO paper kit TR test MIRO:20000036 https://github.com/obi-ontology/obi/issues/1117 VEuPathDB insecticide resistance time response by WHO paper kit assay 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. VEuPathDB ARMS Amplification Refractory Mutation System IRO:0000006 PMID: 18428319 https://github.com/obi-ontology/obi/issues/1117 VEuPathDB insecticide resistance by amplification refractory mutation system assay 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. VEuPathDB PIRA-PCR Primer Introduced Restriction Analysis PCR polymerase chain reaction-primer-introduced restriction analysis IRO:0000007 PMID: 8339229 https://github.com/obi-ontology/obi/issues/1117 VEuPathDB insecticide resistance by primer introduced restriction analysis PCR assay 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. VEuPathDB gene mutation detection by nested PCR IRO:0000127 https://github.com/obi-ontology/obi/issues/1117 VEuPathDB insecticide resistance by nested polymerase chain reaction assay 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. VEuPathDB MIRO:20000103 https://github.com/obi-ontology/obi/issues/1117 VEuPathDB insecticide resistance by ligase detection reaction assay 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. VEuPathDB gene mutation detection by LDR-FMA ligase detection reaction-fluorescent microsphere assay IRO:0000151 https://github.com/obi-ontology/obi/issues/1117 VEuPathDB insecticide resistance by 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. VEuPathDB PASA PCR amplification of specific alleles allele-specific amplification and amplification refractory mutation system PMID: 1734929 https://github.com/obi-ontology/obi/issues/1117 VEuPathDB insecticide resistance by PCR amplification of specific alleles assay 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. VEuPathDB MIRO:20000102 https://github.com/obi-ontology/obi/issues/1117 VEuPathDB insecticide resistance by fluorogenic PCR assay insecticide resistance by PCR-RFLP assay An insecticide resistance by monitoring known mutations assay based on restriction fragment length polymorphism assay. VEuPathDB PCR-RFLP MIRO:20000113 https://github.com/obi-ontology/obi/issues/1117 VEuPathDB insecticide resistance by PCR-RFLP 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). VEuPathDB Short Interspersed Elements PCR IRO:0000013 https://github.com/obi-ontology/obi/issues/1117 VEuPathDB insecticide resistance by short interspersed elements PCR assay pathogen detection assay An organism detection assay that detects pathogens. VEuPathDB pathogen detection method IRO:0000137 https://github.com/obi-ontology/obi/issues/1117 VEuPathDB pathogen detection assay VectorTest assay 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. VEuPathDB VectorTest IRO:0000138 https://github.com/obi-ontology/obi/issues/1117 VEuPathDB VectorTest assay 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. VEuPathDB Rapid Analyte Measurement Platform IRO:0000164 https://github.com/obi-ontology/obi/issues/1117 VEuPathDB pathogen detection by Rapid Analyte Measurement Platform assay pathogen detection by loop-mediated isothermal amplification assay A pathogen detection assay that is based on loop-mediated isothermal amplification. VEuPathDB Loop-mediated isothermal amplification IRO:0000165 https://github.com/obi-ontology/obi/issues/1117 VEuPathDB pathogen detection by loop-mediated isothermal amplification assay blood meal assay An assay that analyzes the specimen taken from blood meal fed organism, such as insect. VEuPathDB blood meal analysis IRO:0000135 https://github.com/obi-ontology/obi/issues/1117 VEuPathDB blood meal assay blood meal by counter current immunoelectrophoresis assay A blood meal assay that uses a counter current immunoelectrophoresis technique. VEuPathDB CIE countercurrent immunoelectrophoresis IRO:0000136 https://github.com/obi-ontology/obi/issues/1117 VEuPathDB blood meal by counter current immunoelectrophoresis assay DNA based blood meal finger printing assay A DNA fingerprinting assay that uses DNA extracted from blood meal fed organism, such as insect. VEuPathDB DNA based blood meal finger printing VEuPathDB VSMO:0001307 https://github.com/obi-ontology/obi/issues/1117 VEuPathDB DNA based blood meal finger printing assay organism detection by size assay An organism detection assay that is based on the size of organism. VEuPathDB by size IRO:0000145 https://github.com/obi-ontology/obi/issues/1117 VEuPathDB organism detection by size assay 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. VEuPathDB cross mating experiment MIRO:30000036 https://github.com/obi-ontology/obi/issues/1117 VEuPathDB organism detection by cross mating assay 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. VEuPathDB cytological chromosome examination MIRO:30000037 https://github.com/obi-ontology/obi/issues/1117 VEuPathDB organism detection by cytological chromosome examination assay 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. VEuPathDB isoenzyme electrophoresis MIRO:30000038 https://github.com/obi-ontology/obi/issues/1117 VEuPathDB organism detection by isoenzyme electrophoresis assay 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. VEuPathDB morphological examination MIRO:30000039 https://github.com/obi-ontology/obi/issues/1117 VEuPathDB organism detection by morphological examination assay organism identification by PCR assay organism detection by PCR assay An organism detection assay that is based on PCR. VEuPathDB PCR-based species identification MIRO:30000040 https://github.com/obi-ontology/obi/issues/1117 VEuPathDB organism detection by PCR assay organism identification by specific DNA hybridization assay organism detection by specific DNA hybridization assay An organism detection assay that is based on DNA hybrdization. VEuPathDB species specific DNA hybridization MIRO:30000041 https://github.com/obi-ontology/obi/issues/1117 VEuPathDB organism detection by specific DNA hybridization assay 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. VEuPathDB salinity tolerance tests MIRO:30000042 https://github.com/obi-ontology/obi/issues/1117 VEuPathDB organism detection by salinity tolerance assay Induced sputum sample induced sputum specimen A sputum specimen that is collected from an organism following its inhalation of a nebulized salt solution. John Judkins PMC3297553 induced sputum specimen 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. John Judkins https://en.wikipedia.org/wiki/Serial_passage https://www.merriam-webster.com/dictionary/passage passage process 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 https://en.wikipedia.org/wiki/Serial_passage https://www.merriam-webster.com/dictionary/passage passage history record 16s ribosomal gene sequencing assay 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. Michelle Giglio Rebecca Jackson Suvarna Nadendla 16S rRNA sequencing assay PMID:31450270 CFDE 16s ribosomal gene sequencing assay amplicon sequencing assay A sequencing assay in which a DNA or RNA input molecule is amplified by PCR and the product sequenced. Michelle Giglio Rebecca Jackson Suvarna Nadendla PMID:29628929 PMID:31450270 CFDE amplicon sequencing assay 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 https://github.com/obi-ontology/obi/issues/1097 VEuPathDB karyotype information partial karyotype information A karyotype information that is about the structural variation of partial genome rather than whole genome. Jie Zheng VEuPathDB https://github.com/obi-ontology/obi/issues/1097 VEuPathDB partial karyotype information full karyotype information A karyotype information that is about the structural variation of the whole genome. Jie Zheng OBI group https://github.com/obi-ontology/obi/issues/1097 full karyotype information 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 IA immunoassay LOINC User's Guide, Version 2.68, PUBLISHED JUNE 2020, page 47 https://github.com/obi-ontology/obi/issues/1203 single-value binding of antibody with reporter to antigen assay tracheal aspirate specimen A specimen that is collected with a suctioning tube from the trachea. Asiyah Yu Lin ORCID:0000-0003-2620-0345 tracheal wash specimen PMID:25338241 tracheal aspirate specimen mid-turbinate nasal swab specimen A specimen that is collected with a mid-turbinate nasal swab from the turbinate area of the nasal cavity. Asiyah Yu Lin ORCID:0000-0003-2620-0345 https://seattlechildrenslab.testcatalog.org/catalogs/185/files/11633 mid-turbinate nasal swab specimen nasal aspirate specimen A specimen that is collected with a suctioning tube from the nasal cavity. Asiyah Yu Lin ORCID:0000-0003-2620-0345 nasal wash specimen|nasopharyngeal aspirate Asiyah Yu Lin ORCID:0000-0003-2620-0345 nasal aspirate specimen lower respiratory tract aspirate specimen A specimen that is collected with a suctioning tube from the lower respiratory tract. Asiyah Yu Lin ORCID:0000-0003-2620-0345 lower respiratory tract wash specimen Asiyah Yu Lin ORCID:0000-0003-2620-0345 lower respiratory tract aspirate specimen upper respiratory specimen A specimen that is derived from the upper respiratory tract Asiyah Yu Lin ORCID:0000-0003-2620-0345 Asiyah Yu Lin ORCID:0000-0003-2620-0345 upper respiratory specimen lower respiratory tract specimen A specimen that is derived from the lower respiratory tract. Asiyah Yu Lin ORCID:0000-0003-2620-0345 Asiyah Yu Lin ORCID:0000-0003-2620-0345 lower respiratory tract specimen anterior nasal swab specimen A specimen that is derived from the anterior nasal wall Asiyah Yu Lin ORCID:0000-0003-2620-0345 Asiyah Yu Lin ORCID:0000-0003-2620-0345 anterior nasal swab specimen aspiration specimen collection Procedure using suction, usually with a thin needle and syringe, to remove bodily fluid or tissue. Asiyah Yu Lin|ORCID:0000-0003-2620-0345 aspiration procedure https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&ns=ncit&code=C15631 aspiration specimen collection surveillance process 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. Chris Stoeckert Shane Babcock, OBI https://github.com/obi-ontology/obi/issues/1181 IDO, VEuPathDB surveillance process cluster study group role 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. Chris Stoeckert, Brianna Lindsay cluster study arm ClinEpiDB cluster study group role compound study group role 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. Chris Stoeckert, Brianna Lindsay compound study arm ClinEpiDB compound study group role ultraviolet light source A light source that provides ultraviolet (UV) light for use in a distant area using a delivery system. Person: Jie Zheng UV light source Person: Jie Zheng https://github.com/obi-ontology/obi/issues/1200 VEuPathDB ultraviolet light source visible light source A light source that provides visible light for use in a distant area using a delivery system. Person: Jie Zheng Person: Jie Zheng https://github.com/obi-ontology/obi/issues/1200 VEuPathDB visible light source solar light source A light source that light is produced from solar energy. Person: Chris Stoeckert Person: Jie Zheng Person: Chris Stoeckert Person: Jie Zheng https://github.com/obi-ontology/obi/issues/1200 VEuPathDB solar light source adult arthropod specimen collection process A live arthropod specimen collection process in which the arthropods are in the adult stage. John Judkins collection of adults MIRO:30000052 https://github.com/obi-ontology/obi/issues/1217 adult arthropod specimen collection process animal-biting arthropod specimen collection by aspiration An arthropod specimen collection by aspiration that occurs while the arthropod is biting an animal. John Judkins animal biting catch MIRO:30000012 https://github.com/obi-ontology/obi/issues/1217 animal-biting arthropod specimen collection by aspiration animal-biting outdoor arthropod specimen collection by aspiration An animal-biting arthropod specimen collection by aspiration that occurs outside a building. John Judkins animal biting catch - outdoors MIRO:30000014 https://github.com/obi-ontology/obi/issues/1217 animal-biting outdoor arthropod specimen collection by aspiration aquatic arthropod specimen collection process An arthropod specimen collection process that has the objective of collecting mosquitoes from an aquatic environment. John Judkins aquatic environment catch MIRO:30000048 https://github.com/obi-ontology/obi/issues/1217 aquatic arthropod specimen collection process arthropod resting in animal house specimen collection by aspiration An arthropod specimen collection by aspiration that catches specimens resting inside an animal house. John Judkins animal shed resting catch MIRO:30000027 https://github.com/obi-ontology/obi/issues/1217 arthropod resting in animal house specimen collection by aspiration arthropod resting outdoors on artificial support 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. John Judkins outdoors shelter catch - artificial MIRO:30000026 https://github.com/obi-ontology/obi/issues/1217 arthropod resting outdoors on artificial support specimen collection by aspiration arthropod resting outdoors on natural support 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. John Judkins outdoors shelter catch - natural MIRO:30000025 https://github.com/obi-ontology/obi/issues/1217 arthropod resting outdoors on natural support specimen collection by aspiration arthropod resting outdoors 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. John Judkins outdoors shelter catch MIRO:30000024 https://github.com/obi-ontology/obi/issues/1217 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. John Judkins catch by aspiration MIRO:30000043 https://github.com/obi-ontology/obi/issues/1217 arthropod specimen collection by aspiration Arthropod collection process arthropod specimen collection process A specimen collection process that has the objective of collecting arthropods as specimens. John Judkins collection of arthropods field population catch MIRO:30000044 https://github.com/obi-ontology/obi/issues/1217 arthropod specimen collection process human-biting arthropod specimen collection by aspiration An arthropod specimen collection by aspiration that occurs while the arthropod is biting a human. John Judkins man biting catch MIRO:30000017 https://github.com/obi-ontology/obi/issues/1217 human-biting arthropod specimen collection by aspiration human-biting indoor arthropod specimen collection by aspiration An arthropod specimen collection by aspiration that occurs while the arthropod is biting a human inside a building. John Judkins man biting catch - indoors MIRO:30000019 https://github.com/obi-ontology/obi/issues/1217 human-biting indoor arthropod specimen collection by aspiration human-biting outdoor 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. John Judkins man biting catch - outdoors MIRO:30000018 https://github.com/obi-ontology/obi/issues/1217 human-biting outdoor arthropod specimen collection by aspiration knockdown arthropod specimen collection by pyrethrum spray A knockdown arthropod specimen collection process in which the pesticide is pyrethrum. John Judkins pyrethrum spray catch MIRO:30000023 https://github.com/obi-ontology/obi/issues/1217 knockdown arthropod specimen collection by pyrethrum spray knockdown arthropod specimen collection process An arthropod specimen collection process that involves exposing arthropods to pesticide, then collecting them once they become dead or immobilized. John Judkins knockdown collection IRO:0000014 https://github.com/obi-ontology/obi/issues/1217 knockdown arthropod specimen collection process live arthropod specimen collection process An arthropod specimen collection process meant to collect live specimens. John Judkins catch of live specimens MIRO:30000044 VSMO:0001445 https://github.com/obi-ontology/obi/issues/1217 live arthropod specimen collection process Mosquito trap arthropod trap A device designed to catch arthropods. John Judkins MIRO:30000011 https://github.com/obi-ontology/obi/issues/1217 arthropod trap artificial pit shelter An arthropod trap, consisting of a pit dug in the ground to provide a space for arthropods to rest and be collected. John Judkins IRO:0000005 https://github.com/obi-ontology/obi/issues/1217 artificial pit shelter baited net trap 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. John Judkins https://github.com/obi-ontology/obi/issues/1217 baited net trap barrier trap An arthropod trap consisting of a static physical barrier designed to funnel arthropods in flight into a container. John Judkins IRO:0000017 https://github.com/obi-ontology/obi/issues/1217 barrier trap BG-Counter A device manufactured by BioGents that is designed to count mosquitoes passing through the device, differentiating the mosquitoes from other arthropods. John Judkins IRO:0000143 https://github.com/obi-ontology/obi/issues/1217 BG-Counter BG-Sentinel 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. John Judkins IRO:0000028 VSMO:0001906 https://github.com/obi-ontology/obi/issues/1217 BG-Sentinel trap CDC light trap 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. John Judkins CDC light trap IRO:0000163 https://github.com/obi-ontology/obi/issues/1217 Centers for Disease Control and Prevention light trap dipper for arthropod immatures 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. John Judkins dipper for immatures VSMO:0001479 https://github.com/obi-ontology/obi/issues/1217 dipper for arthropod immatures encephalitis virus surveillance trap 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. John Judkins EVS trap IRO:0000029 VSMO:0001295 https://github.com/obi-ontology/obi/issues/1217 encephalitis virus surveillance trap gravid trap An arthropod trap that is designed to collect gravid female arthropods or their eggs. John Judkins IRO:0000030 https://github.com/obi-ontology/obi/issues/1217 gravid trap light trap An arthropod trap that uses light as an attractant. John Judkins MIRO:30000065 https://github.com/obi-ontology/obi/issues/1217 light trap light trap for indoor use A light trap designed to be placed inside a building. John Judkins indoor light trap MIRO:30000009 https://github.com/obi-ontology/obi/issues/1217 light trap for indoor use light trap for outdoor use A light trap designed to be placed outside a building. John Judkins outdoor light trap MIRO:30000010 https://github.com/obi-ontology/obi/issues/1217 light trap for outdoor use Mosquito Magnet Pro trap 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. John Judkins IRO:0000022 https://github.com/obi-ontology/obi/issues/1217 Mosquito Magnet Pro trap MosquiTRAP A gravid trap consisting of an arthropod attractant and adhesive surface. John Judkins IRO:0000140 https://github.com/obi-ontology/obi/issues/1217 MosquiTRAP New Jersey light trap A light trap that is designed to use motorized suction to trap arthropods in a collection bag once they approach the light attractant. John Judkins New Jersey trap IRO:0000031 https://github.com/obi-ontology/obi/issues/1217 New Jersey light trap Onderstepoort Veterinary Institute light-suction trap 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. John Judkins OVI light-suction trap IRO:0000154 Parasites Vectors 8, 239 (2015) https://github.com/obi-ontology/obi/issues/1217 Onderstepoort Veterinary Institute light-suction trap outlet window trap An arthropod trap that is positioned adjacent to a window of a building and is designed to collect arthropods flying out of the building. John Judkins outlet window trap MIRO:30000020 https://github.com/obi-ontology/obi/issues/1217 outlet window trap ovitrap 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. John Judkins oviposition trap MIRO:30000016 VSMO:0001501 https://github.com/obi-ontology/obi/issues/1217 ovitrap resting arthropod trap An arthropod trap that is designed to be attractive to an arthropod as a place to rest during a period of inactivity. John Judkins https://github.com/obi-ontology/obi/issues/1217 resting arthropod trap resting box 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. John Judkins resting box catch IRO:0000021 https://github.com/obi-ontology/obi/issues/1217 resting box trap resting bucket 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). John Judkins resting bucket catch IRO:0000141 https://github.com/obi-ontology/obi/issues/1217 resting bucket Shannon trap 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. John Judkins shannon trap catch IRO:0000191 https://github.com/obi-ontology/obi/issues/1217 Shannon trap sticky resting bucket 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. John Judkins sticky resting bucket catch IRO:0000142 https://github.com/obi-ontology/obi/issues/1217 sticky resting bucket sticky trap An arthropod trap that is designed to capture arthropods resting on a surface by coating the surface with adhesive. John Judkins sticky trap catch IRO:0000128 https://github.com/obi-ontology/obi/issues/1217 sticky trap population based design 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. Chris Stoeckert https://link.springer.com/referenceworkentry/10.1007%2F978-1-4419-1005-9_45, EFO_0001430 population based design https://github.com/obi-ontology/obi/issues/1090 population based design Endotracheal tube sample endotracheal tube specimen 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. John Judkins ORCID:0000-0001-6595-0902 https://bmcpulmmed.biomedcentral.com/articles/10.1186/s12890-019-0926-3 endotracheal tube specimen Endotracheal tube aspirate sample endotracheal aspirate specimen 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. John Judkins ORCID:0000-0001-6595-0902 https://bmcpulmmed.biomedcentral.com/articles/10.1186/s12890-019-0926-3 endotracheal aspirate specimen Altitude altitude measurement datum A length measurement datum between a point at sea or ground level and some point above it. Chris Stoeckert Adapted from https://www.merriam-webster.com/dictionary/altitude altitude measurement datum duration of specimen collection 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. specimen collection duration VEuPathDB specimen collection duration prevalence of pathogen in specimens 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. Chris Stoeckert prevalence of pathogen VEuPathDB prevalence of pathogen in 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. Chris Stoeckert host blood index VEuPathDB prevalence of blood meal specimens from a host organism 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. Chris Stoeckert presence of blood meal host organism VEuPathDB presence of blood from host organism in blood meal specimen blood meal source organism An organism that is the source of a blood meal. Chris Stoeckert blood meal host organism VEuPathDB blood meal source organism blood meal source role A mosquito feeds on a human whereby the human acquires the blood meal source 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. Will deprecate this term in VEuPathDB ontology once in OBI. Chris Stoeckert http://purl.obolibrary.org/obo/EUPATH_0000791 blood meal source role arthropod attractor role A role of a material entity realized in drawing an arthropod in the direction of the material. John Judkins attractant IRO:0000034 https://github.com/obi-ontology/obi/issues/1302 VEuPathDB arthropod attractor role arthropod collection process with automated identification An arthropod specimen collection process that involves a device that produces data specifying the types of arthropod collected. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1302 VEuPathDB arthropod collection process with automated identification gravid female arthropod specimen collection process An arthropod specimen collection process that has the objective of collecting gravid female arthropods. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1302 VEuPathDB gravid female arthropod specimen collection process resting flight-capable arthropod specimen collection process An arthropod specimen collection process that occurs while an arthropod that is capable of flight is resting outdoors during a period of inactivity. John Judkins VSMO:0000514 https://github.com/obi-ontology/obi/issues/1302 VEuPathDB resting flight-capable arthropod specimen collection process daytime arthropod specimen collection by aspiration An arthropod specimen collection by aspiration that occurs in the daytime. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1302 VEuPathDB daytime arthropod specimen collection by aspiration arthropod resting in human house specimen collection by aspiration An arthropod specimen collection by aspiration that catches specimens resting inside a human house. John Judkins https://github.com/obi-ontology/obi/issues/1302 VEuPathDB arthropod resting in human house specimen collection by aspiration landing arthropod specimen collection process An arthropod specimen collection process that occurs while the arthropods land on a surface. John Judkins collection of landing insects VSMO:0001457 https://github.com/obi-ontology/obi/issues/1302 VEuPathDB landing arthropod specimen collection process flying adult arthropod collection process by passive interception An adult arthropod specimen collection process that has the objective of collecting arthropods capable of flight, through the use of a barrier trap. John Judkins https://github.com/obi-ontology/obi/issues/1302 VEuPathDB flying adult arthropod collection process by passive interception device for collection of resting adult arthropods 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. John Judkins VSMO:0001355 https://github.com/obi-ontology/obi/issues/1302 VEuPathDB device for collection of resting adult arthropods well net for arthropod immatures A device that is designed for the collection of arthropod larvae or pupae from water and consists of a conical net. John Judkins https://github.com/obi-ontology/obi/issues/1302 VEuPathDB well net for arthropod immatures arthropod trap containing small non-human animal bait An arthropod trap that uses as attractant an animal that is not human and is the size of a chicken or smaller. John Judkins trap containing small non-human animal bait VSMO:0001595 https://github.com/obi-ontology/obi/issues/1302 VEuPathDB arthropod trap containing small non-human animal bait trap for emerging adult arthropods An arthropod trap that is designed to trap an arthropod as it emerges from water at the beginning of its adult stage. John Judkins American Midland Naturalist, Vol. 97, No. 2 (Apr., 1977), pp. 381-389 VSMO:0001352 https://github.com/obi-ontology/obi/issues/1302 VEuPathDB trap for emerging adult arthropods barcode target locus role 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 VEuPathDB https://github.com/obi-ontology/obi/issues/1325 barcode target locus role oligonucleotide primer set A processed material that consists of oligonucleotides that bear a primer role. Chris Stoeckert https://orcid.org/0000-0002-5714-991X VEuPathDB https://github.com/obi-ontology/obi/issues/1325 oligonucleotide primer set fluorogenic PCR assay A polymerase chain reaction assay that uses target specific probes labeled with fluorogenic chromophores. John Judkins TaqMan MIRO:20000102 https://github.com/obi-ontology/obi/issues/1320 fluorogenic PCR assay genotyping by PCR assay 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 Jie Zheng, ORCID:0000-0002-2999-0103 VEuPathDB https://github.com/obi-ontology/obi/issues/1348 VEuPathDB genotyping by PCR assay coma severity assay 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. John Judkins https://github.com/obi-ontology/obi/issues/1357 John Judkins coma severity assay Gametocyte detection Plasmodium gametocyte detection assay An assay that detects Plasmodium gametocytes in a specimen. Chris Stoeckert Jie Zheng John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1322 Plasmodium gametocyte detection assay malaria rapid diagnosis assay An assay that is quick and easy in the diagnosis of malaria by detecting evidence of malaria parasites (antigens) in human blood. Chris Stoeckert Jie Zheng malaria rapid diagnosis test VEuPathDB https://github.com/obi-ontology/obi/issues/1322 malaria rapid diagnosis assay Parasite detection parasite detection assay An assay that detects parasite in a specimen. Chris Stoeckert Jie Zheng VEuPathDB https://github.com/obi-ontology/obi/issues/1322 parasite detection assay Stool microbiology test feces microbiology assay An organism detection assay that detects microorganisms in a feces specimen. John Judkins stool test for microorganisms VEuPathDB https://github.com/obi-ontology/obi/issues/1322 feces microbiology assay Blood test blood assay An assay that has a blood specimen as evaulant. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1322 blood assay Plasmodium species, by FalciVax RDT falcivax rapid diagnostic test 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. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1322 falcivax rapid diagnostic test Plasmodium species, by OptiMAL RDT optimal-IT rapid diagnostic test A parasite detection assay that is rapid, sensitive, and able to differentiate between P. falciparum and other malaria parasites. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1322 optimal-IT rapid diagnostic test Urine test urine assay An assay that has a urine specimen as evaluant. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1322 urine assay Plasmodium species, by qPCR parasite species identification by PCR assay A parasite detection by PCR assay that identifies the species of parasite. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1322 parasite species identification by PCR assay PCR method parasite detection by PCR assay A parasite detection assay that uses PCR. Chris Stoeckert Jie Zheng VEuPathDB https://github.com/obi-ontology/obi/issues/1322 parasite detection by PCR assay free-standing window trap 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] 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. VEuPathDB VSMO:0001649 free-standing window trap BG-lure scent dispenser 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. VEuPathDB BG-lure IRO:0001060 BG-lure scent dispenser hand-held sweep net A device that consists of a network of mesh and is designed to capture adult arthropods. VEuPathDB VSMO:0001522 hand-held sweep net Centers for Disease Control and Prevention gravid trap 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. VEuPathDB CDC gravid trap VSMO:0001510 Centers for Disease Control and Prevention gravid trap egg specimen collection process An arthropod specimen collection process in which the arthropods are in the embryo stage. VEuPath collection of eggs MIRO:30000049 https://github.com/obi-ontology/obi/issues/1322 egg specimen collection process larval specimen collection process An arthropod specimen collection process in which the arthropods are in the larval stage. VEuPath collection of larvae MIRO:30000022 https://github.com/obi-ontology/obi/issues/1322 larval specimen collection process pupal specimen collection process An arthropod specimen collection process in which the arthropods are in the pupal stage. VEuPath collection of pupae MIRO:30000050 https://github.com/obi-ontology/obi/issues/1322 pupal specimen collection process Vacutainer sample blood specimen in vacutainer A blood specimen that is located in a vacutainer. John Judkins Vacutainer sample VEuPathDB blood specimen in vacutainer Filter paper sample blood specimen on filter paper A blood specimen that is located on a filter paper. Chris Stoeckert Jie Zheng Filter paper sample Penn Group blood specimen on filter paper Proportion mapped reads proportion mapped reads 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. John Judkins VEuPathDB proportion mapped reads Antibiotic administration antibiotic administration process Administering substance in vivo where an antibiotic substance is administered to a living organism. Chris Stoeckert Cristian Cocos Jie Zheng Penn Group antibiotic administration process insecticide resistance datum A data item that is about resistance to an insecticide. John Judkins VEuPathDB insecticide resistance datum organism detection datum A data item that is the specified output of an organism detection assay. John Judkins VEuPathDB organism detection datum easting coordinate measurement datum 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. John Judkins https://en.wikipedia.org/wiki/Grid_reference_system easting coordinate measurement datum northing coordinate measurement datum A one dimensional Cartesian spatial coordinate datum that is the northward component of a distance from a point on a map projection. Easting and northing coordinates are commonly measured in meters from a horizontal datum. John Judkins https://en.wikipedia.org/wiki/Grid_reference_system northing coordinate measurement datum Study center clinical study center Organization that undertakes a clinical study at some point in time. Chris Stoeckert Cristian Cocos Jie Zheng Penn Group clinical study center Sequencing sequencing protocol A protocol that, when concretized, is realized in an assay that uses chemical or biological means to infer the sequence of a biomaterial. John Judkins VEuPathDB sequencing protocol Sample collection device or method specimen collection protocol A protocol that specifies processes to fulfill a specimen collection objective. John Judkins VEuPathDB specimen collection protocol Subject ID participant identifier A symbol that denotes a participant under investigation. John Judkins VEuPathDB participant identifier Axillary temperature axillary temperature measurement datum A temperature measurement datum that is about an axilla. John Judkins VEuPathDB axillary temperature measurement datum Temperature organismal body temperature measurement datum A temperature measurement datum that is about an organism. Chris Stoeckert Jie Zheng Penn Group organismal body temperature measurement datum Subject common name common name of organism 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. John Judkins https://en.wikipedia.org/wiki/Common_name common name of organism Age at enrollment age since birth at time of enrollment An age since birth measurement datum at the time of subject enrollment. Jie Zheng Penn Group age since birth at time of enrollment age since birth at time of visit An age since birth measurement datum at the time of a clinical visit. Chris Stoeckert Grant Dorsey Jie Zheng Shon Cade Penn Group age since birth at time of visit entomological data item A data item that is about a collection of insects. John Judkins entomological measurement datum VEuPathDB entomological data item temperature measurement datum A scalar measurement datum that is the result of measuring temperature. John Judkins VEuPathDB temperature measurement datum Temperature measurement method organismal body temperature measurement assay An assay that detects body temperature of an organism. Chris Stoeckert Jie Zheng VEuPathDB https://github.com/obi-ontology/obi/issues/1322 organismal body temperature measurement assay Sample collection time post infection (days) specimen collection time post infection A specimen collection time measurement datum that is the measure of a time when specimens are collected after an infection starts. Chris Stoeckert, ORCID: 0000-0002-5714-991X VEuPathDB, EUPATH:0000613 https://github.com/obi-ontology/obi/issues/1286 specimen collection time post infection laboratory-based population 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. Chris Stoeckert, ORCID: 0000-0002-5714-991X VEuPathDB https://github.com/obi-ontology/obi/issues/1370 laboratory-based population Cerebrospinal fluid test cerebrospinal fluid assay An assay that has a cerebrospinal fluid specimen as evaluant. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1429 cerebrospinal fluid assay Endotracheal tube aspirate test endotracheal aspirate assay An assay that has an endotracheal aspirate specimen as evaluant. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1429 endotracheal aspirate assay Induced sputum test induced sputum assay An assay that has an induced sputum specimen as evaluant. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1429 induced sputum assay lung assay An assay that has a lung specimen as evaluant. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1429 lung assay milk assay An assay that has a milk specimen as evaluant. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1429 milk assay Stool test feces assay An assay that has a feces specimen as evaluant. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1429 feces assay Umbilical cord blood test umbilical cord blood assay An assay that has an umbilical cord blood specimen as evaluant. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1429 umbilical cord blood assay saliva assay An assay that has a saliva specimen as evaluant. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1429 saliva assay Cerebrospinal fluid microbiology test cerebrospinal fluid microbiology assay An organism detection assay that detects microorganisms in a cerebrospinal fluid specimen. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1429 cerebrospinal fluid microbiology assay Endotracheal tube aspirate microbiology test endotracheal tube aspirate microbiology assay An organism detection assay that detects microorganisms in an endotracheal aspirate specimen. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1429 endotracheal tube aspirate microbiology assay Induced sputum microbiology test induced sputum microbiology assay An organism detection assay that detects microorganisms in an induced sputum specimen. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1429 induced sputum microbiology assay blood assay datum A data item that is the specified output of a blood assay. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 blood assay datum Raw test result for blood blood microbiology datum An organism detection datum that is the specified output of a blood microbiology assay. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 blood microbiology datum feces assay datum A data item that is the specified output of a feces assay. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 feces assay datum Raw test result for stool feces microbiology datum An organism detection datum that is the specified output of a feces microbiology assay. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 feces microbiology datum urine assay datum A data item that is the specified output of a urine assay. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 urine assay datum Raw test result for urine urine microbiology datum An organism detection datum that is the specified output of a urine microbiology assay. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 urine microbiology datum induced sputum assay datum A data item that is the specified output of a induced sputum assay. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 induced sputum assay datum 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 Jie Zheng ORCID:0000-0002-2999-0103 laboratory OBIB eagle-i resource ontology ERO_0000001 https://github.com/obi-ontology/obi/issues/1436 OBIB biomedical laboratory organization Raw test result for induced sputum induced sputum microbiology datum An organism detection datum that is the specified output of an induced sputum microbiology assay. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 induced sputum microbiology datum cerebrospinal fluid assay datum A data item that is the specified output of a cerebrospinal fluid assay. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 cerebrospinal fluid assay datum cerebrospinal fluid microbiology datum An organism detection datum that is the specified output of a cerebrospinal fluid microbiology assay. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 cerebrospinal fluid microbiology datum endotracheal aspirate assay datum An organism detection datum that is the specified output of an endotracheal aspirate assay. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 endotracheal aspirate assay datum 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. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 endotracheal tube aspirate microbiology datum Raw test result for lung aspirate lung microbiology datum An organism detection datum that is the specified output of a lung microbiology assay. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 lung microbiology datum 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. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 nasopharyngeal or oropharyngeal swab microbiology datum Raw test result for pleural fluid pleural fluid microbiology datum An organism detection datum that is the specified output of a pleural fluid microbiology assay. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 pleural fluid microbiology datum umbilical cord blood assay datum A data item that is the specified output of an umbilical cord blood assay. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 umbilical cord blood assay datum Raw test result for umbilical cord blood umbilical cord blood microbiology datum An organism detection datum that is the specified output of an umbilical cord blood microbiology assay. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 umbilical cord blood microbiology datum Raw bacteria data for blood bacteria in blood datum A blood microbiology datum that is about bacteria. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 bacteria in blood datum Raw virus data for blood virus in blood datum A blood microbiology datum that is about a virus. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 virus in blood datum Raw eukaryota data for blood eukaryota in blood datum A blood microbiology datum that is about eukaryota. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 eukaryota in blood datum Raw bacteria data for stool bacteria in feces datum A feces microbiology datum that is about bacteria. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 bacteria in feces datum Raw eukaryota data for stool eukaryota in feces datum A feces microbiology datum that is about eukaryota. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 eukaryota in feces datum Raw virus data for stool virus in feces datum A feces microbiology datum that is about a virus. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 virus in feces datum Raw eukaryota data for urine eukaryota in urine datum A urine microbiology datum that is about eukaryota. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 eukaryota in urine datum Raw bacteria data for induced sputum bacteria in induced sputum datum An induced sputum microbiology datum that is about bacteria. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 bacteria in induced sputum datum Raw eukaryota data for induced sputum eukaryota in induced sputum datum An induced sputum microbiology datum that is about eukaryota. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 eukaryota in induced sputum datum Raw virus data for induced sputum virus in induced sputum datum An induced sputum microbiology datum that is about a virus. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 virus in induced sputum datum bacteria in endotracheal tube aspirate datum An endotracheal tube aspirate microbiology datum that is about bacteria. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 bacteria in endotracheal tube aspirate datum Raw bacteria data for lung aspirate bacteria in lung datum A lung microbiology datum that is about bacteria. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 bacteria in lung datum Raw eukaryota data for lung aspirate eukaryota in lung datum A lung microbiology datum that is about eukaryota. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 eukaryota in lung datum Raw virus data for lung aspirate virus in lung datum A lung microbiology datum that is about a virus. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 virus in lung datum 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. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 bacteria in nasopharyngeal or oropharyngeal swab datum 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. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 eukaryota in nasopharyngeal or oropharyngeal swab datum 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. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 virus in nasopharyngeal or oropharyngeal swab datum bacteria in pleural fluid datum A pleural fluid microbiology datum that is about bacteria. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 bacteria in pleural fluid datum eukaryota in pleural fluid datum A pleural fluid microbiology datum that is about eukaryota. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 eukaryota in pleural fluid datum virus in pleural fluid datum A pleural fluid microbiology datum that is about a virus. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 virus in pleural fluid datum Raw eukaryota data for umbilical cord blood eukaryota in umbilical cord blood datum An umbilical cord blood microbiology datum that is about eukaryota. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 eukaryota in umbilical cord blood datum lung microbiology assay An organism detection assay that detects microorganisms in a lung specimen. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1429 lung microbiology assay Pleural fluid microbiology test pleural fluid microbiology assay An organism detection assay that detects microorganisms in a pleural fluid specimen. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1429 pleural fluid microbiology assay umbilical cord blood microbiology assay An organism detection assay that detects microorganisms in an umbilical cord blood specimen. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1429 umbilical cord blood microbiology assay nasopharyngeal or oropharyngeal swab microbiology assay An organism detection assay that detects microorganisms in a nasopharyngeal or oropharyngeal swab specimen. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1429 nasopharyngeal or oropharyngeal swab microbiology assay Urine microbiology test urine microbiology assay An organism detection assay that detects microorganisms in a urine specimen. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1429 urine microbiology assay 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. John Judkins multiplexed real time polymerase chain reaction assay VEuPathDB https://github.com/obi-ontology/obi/issues/1431 multiplex 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. John Judkins multiplexed real time reverse-transcription polymerase chain reaction assay VEuPathDB https://github.com/obi-ontology/obi/issues/1431 multiplex real time reverse-transcription polymerase chain reaction assay mosquito membrane feeding device A device that contains blood in a membrane penetrable to mosquitoes, designed to feed mosquitoes without the need for an animal host. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1439 mosquito membrane feeding device mosquito membrane feeding assay 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. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1439 mosquito membrane feeding assay 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. John Judkins NCIT:C85736 https://www.cdc.gov/dpdx/diagnosticprocedures/stool/staining.html https://github.com/obi-ontology/obi/issues/1444 modified acid-fast stain microscopy assay 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. John Judkins ALS assay antibodies from lymphocyte supernatant assay OBI VEuPathDB https://github.com/obi-ontology/obi/issues/1443 antibodies from lymphocyte secretions assay milk assay datum A data item that is the specified output of a milk assay. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1515 milk assay datum detection technique 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. Bjoern Peters Hector Guzman-Orozco OBI https://github.com/obi-ontology/obi/issues/1488 detection technique assay kit 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. John Judkins OBI, VEuPathDB https://github.com/obi-ontology/obi/issues/1456 VEuPathDB assay kit placental blood specimen A specimen that is derived from placental blood. John Judkins VEuPathDB placental blood specimen Placental blood microbiology test placental blood microbiology assay A blood microbiology assay that detects microorganisms in a placental blood specimen. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1297 placental blood microbiology assay Raw test result for placental blood placental blood microbiology datum An organism detection datum that is the specified output of a placental blood microbiology assay. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1297 placental blood microbiology datum eukaryota in placental blood datum A placental blood microbiology datum that is about eukaryota. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1297 eukaryota in placental blood datum mid-upper arm circumference datum 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. The Mother and Child Health and Education Trust mid-upper arm circumference datum antigen specific antibodies assay datum A data item that is the specified output of an antigen specific antibodies assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB https://github.com/obi-ontology/obi/issues/1526 antigen specific antibodies assay datum antigen specific antibodies in blood assay An antigen specific antibodies assay that has a blood specimen as evaluant. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB https://github.com/obi-ontology/obi/issues/1526 VEuPathDB antigen specific antibodies in blood assay antigen specific antibodies in milk assay An antigen specific antibodies assay that has a milk specimen as evaluant. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB https://github.com/obi-ontology/obi/issues/1526 VEuPathDB antigen specific antibodies in milk assay 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. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB https://github.com/obi-ontology/obi/issues/1526 antigen specific antibodies in blood assay datum 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. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB https://github.com/obi-ontology/obi/issues/1526 antigen specific antibodies in milk assay datum Mosquito Magnet Liberty Plus trap 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. VEuPathDB https://github.com/obi-ontology/obi/issues/1523 Mosquito Magnet Liberty Plus trap cow-baited arthropod trap 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. John Judkins ORCID:0000-0001-6595-0902 Sarah Kelly https://github.com/obi-ontology/obi/issues/1602 cow-baited arthropod trap Scrub Typhus Detect IgM ELISA kit 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. John Judkins ORCID:0000-0001-6595-0902 https://inbios.com/scrub-typhus-detecttm-igm-elisa-kit-intl/ Scrub Typhus Detect IgM ELISA kit Panbio Dengue IgM capture ELISA kit 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. John Judkins ORCID:0000-0001-6595-0902 Panbio Dengue IgM capture ELISA kit Panbio Dengue Early ELISA kit 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. John Judkins ORCID:0000-0001-6595-0902 Panbio Dengue Early ELISA kit SD Bioline Chikungunya IgM RDT kit A device manufactured by Abbott for rapid detection of human IgM antibodies for Chikungunya virus in blood, using analytical chromatography. John Judkins ORCID:0000-0001-6595-0902 https://www.indiamart.com/proddetail/abbott-sd-bioline-chikungunya-igm-test-kit-12908515588.html SD Bioline Chikungunya IgM RDT kit 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. John Judkins ORCID:0000-0001-6595-0902 SD Bioline Chikungunya IgM capture ELISA kit Advantage Chikungunya IgM Card kit 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. John Judkins ORCID:0000-0001-6595-0902 Advantage Chikungunya IgM Card kit organism detection assay 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. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB https://github.com/obi-ontology/obi/issues/1633 organism detection assay ELISA measuring Orientia tsutsugamushi IgM antibody An enzyme-linked immunosorbent assay that detects the IgM antibody that binds Orientia tsutsugamushi. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB https://github.com/obi-ontology/obi/issues/1456 ELISA measuring Orientia tsutsugamushi IgM antibody microarray assay measuring Dengue IgM antibody A microarray assay that detects the IgM antibody that binds Dengue. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB https://github.com/obi-ontology/obi/issues/1456 microarray assay measuring Dengue IgM antibody microarray assay measuring NS1 A microarray assay that detects NS1. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB https://github.com/obi-ontology/obi/issues/1456 microarray assay measuring NS1 analytical chromatography measuring Chikungunya IgM antibody Analytical chromatography that detects the IgM antibody that binds Chikungunya. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB https://github.com/obi-ontology/obi/issues/1456 analytical chromatography measuring Chikungunya IgM antibody ELISA measuring Chikungunya IgM antibody An enzyme-linked immunosorbent assay that detects the IgM antibody that binds Chikungunya. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB https://github.com/obi-ontology/obi/issues/1456 ELISA measuring Chikungunya IgM antibody 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. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB https://github.com/obi-ontology/obi/issues/1456 microarray ELISA measuring Chikungunya IgM antibody Plasma sample 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 PERSON: Melanie Courtot PERSON: Philippe Rocca-Serra plasma WEB: http://en.wikipedia.org/wiki/Blood_plasma blood plasma specimen 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. PERSON: Maura Gasparetto PERSON: Melanie Courtot PERSON: Philippe Rocca-Serra WEB: http://en.wikipedia.org/wiki/Blood_plasma blood serum specimen Host organism organism animal fungus plant virus A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs. 10/21/09: This is a placeholder term, that should ideally be imported from the NCBI taxonomy, but the high level hierarchy there does not suit our needs (includes plasmids and 'other organisms') 13-02-2009: OBI doesn't take position as to when an organism starts or ends being an organism - e.g. sperm, foetus. This issue is outside the scope of OBI. GROUP: OBI Biomaterial Branch WEB: http://en.wikipedia.org/wiki/Organism organism Sample type specimen Biobanking of blood taken and stored in a freezer for potential future investigations stores specimen. A material entity that has the specimen 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. PERSON: James Malone PERSON: Philippe Rocca-Serra GROUP: OBI Biomaterial Branch specimen cultured cell population 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. PERSON:Matthew Brush cell culture sample PERSON:Matthew Brush 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. cultured cell population 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. PERSON: Bjoern Peters BAL GROUP: IEDB bronchial alveolar lavage Data analysis 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 James Malone Melanie Courtot Philippe Rocca-Serra Richard Scheuermann Ryan Brinkman Tina Hernandez-Boussard data analysis data processing Branch editors data transformation data transformation objective normalize objective An objective specification to transformation input data into output data Modified definition in 2013 Philly OBI workshop James Malone PERSON: James Malone data transformation objective averaging data transformation An averaging data transformation is a data transformation that has objective averaging. James Malone PERSON: James Malone averaging data transformation 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. James Malone PERSON: James Malone center calculation objective center calculation data transformation A center calculation data transformation is a data transformation that has objective of center calculation. James Malone PERSON: James Malone center calculation data transformation Observational observation design 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. Philippe Rocca-Serra OBI branch derived observation design 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 PERSON: Jennifer Fostel GROUP: CEBS pool of specimens 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. PERSON: Bjoern Peters PERSON: Philippe Rocca-Serra liquid chemical solution GROUP: OBI Biomaterial Branch chemical solution solvent role 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 Philippe Rocca-Serra adpated from wikipedia (http://en.wikipedia.org/wiki/Solvatation) solvent role solute 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 Philippe Rocca-Serra adapted from wikipedia (http://en.wikipedia.org/wiki/Solute) solute role extraction 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. Person:Bjoern Peters Philippe Rocca-Serra extraction filtration 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 Philippe Rocca-Serra OBI-Branch: adapted from wikipedia and wordnet filtration centrifugation PMID: 18428461.Purification of oligodendrocytes and their progenitors using immunomagnetic separation and Percoll gradient centrifugation. Curr Protoc Neurosci. 2001 May;Chapter 3:Unit 3.12. centrifugation is a process separating molecules by size or density using centrifugal forces generated by a spinning rotor. G-forces of several hundred thousand times gravity are generated in ultracentrifugation Philippe Rocca-Serra adapted from http://www.fao.org/DOCREP/003/X3910E/X3910E06.htm centrifugation staining 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. Philippe Rocca-Serra adapted from Wikipedia: http://en.wikipedia.org/wiki/Staining staining polymerization 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 Philippe Rocca-Serra OBI-Branch polymerization storage 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 Philippe Rocca-Serra OBI-Branch storage nucleic acid hybridization 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. Philippe Rocca-Serra adapted from wikipedia [http://en.wikipedia.org/wiki/Nucleic_acid_hybridization] hybridization assay nucleic acid hybridization elution 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) Philippe Rocca-Serra wordnet.princeton.edu/perl/webwn elution light source light source 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. Elizabeth M. Goralczyk John Quinn Olga Tchuvatkina Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253 light source 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 http://www.nuncbrand.com/page.aspx?ID=301 multi-well plate DNA sequencer ABI 377 DNA Sequencer, ABI 310 DNA Sequencer A DNA sequencer is an instrument that determines the order of deoxynucleotides in deoxyribonucleic acid sequences. Trish Whetzel MO DNA sequencer centrifuge A device with a rapidly rotating container that applies centrifugal force to its contents Melanie Courtot Person: Jennifer Fostel Trish Whetzel http://en.wikipedia.org/wiki/Centrifuge centrifuge hybridization chamber Glass Array Hybridization Cassette A device which is used to maintain constant contact of a liquid on an array. This can be either a glass vial or slide. Trish Whetzel MO_563 hybridization_chamber hybridization chamber gel tank 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. Person:Frank Gibson Person:Kevin Clancy electrophoresis box electrophoresis unit sep:00095 gel tank power supply 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. Daniel Schober Frank Gibson PSU electrical power supply power pack power supply unit PERSON: Daniel Schober sep:00093 was power_pack, maps to SEP electrical_power_supply power supply microscope 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) PERSON: Phillippe Rocca-Serra wikipedia microscope animal cage 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. PERSON: Phillippe Rocca-Serra laboratory cage OBI biomaterial branch animal cage Study design 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. PERSON: Chris Stoeckert experimental design rediscussed at length (MC/JF/BP). 12/9/08). The definition was clarified to differentiate it from protocol. study design 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 eligibility criterion 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 Bjoern Peters IEDB criteria come from plan / clinical trial branch human subject enrollment collecting specimen from organism taking a sputum sample from a cancer patient, taking the spleen from a killed mouse, collecting a urine sample from a patient a process with the objective to obtain a material entity that was part of an organism for potential future use in an investigation PERSON:Bjoern Peters IEDB collecting specimen from organism 1 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. Bjoern Peters Person:Bjoern Peters IEDB administering substance in vivo 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 Bjoern Peters IEDB material component separation 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. PERSON:Bjoern Peters aliquoting apportioning OBI branch derived material portioning 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 PlanAndPlannedProcess Branch OBI branch derived maintaining cell culture 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 OBI branch derived artificially induced reverse transcription 'establishing cell culture' 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). PERSON:Matthew Brush PERSON:Matthew Brush 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. establishing cell culture 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 PlanAndPlannedProcess Branch OBI branch derived lavage 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 OBI branch derived preparative chromatography Sequencing assay sequencing assay The use of the Sanger method of DNA sequencing to determine the order of the nucleotides in a DNA template An assay the uses chemical or biochemical means to infer the sequence of a biomaterial PlanAndPlannedProcess Branch OBI branch derived sequencing assay 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 PERSON:Kevin Clancy OBI branch derived specific enzymatic cleavage dialysis the use of a dialysis bag of select pore size to remove salt from collagen isolated from mouse cartilage a protocol application that uses diffusion through a semi-permeable membrane to separate an input material into two fractions of different composition PERSON:Kevin Clancy OBI branch derived dialysis 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 PERSON:Kevin Clancy OBI branch derived 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. electrophoresis 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 PERSON:Kevin Clancy 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 PERSON:Kevin Clancy OBI branch derived enzymatic amplification RNA extraction A RNA extraction is a nucleic acid extraction where the desired output material is RNA PlanAndPlannedProcess Branch OBI branch derived requested by Helen Parkinson for MO RNA extraction 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 PlanAndPlannedProcess Branch OBI branch derived requested by Helen Parkinson for MO. Could be defined class nucleic acid extraction 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. OBI bead assay bead infection process the detrimental process in which an infectious agent colonizes or replicates in a host environment IEDB IEDB infection process adaptive immune receptor is a receptor produced by cells of the adaptive immune system with the purpose of binding epitopes. IEDB IEDB adaptive immune receptor lymph node cell specimen 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. IEDB IEDB lymph node cell specimen organ harvesting The process of removing an organ from its source organism IEDB IEDB organ harvesting disposition to infect an organism 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 IEDB IEDB disposition to infect an organism pathologic process abnormal, harmful processes caused by or associated with a disease IEDB IEDB pathologic process bodily fluid specimen A specimen that is derived from some bodily fluid Christian Stoeckert ORCID:0000-0002-5714-991X Mark A. Miller ORCID:0000-0001-9076-6066 Christian Stoeckert ORCID:0000-0002-5714-991X Mark A. Miller ORCID:0000-0001-9076-6066 bodily fluid specimen Umbilical cord blood sample umbilical cord blood specimen A specimen that is derived from some umbilical cord blood Christian Stoeckert ORCID:0000-0002-5714-991X Mark A. Miller ORCID:0000-0001-9076-6066 Christian Stoeckert ORCID:0000-0002-5714-991X Mark A. Miller ORCID:0000-0001-9076-6066 umbilical cord blood specimen Erythrocyte sample erythrocyte specimen A specimen that is derived from some erythrocytes Christian Stoeckert ORCID:0000-0002-5714-991X Mark A. Miller ORCID:0000-0001-9076-6066 Christian Stoeckert ORCID:0000-0002-5714-991X Mark A. Miller ORCID:0000-0001-9076-6066 erythrocyte specimen A representation that is either the output of a clinical history taking or a physical examination or an image finding, or some combination thereof. clinical finding Clinical history A series of statements representing health-relevant qualities of a patient and of a patient's family. clinical history 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. laboratory finding Clinical phenotype A clinically abnormal phenotype. clinical phenotype Laboratory test 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. clinical laboratory test The totality of all processes through which a given disease instance is realized. disease course Diagnosis The representation of a conclusion of a diagnostic process. diagnosis Physical examination TODO: Define. physical examination finding 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. congenital malformation congenital disorder Treatment 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 treatment 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 health care process 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 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). diagnostic process Health status 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. medication role Anti-fungal agent resistance 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. antibiotic resistance phenotype antibiotic sensitivity phenotype antifungal resistance phenotype antimetabolite resistance phenotype antimicrobial compound sensitivity phenotype antiviral resistance phenotype antimicrobial agent resistance phenotype Resistance to azole An azole compound resistance phenotype where an organism or cell is resistant to one or more azole compounds. resistant to azole 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. employee job role health care facility A deontic document act that concludes an inpatient encounter. discharge process patient discharge Travel details 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 Ethnicity A social identity information content entity that is about whether some person identifies as some ethnicity. ethnic identity information content entity Gender 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 Education level 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. highest level of education data item 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 24 hour food recall 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 24-hour dietary recall 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 Obstetric history TO DO 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 Gestational age 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 Preterm birth 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. oocyst stage A life cycle stage where a cell differentiates into male or female sexual forms. gametocyte stage A parasite lifecycle stage of some sporozoans where cells divide through sporogony producing daughter cells called sporozoites that infect new hosts. sporozoite stage Parasite lifecycle stage A life cycle stage of a parasite. parasite lifecycle stage Parasite organism 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. parasite organism 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 blood stage 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 Plasmodium gametocyte A time quality inhering in a bearer by virtue of how long the bearer has existed. age 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. fluorescence A quality inhering in a substance by virtue of the amount of the bearer's there is mixed with another substance. concentration concentration of Sex 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. biological sex A quality of a single physical entity inhering in the bearer by virtue of the bearer's size or shape or structure. morphology qualitative The number of entities of this type that are part of the whole organism. count in organism number presence presence or absence in organism quantitative amount A morphology quality inhering in a bearer by virtue of the bearer's physical magnitude. size A 1-D extent quality which is equal to the distance between two points. length A physical quality that inheres in a bearer by virtue of the proportion of the bearer's amount of matter. mass A physical quality of the thermal energy of a system. temperature A quality of a single process inhering in a bearer by virtue of the bearer's occurrence per unit time. rate female A biological sex quality inhering in an individual or a population that only produces gametes that can be fertilised by male gametes. female male A biological sex quality inhering in an individual or a population whose sex organs contain only male gametes. male A quality denoting the lack of an entity. absence absent from organism absent A quality inhering in a bearer by virtue of the bearer's existence. present in organism present Decreased activity A behavioral quality of a process inhering in a bearer by virtue of the bearer's exhibiting reduced activity. hypoactive decreased behavioural activity A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities. relational physical quality physical quality A quality inhering in a bearer by virtue of the bearer's having susceptibilty toward an external stimulus. susceptible susceptible toward A resistance quality inhering in a bearer by virtue of the bearer's resistance to a stimulus. resistant resistant to A quality which inheres in a continuant. monadic quality of a continuant monadic quality of an object monadic quality of continuant multiply inhering quality of a physical entity quality of a continuant quality of a single physical entity quality of an object quality of continuant physical object quality A 2-D extent quality inhering in a bearer by virtue of the bearer's two dimensional extent. area A biological sex quality inhering in a population of multiple sexes. mixed sex Morbidity A quality inhering in a population by virtue of the proportion of its members that are ill at a given time. morbidity A viability quality inhering in a bearer by virtue of the bearer's condition before death. alive An organismal quality inhering in a bearer by virtue of the bearer's ability to produce new life or offspring. reproductive quality An organismal quality inhering in a bearer by virtue of the bearer's physical expression of sexual characteristics. phenotypic sex Mating type A biological sex quality inhering in an individual or a population that undergo sexual reproduction. mating type A quality that inheres in an entire organism or part of an organism. organismal quality A quality that inheres in an entire population or part of a population. population quality A quality inhering in a bearer by virtue of the severity of infectious disease caused by the bearer in a target organism. virulence A quality of an object that has a value that is decreased compared to normal or average. decreased object quality A viviparous organism having never given birth. nulliparous 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. lesioned An organismal quality of having successfully reproduced. parous A material entity that consists of two or more organisms, viruses, or viroids. group of organism organism collection collection of organisms Household 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 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. prescription health care prescription prescription de santé Resistance to voriconazole 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 Resistance to posaconazole 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). aggregate fruit (broad) coenocarp (narrow) compound fruit (broad) dehiscent fruit (broad) diaspore (broad) frucht (exact, German) fruto (exact, Spanish) indehiscent fruit (broad) multiple fruit (broad) propagule (broad) syncarp (narrow) 果実 (exact, Japanese) fruit 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. Asteraceae floret (narrow) basal flower (narrow) double flower (narrow) flor (Spanish, exact) floret (related) hermaphrodite flower (narrow) monoclinous flower (narrow) perfect flower (narrow) 花 (Japanese, exact) flower An anatomical entity that is or was part of a plant. entidad anat&#243mica vegetal (Spanish, exact) 植物 解剖学（形態）的実体 (Japanese, exact) plant anatomical entity An amino acid chain that is produced de novo by ribosome-mediated translation of a genetically-encoded mRNA, and any derivatives thereof. native protein natural protein protein 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. IFN-gamma IFNG immune interferon interferon gamma 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. TNF TNF-a TNF-alpha TNFA TNFSF2 TNFa cachectin tumor necrosis factor alpha tumor necrosis factor ligand superfamily member 2 tumor necrosis factor An interleukin-1 that is a translation product of the human IL1B gene or a 1:1 ortholog thereof. IL-1 beta IL1B IL1F2 catabolin interleukin-1 beta A protein that is a translation product of the human IL1RN gene or a 1:1 ortholog thereof. ICIL-1RA IL-1RN IL-1ra IL1 inhibitor IL1F3 IL1RA IL1RN IRAP anakinra 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. CTLA-8 CTLA8 IL-17 IL-17A IL17 IL17A cytotoxic T-lymphocyte-associated antigen 8 interleukin-17A A protein that is a translation product of the human IL7 gene or a 1:1 ortholog thereof. IL-7 IL7 interleukin-7 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. IL-13 IL13 NC30 T-cell activation protein P600 interleukin-13 A protein that is a translation product of the human IL15 gene or a 1:1 ortholog thereof. IL-15 IL15 interleukin-15 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. IL-2 IL2 T-cell growth factor TCGF aldesleukin interleukin-2 A protein that is a translation product of the human IL4 gene or a 1:1 ortholog thereof. B-cell IgG differentiation factor B-cell growth factor 1 B-cell stimulatory factor 1 BSF-1 IGG1 induction factor IL-4 IL4 binetrakin lymphocyte stimulatory factor 1 pitrakinra interleukin-4 A protein that is a translation product of the human IL5 gene or a 1:1 ortholog thereof. B-cell differentiation factor I B-cell growth factor II BCGF-II IL-5 IL5 T-cell replacing factor TRF cytotoxic T-lymphocyte inducer eosinophil differentiation factor interleukin-5 A protein that is a translation product of the human IL6 gene or a 1:1 ortholog thereof. B-cell hybridoma growth factor B-cell stimulatory factor 2 BSF-2 CDF CTL differentiation factor IFN-beta-2 IFNB2 IL-6 IL6 hybridoma growth factor interferon beta-2 interleukin HP-1 interleukin-6 A protein that is a translation product of the human CXCL8 gene or a 1:1 ortholog thereof. C-X-C motif chemokine 8 CXCL8 GCP-1 IL-8 IL8 MDNCF MONAP NAP-1 T-cell chemotactic factor emoctakin granulocyte chemotactic protein 1 monocyte-derived neutrophil chemotactic factor monocyte-derived neutrophil-activating peptide neutrophil-activating protein 1 protein 3-10C interleukin-8 A protein that is a translation product of the human IL9 gene or a 1:1 ortholog thereof. IL-9 IL9 T-cell growth factor P40 cytokine P40 interleukin-9 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. CSIF IL-10 IL10 cytokine synthesis inhibitory factor interleukin-10 A protein with core architecture consisting of a Small cytokines (intecrine/chemokine), interleukin-8 like (Pfam:PF00048) domain. fam:C/C-C chemokine C/C-C motif small inducible chemokine A protein that is a translation product of the human CD14 gene or a 1:1 ortholog thereof. CD14 monocyte differentiation antigen CD14 myeloid cell-specific leucine-rich glycoprotein CD14 molecule A C/C-C motif small inducible chemokine that is a translation product of the CCL3, CCL3L1/CCL3L3, or CCL4 gene. C-C motif chemokine 3/4 A C/C-C motif small inducible chemokine that is a member of a subfamily that includes eotaxin. eotaxin-like cytokine A C/C-C motif small inducible chemokine that is a translation product of the human CCL5 gene or a 1:1 ortholog thereof. CCL5 D17S136E EoCP RANTES SCYA5 SIS-delta T cell-specific protein P228 T-cell-specific protein RANTES TCP228 eosinophil chemotactic cytokine small inducible cytokine A5 small-inducible cytokine A5 C-C motif chemokine 5 An eotaxin-like cytokine that is a translation product of the human CCL2 gene or a 1:1 ortholog thereof. CCL2 HC11 Je MCAF MCP-1 MCP1 SCYA2 monocyte chemoattractant protein 1 monocyte chemotactic and activating factor monocyte chemotactic protein 1 monocyte secretory protein JE platelet-derived growth factor-inducible protein JE small-inducible cytokine A2 C-C motif chemokine 2 A C-C motif chemokine 3/4 that is a translation product of the human CCL3 gene or a 1:1 ortholog thereof. CCL3 G0/G1 switch regulatory protein 19-1 G0S19-1 L2G25B MIP-1-alpha MIP1A PAT 464.1 SCYA3 SIS-alpha SIS-beta TY-5 heparin-binding chemotaxis protein macrophage inflammatory protein 1-alpha small-inducible cytokine A3 tonsillar lymphocyte LD78 alpha protein C-C motif chemokine 3 A C-C motif chemokine 3/4 that is a translation product of the human CCL4 gene or a 1:1 ortholog thereof. ACT-2 ACT2 CCL4 G-26 T-lymphocyte-secreted protein HC21 LAG-1 LAG1 MIP-1-beta MIP-1-beta(1-69) MIP1B PAT 744 SCYA4 SIS-gamma T-cell activation protein 2 immune activation protein 2 lymphocyte activation gene 1 protein macrophage inflammatory protein 1-beta protein H400 small-inducible cytokine A4 C-C motif chemokine 4 An eotaxin-like cytokine that is a translation product of the human CCL11 gene or a 1:1 ortholog thereof. C-C motif chemokine 11 CCL11 SCYA11 eosinophil chemotactic protein small-inducible cytokine A11 eotaxin A protein that is a translation product of the human CRP gene or a 1:1 ortholog thereof. CRP PTX1 C-reactive protein A protein that is a translation product of the human CSF2 gene or a 1:1 ortholog thereof. CSF CSF2 Csfgm GM-CSF GMCSF colony-stimulating factor molgramostin sargramostim granulocyte-macrophage colony-stimulating factor A protein that is a translation product of the human CSF3 gene or a 1:1 ortholog thereof. C17orf33 CSF3 Csfg G-CSF GCSF filgrastim lenograstim pluripoietin granulocyte colony-stimulating factor A protein that is a translation product of the human EGF gene or a 1:1 ortholog thereof. EGF pro-epidermal growth factor A protein that is a translation product of the human MFGE8 gene or a 1:1 ortholog thereof. HMFG MFG-E8 MFGE8 MFGM MP47 SED1 breast epithelial antigen BA46 milk fat globule-EGF factor 8 sperm surface protein SP47 lactadherin A protein that is a translation product of the human MPO gene or a 1:1 ortholog thereof. MPO myeloperoxidase A protein that is a translation product of the human REG1B gene or a 1:1 ortholog thereof. PSP-2 PSPS2 REG-1-beta REG1B REGL pancreatic stone protein 2 regenerating islet-derived protein 1-beta regenerating protein I beta lithostathine-1-beta A serpin that is a translation product of the human SERPINA1 gene or a 1:1 ortholog thereof. AAT PI PRO0684 PRO2209 SERPINA1 alpha-1 protease inhibitor alpha-1-antiproteinase serpin A1 alpha-1-antitrypsin A protein that is a translation product of the Escherichia coli K-12 aspC gene or a 1:1 ortholog thereof. AspAT aspC transaminase A aspartate aminotransferase A protein that is a translation product of the Escherichia coli K-12 phoA gene or a 1:1 ortholog thereof. APase phoA alkaline phosphatase 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. DenV-NS1 non-structural protein 1 NS1 A protein that is a translation product of the human GPT or GPT2 genes, 1:1 orthologs thereof, or a semi-ortholog thereof. fam:ALAT alanine aminotransferase An acetylcholinesterase that is a translation product of the Anopheles gambiae Ace gene or a 1:1 ortholog thereof. ACHE1 AChE Ace insect-type acetylcholinesterase A voltage-gated sodium channel subunit alpha that is a translation product of the fruit fly para gene or a 1:1 ortholog thereof. Nav1 para protein paralytic sodium channel 1 sodium channel protein para 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. para/var:not_S989 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. para/var:not_I1011 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. para/var:not_L1014 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. para/var:not_V1016 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. para/var:not_I1532 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. para/var:not_F1534 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. para/var:not_N1575 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. para/var:not_D1763 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. para/var:V1021G Kdr V1016G A protein that is a translation product of the fruit fly Rdl gene or a 1:1 ortholog thereof. Rdl 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. para/var:I784M Kdr I1011M 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. para/var:I784V Kdr I1011V 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. para/var:S762P Kdr S989P 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. para/var:L1014S Kdr L1014S 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. para/var:I1472T Kdr I1532T 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. para/var:F1318C Kdr F1534C 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. para/var:F1474L Kdr F1534L 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. para/var:F1474S Kdr F1534S 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. para/var:N1515Y Kdr N1575Y 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. para/var:D1763Y Kdr D1763Y A sodium channel protein para that is resistant to some insecticide. para/kdr 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. para/var:V1021I Kdr V1016I 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. ACHE1/var:not_G119 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. ACHE1/var:not_F290 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. ACHE1/var:not_F331 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. ACHE1/var:G119S AChE1 G119S 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. Rdl/var:not_A296 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. Rdl/var:A296G Rdl A296G 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. Rdl/var:A296S Rdl A296S An insect-type acetylcholinesterase that is resistant to some insecticide. ACHE1/resistant insecticide resistant acetylcholinesterase A gamma-aminobutyric acid receptor subunit beta that is resistant to some insecticide. Rdl/resistant 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. Gste2 glutathione S-transferase epsilon 2 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. Gste2/var:not_I114 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. Gste2/var:not_L119 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. Gste2/var:L119F Gste2 L119F A glutathione S-transferase epsilon 2 that is resistant to some insecticide. Gste2/resistant 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. para/var:L1014C Kdr L1014C 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. para/var:L1014F Kdr L1014F 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. sequence region 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. chromosome arm chromosome_arm SSLP are a kind of sequence alteration where the number of repeated sequences in intergenic regions may differ. SSLP simple sequence length polymorphism simple sequence length variation simple_sequence_length_variation A repeat_region containing repeat_units of 2 to 10 bp repeated in tandem. INSDC_feature:repeat_region INSDC_qualifier:microsatellite STR microsatellite locus microsatellite marker short tandem repeat microsatellite A sequence of nucleotides that has been algorithmically derived from an alignment of two or more different sequences. sequence assembly sequence_assembly A region of sequence implicated in an experimental result. experimental result region experimental_result_region 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. INSDC_feature:gene gene Region of 16S rRNA sequenced Cytosolic 16S rRNA is an RNA component of the small subunit of cytosolic ribosomes in prokaryotes. cytosolic 16S SSU RNA cytosolic 16S rRNA cytosolic 16S ribosomal RNA cytosolic rRNA 16S cytosolic_16S_rRNA A genome is the sum of genetic material within a cell or virion. genome A genotype is a variant genome, complete or incomplete. genotype A collection of sequences (often chromosomes) taken as the standard for a given organism and genome assembly. reference genome reference_genome A collection of one or more sequences of an individual. variant collection variant_collection A sequence variant where the structure of the gene is changed. Jannovar:gene_variant VAAST:gene_variant gene structure variant snpEff:GENE gene_variant A physical quality which inheres to the variant by virtue of the number instances of the variant within a population. variant frequency variant_frequency A quality inhering in a variant by virtue of its phenotype. variant phenotype variant_phenotype A continuous nucleotide sequence is inverted in the same position. inversion inversion A chromosomal inversion that does not include the centromere. paracentric inversion paracentric_inversion 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. Cq Ct threshold cycle Spontaneous bleeding 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. bleeding A pain that is characterized by a pain situated, or occurring, in or around a joint. arthralgia arthromyalgia joint pain Prostration Prostration is a general symptom characterized by complete physical or mental exhaustion. prostration Seizures seizure dry mouth Sore throat A pain that is characterized by a painful throat due to inflammation of the fauces and pharynx. sore throat throat pain Anorexia A nutrition, metabolism, and development symptom that is characterized by a loss of appetite especially when prolonged. anorexia Convulsions A nervous system symptom that is characterized by an abnormal violent and involuntary contraction or series of contractions of the muscles. convulsion Dizziness A balance symptom that is characterized by a sensation of unsteadiness accompanied by a feeling of movement within the head. dizzy dizziness septicemia Chills rigors chills Malaise 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. malaise Fatigue A neurological and physiological symptom that is characterized by a weariness or exhaustion from labor, exertion, or stress. fatigue Any portion of the organ that covers that body and consists of a layer of epidermis and a layer of dermis. portion of skin region of skin skin skin region skin zone zone of skin An organ that is capable of transducing sensory stimulus to the nervous system. Sinnesorgan organ of sense organ system organ of sensory organ system organ of sensory system sense organ system organ sensillum sensor sensory organ sensory organ system organ sensory system organ sense organ 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. lymph gland nodus lymphaticus lymph node The head is the anterior-most division of the body [GO]. adult head cephalic area head (volume) head Host body site Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome. biological structure connected biological structure anatomical structure Anatomical structure that performs a specific function or group of functions [WP]. anatomical unit body organ element organ A multicellular structure that is a part of an organ. cardinal organ part regional part of organ organ part The stage of development at which the animal is fully formed, including immaturity and maturity. Includes both sexually immature stage, and adult stage. adult stage fully formed animal stage juvenile-adult stage fully formed 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. ammocoete ammocoete stage bipinnaria bipinnaria stage caterpillar caterpillar stage glochidium glochidium stage grub grub stage larva larva stage leptocephalus leptocephalus stage maggot maggot stage metacestode naiad, nymph naiad, nymph stage nauplius nauplius stage nymph nymph stage planula planula stage tornaria trochophore trochophore stage veliger veliger stage wriggler wriggler stage zoea zoea stage larval stage 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. aurelia stage chrysalides stage chrysalis stage pupa stage pupal stage End of the life of an organism. death death stage An section of a respiratory tract. respiratory tract subdivision of respiratory tract proximo-distal subdivision of respiratory tract An anatomical structure that develops from the endoderm and the mesoderm. mixed endoderm/mesoderm-derived structure Host life stage A spatiotemporal region encompassing some part of the life cycle of an organism. developmental stage stage life cycle stage A tube in the respiratory system. Examples: bronchus, bronchiole, trachea. airway respiratory conducting tube segment of tracheobronchial tree tracheobronchial tree segment respiratory tube 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. bowel intestinal tract 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). bucca buccal cavity cavity of mouth oral cavity 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. excreted substance excretion portion of excreted substance waste substance excreta A fluid that is composed of blood plasma and erythrocytes. portion of blood vertebrate blood whole blood blood 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]. mucosa of organ mucosa of organ part mucosal region mucous membrane organ mucosa region of mucosa tunica mucosa mucosa A portion of organism substance that is produced by exocrine glands. bodily secretion exocrine gland fluid exocrine gland fluid or secretion exocrine gland fluid/secretion exocrine gland secretion external secretion secreted substance secretion secretion of exocrine gland Host body product Material anatomical entity in a gaseous, liquid, semisolid or solid state; produced by anatomical structures or derived from inhaled and ingested substances that have been modified by anatomical structures as they pass through the body. body fluid or substance body substance organism substance portion of body substance portion of organism substance organism substance Anatomical entity that has mass. material anatomical entity Host body habitat Anatomical entity that has no mass. immaterial physical anatomical entity immaterial anatomical entity 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. anatomic region body part body region cardinal body part organism subdivision Anatomical group whose component anatomical structures lie in close proximity to each other. anatomical cluster 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 simple tissue tissue portion tissue 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]. epithelial tissue portion of epithelium epithelium Unilaminar epithelium, which consists of a single layer of columnar cells. Examples: ciliated columnar epithelium, gastric epithelium, microvillus columnar epithelium.[FMA]. columnar epithelium columnar epithlium epithelium simplex columnare simple columnar epithelia simple columnar epithelium simple columnar epithelium 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. anterior intestine gaster mesenteron stomach chamber ventriculus stomach A myogenic muscular circulatory organ found in the vertebrate cardiovascular system composed of chambers of cardiac muscle. It is the primary circulatory organ. branchial heart cardium chambered heart vertebrate heart heart 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]. encephalon suprasegmental levels of nervous system suprasegmental structures synganglion the brain brain The transparent anterior portion of the fibrous coat of the eye that serves as the chief refractory structure. cornea of camera-type eye corneas tunica cornea cornea An organ that detects light. light-detecting organ visual apparatus eye 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. haemolymph hemolymph Saliva-secreting exocrine glands of the oral cavity[GO]. glandulae salivariae salivary gland saliva-secreting gland 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]. mesenteron midgut The caudalmost subdivision of a digestive tract. metenteron hindgut Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species. anatomical entity Transudate contained in the pleural cavity. pleural fluid Excretion that is the output of a kidney. urine A thin musculomebranous barrier that separates the abdominal and thoracic cavities. Often used for breathing control. diaphragm muscle diaphragm of thorax midriff phren thoracic diaphragm diaphragm Muscle tissue that consists primarily of skeletal muscle fibers. skeletal muscle skeletal muscle system somatic muscle skeletal muscle tissue 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.. back back of body proper dorsal part of organism dorsum 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. blind intestine blindgut caeca caecum ceca cecum intestinum caecum intestinum crassum caecum intestinum crassum cecum caecum Anatomical cavity bounded by visceral and parietal peritoneum. cavitas peritonealis saccus serosus peritonei peritoneal cavity Mucosal layer that lines the intestine. bowel mucosa bowel mucosa of organ bowel mucous membrane bowel organ mucosa intestine mucosa intestine mucosa of organ intestine mucous membrane intestine organ mucosa mucosa of bowel mucosa of intestine mucosa of organ of bowel mucosa of organ of intestine mucous membrane of bowel mucous membrane of intestine organ mucosa of bowel organ mucosa of intestine tunica mucosa intestini intestinal mucosa A clear, colorless, bodily fluid, that occupies the subarachnoid space and the ventricular system around and inside the brain and spinal cord. CSF cerebral spinal fluid liquor cerebrospinalis spinal fluid cerebrospinal fluid head region head subdivision region of head subdivision of head The part of the forelimb extending from the shoulder to the autopod[cjm]. brachium upper extremity arm Skeletal element that is composed of bone tissue. bone bone organ bones bone element The segment of the respiratory tract that starts proximally with the nose and ends distally with the cricoid cartilage, before continuing to the trachea. upper respiratory tract The segment of the respiratory tract that starts proximally with the trachea and includes all distal structures including the lungs[WP,modified]. lower respiratory system lower respiratory tract 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. cavitas nasalis cavitas nasi cavity of nose cavity of olfactory apparatus cavum nasi nasal canal nasal conduit space nasal fossa nasal pit olfactory cavity olfactory chamber olfactory chamber cavity olfactory pit nasal cavity A muscular organ in the floor of the mouth. glossus tongue The section of the pharynx that lies above the soft palate. Nasenrachenraum epipharynx nasal part of pharynx pars nasalis pharyngis rhinopharynx nasopharynx The portion of the pharynx that lies between the soft palate and the upper edge of the epiglottis. mesopharynx oral part of pharynx pars oralis pharyngis oropharynx The part of the ear that projects from the head, connecting to the external acoustic meatus. auricle auricle of ear auricle of external ear auricula auricula (auris externa) pinna of ear pinnae pinna The small curved bones that extends horizontally along the lateral wall of the nasal passage. concha ossified nasal turbinal ossified nasal turbinate ossified turbinate turbinal bone turbinate bone turbinate bone The smooth stratified squamous epithelium that covers the outer surface of the cornea. anterior corneal epithelium anterior endothelium of cornea cornea epithelial tissue cornea epithelium e. anterius corneae endothelium anterius corneae endothelium camerae anterioris bulbi endothelium corneale epithelial tissue of cornea epithelium anterius (cornea) epithelium anterius corneae epithelium corneæ anterior layer epithelium of cornea epithelium posterius corneae external epithelium of cornea corneal epithelium A thick watery refractive medium that fills the space between the lens and the cornea[WP]. aqueous humor aqueous humour humor aquosus aqueous humor of eyeball The mucous membrane that lines the nasal cavity[MP]. mucosa of nose mucous membrane of nose nasal mucosa tunica mucosa nasalis tunica mucosa nasi nasal cavity mucosa A fluid produced in the oral cavity by salivary glands, typically used in predigestion, but also in other functions. sailva normalis saliva atomaris saliva molecularis salivary gland secretion saliva 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]. bulb bulbus medulla medulla oblonzata metepencephalon medulla oblongata An emulsion of fat globules within a fluid that is secreted by the mammary gland during lactation. mammary gland milk milk Organism substance that is composed of sperm cells suspended in seminal fluid. ejaculate sperm semen 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. allantoic placenta eutherian placenta placenta Portion of semisolid bodily waste discharged through the anus[MW,modified]. cow dung cow pat droppings dung excrement excreta faeces fecal material fecal matter fewmet frass guano ordure piece of shit portion of dung portion of excrement portion of faeces portion of fecal material portion of fecal matter portion of feces portion of guano portion of scat portionem cacas scat spoor spraint stool feces Respiration organ that develops as an outpocketing of the esophagus. pulmo lung 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. splanchnic tissue viscera visceral organ visceral organ system visceral tissue viscus The organ that functions to filter blood and to store red corpuscles and platelets. lien spleen 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]. iecur jecur liver An organ that aids digestion and stores bile produced by the liver[WP]. cholecyst gall bladder vesica biliaris vesica fellea gallbladder A paired organ of the urinary tract which has the production of urine as its primary function. reniculate kidney kidney The middle layer of the heart, comprised mainly of striated cardiac muscle fibers. cardiac muscle heart muscle heart myocardium muscle of heart myocardium 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. ducted gland glandula exocrina exocrine gland Endocrine glands are glands of the endocrine system that secrete their products directly into the circulatory system rather than through a duct.[WP, modified]. ductless gland glandula endocrina glandulae endocrinae endocrine gland Anatomical structure of largely lymphoid tissue that functions in cell-mediated immunity by being the site where T cells develop. thymus gland thymus organ thymus The soft tissue that fills the cavities of bones. medulla of bone medulla ossea medulla ossium medullary bone bone marrow Muscle tissue is a contractile tissue made up of actin and myosin fibers[GO]. muscular tissue portion of muscle tissue textus muscularis muscle tissue An external caudal extension of the body. In chordates, the tail is post-anal, in other animals the anus ends in the tail. caudal subdivision tail Replacement bone that forms within cartilage. cartilaginous bone endochondral bones ossified chondrogenic bone endochondral bone An organ that functions as a secretory or excretory organ. Druese glandula glandular organ gland 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. gill 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. ammocoete bipinnaria caterpillar glochidium grub larval organism leptocephalus maggot naiad nymph planula tadpole trochophore veliger wriggler zoea larva 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. cavity anatomical cavity Anatomical structure that overlaps the outer epithelial layer and is adjacent to the space surrounding the organism. anatomical surface feature surface feature surface region surface structures surface structure 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. organ compound organ The trachea is the portion of the airway that attaches to the bronchi as it branches [GO:dph]. cartilaginous trachea tracheal tubule vertebrate trachea windpipe trachea A gland that is part of a digestive tract [Automatically generated definition]. digestive tract gland gland of digestive tract gland of lower gastrointestinal tract gut gland lower gastrointestinal tract gland gland of digestive tract A bone that is part of a head [Automatically generated definition]. adult head bone adult head bone organ bone of adult head bone of head bone organ of adult head bone organ of head craniofacial bone head bone organ head bone A bone that is part of a facial skeleton [Automatically generated definition]. bone of facial skeleton bone of viscerocranium facial bone facial skeleton bone viscerocranium bone facial bone 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]. ethmo-turbinate ethmoturbinal ethmoturbinate nasal turbinate of ethmoid bone turbinate of ethmoid bone nasal concha of ethmoid bone An anatomical structure that develops (entirely or partially) from the endoderm. endoderm-derived structure An anatomical structure that develops (entirely or partially) from the mesoderm. mesodermal derivative mesoderm-derived structure An anatomical structure that develops (entirely or partially) from the ectoderm. ectodermal deriviative ectoderm-derived structure Organ that is part of the hematopoietic system. haematological system organ haemopoietic system organ hematopoeitic or lymphoid organ hematopoeitic organ hematopoietic system organ lymph organ lymphoid organ organ of haematological system organ of haemopoietic system organ of hematopoietic system organ of organa haemopoietica organa haemopoietica organ hemopoietic organ 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. instar larval stage Organ consisting of skeletal tissue. Encompasses whole bones, fused bones, cartilaginious elements, teeth, dermal denticles. skeletal element A mucosa that is part of a gastrointestinal system. digestive tract mucosa gut mucosa gut mucuous membrane mucosa of gut gastrointestinal system mucosa 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. airway epithelium epithelial tissue of respiratory tract epithelium of respiratory tract respiratory epithelium respiratory tract epithelial tissue respiratory tract epithelium A proximal-distal subdivision of the digestive tract. alimentary system subdivision gut section intestinal tract segment of intestinal tract subdivision of alimentary system subdivision of digestive tract A part of a wall of an organ that forms a layer. organ component layer An organ that is part of a immune system [Automatically generated definition]. immune system organ immune organ Muscle structures are contractile cells, tissues or organs that are found in multicellular organisms[GO]. muscle muscle element musculus muscle structure 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. avian beak bill rostrum beak An organ or element that is in the abdomen. Examples: spleen, intestine, kidney, abdominal mammary gland. abdomen organ abdomen element 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. trunk organ trunk region element An organ or element that is in the thoracic cavity. Examples: lung, heart, longus colli. thoracic cavity organ thoracic cavity element An organ that part of the thoracic segment region. This region can be further subdividied chest and thoracic cavity regions. upper body organ thoracic segment organ An epithelium that lines the nasal cavity. nasal epithelium nasal mucosa nasal cavity epithelium Epithelium that derives from the endoderm. Examples: urothelium, transitional epithelium of ureter, epithelium of prostatic gland.[FMA]. endoderm-derived epithelium endoepithelium endo-epithelium bone organ zone zone of bone organ 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. middle concha middle nasal turbinate middle turbinate middle nasal concha The laminar structure of the heart. heart layer Body substance in a liquid or semi-solid state in the eyeball which serves to refract light. ocular refractive media Liquid components of living organisms. includes fluids that are excreted or secreted from the body as well as body water that normally is not. body fluid fluid bodily fluid A portion of organism substance that secreted_by a respiratory system. respiratory system fluid respiratory system secretion respiratory system fluid/secretion digestive fluid digestive juice digestive system fluid or secretion digestive system secreted substance Any gland that is part of the digestive system. digestive gland digestive system gland Matter ejected from the lungs, bronchi, and trachea, through the mouth. expectoration sputum A pouched enlargement of the gullet of many birds that serves as a receptacle for food and for its preliminary maceration. esophageal diverticulum esophageal pouch crop Simple columnar epithelium in which the luminal side of the cells bears cilia. Examples: epithelium of trachea, epithelium of uterine tube.[FMA]. ciliated columnar epithelium Any bodily fluid that has passed through a membrane such as the capillary wall, as a result of unbalanced hydrostatic and osmotic forces. plasma ultrafiltrate transudate The external junctural region between the lower part of the abdomen and the thigh. groin groin area groin region iliac fossa viewed surgically iliac region inguen inguinal region inguinal part of abdomen Pregnant An organism containing a developing embryo, fetus, or unborn offspring within the body. gravid pregnant adult pregnant adult stage pregnant organism pregnant stage gravid organism The axilla is the area directly under the joint where the forelimb connects to the shoulder. arm pit armpit armpits axilla axillae axillary region oxter regio axillaris underarm axilla Branch or outpocketing of the digestive tract. diverticulum of gut intestinal pouch digestive tract diverticulum diverticulum pouch sac An anatomical structure that has more than one cell as a part. multicellular structure multicellular anatomical structure An organ of the digestive tract that is capable of retaining and storing food. food storage organ Gland of the epithelium lining the oral cavity. The most common are the salivary glands. buccal gland gland of oral opening gland of oral region mouth gland oral cavity gland oral region gland oral gland An anatomical structure that develops from the neural crest. neural crest-derived structure 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. endochondral replacement element endochondral element Epithelium composed of cells that develops from the ectoderm[FMA,modified]. ectoderm-derived epithelium ecto-epithelium 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. appendage segment appendicular segment 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. axial subdivision of organism body segment main body segment subdivision of organism along main body axis Blood that remains in the placenta and in the attached umbilical cord after childbirth[WP]. cord blood fetal blood umbilical cord blood umbilical cord blood subdivision of tube Any of the organs or elements that are part of the digestive system. Examples: tongue, esophagus, spleen, crop, lunge feeding organ, tooth elements. digestive organ digestive system organ digestive system element A larval stage of that is the immature stage of some invertebrates that undergoe gradual metamorphosis (hemimetabolism) before reaching its adult stage. nymph nymph stage Any structure that is placed on one side of the left-right axis of a bilaterian. lateral structure An epithelium that is part of a camera-type eye. eye epithelium A viscus that is part of a abdomen. abdominal viscera abdominal viscera set set of abdominal viscera abdominal viscera A life cycle stage that starts at completion of development and growth of the sexually mature adult animal, and ends before senescence. adulthood stage prime adult stage Any organ component layer that consists of muscle tissue. layer of muscle tissue A membranous sac in animals that serves as the receptacle of a liquid or contains gas. bladder bladder organ Any region of epithelium that is part of a skin region. skin epithelium sensory organ epithelium nose epithelium 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. external soft tissue zone A skeletal element of the ethmoid region with complex morphology that are lined with mucuous membranes involved in either olfaction or air conditioning. concha conchae nasales nasal concha nasal turbinal nasal turbinal element nasal turbinate turbinal turbinate nasal turbinal Paired, vertical, and relatively straight plates that form the anterior limit of the nasal capsule. prenasal wall solum anterius anterior nasal wall Left part of the organism dorsal to a horizontal plane and bounded on one side by the same transverse plane. left side of back Right part of the organism dorsal to a horizontal plane and bounded on one side by the same transverse plane. right side of back Blood located in the placenta. placental blood "A unit which is a standard measure of the distance between two points." [Wikipedia:Wikipedia] length unit "A unit which is a standard measure of the amount of matter/energy of a physical object." [Wikipedia:Wikipedia] mass unit "A unit which is a standard measure of the dimension in which events occur in sequence." [Wikipedia:Wikipedia] time unit "A unit which is a standard measure of the average kinetic energy of the particles in a sample of matter." [Wikipedia:Wikipedia] temperature unit "A unit which is a standard measure of the amount of a 2-dimensional flat surface." [UOC:GVG] area unit "A unit which represents a standard measurement of how much of a given substance there is mixed with another substance." [UOC:GVG] concentration unit "A density unit which is a standard measure of the mass of a substance in a given volume." [UOC:GVG] mass density unit "A density unit which is a standard measure of the mass exerting an influence on a given area." [Wikipedia:Wikipedia] area density unit "A unit which is a standard measure of the amount of space occupied by any substance, whether solid, liquid, or gas." [NIST:NIST] volume unit "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] parts per notation unit "A unit which is a standard measure of the influence exerted by some mass." [Wikipedia:Wikipedia] density unit "A unit which is a standard measure of physical quantity consisting of only a numerical number without any units." [Wikipedia:Wikipedia] dimensionless unit "A dimensionless ratio unit which denotes numbers as fractions of 100." [Wikipedia:Wikipedia] percent "A dimensionless unit which denotes a simple count of things." [MGED:MGED] count unit "A dimensionless unit which denotes an amount or magnitude of one quantity relative to another." [Wikipedia:Wikipedia] ratio "A dimensionless ratio unit which relates the part (the numerator) to the whole (the denominator)." [Wikipedia:Wikipedia] fraction "A concentration unit which denotes the average cell number in a given volume." [Bioedonline:Bioedonline] cell concentration unit "A concentration unit which is a standard measure of the amount of the action of a catalyst in a given volume." [UOC:GVG] catalytic (activity) concentration unit "A dimensionless concentration unit which denotes the given volume of the solute in the total volume of the resulting solution." [NIST:NIST] volume per unit volume "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] dose unit 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. route of administration Haemophilus influenzae serotype b 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. antibody 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. replicate Platelets The number of PLATELETS per unit volume in a sample of venous BLOOD. platelet count Heart rate The number of times the HEART VENTRICLES contract per unit of time, usually per minute. heart rate Birth weight The mass or quantity of heaviness of an individual at BIRTH. It is expressed by units of pounds or kilograms. birth weight Hematocrit (%) 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. hematocrit An fasting blood glucose measurement is a measurement of glucose in the blood of a patient at some defined time point after eating. fasting blood glucose measurement Birth date The point in time at which an individual was born. date of birth The age at which death occurs. age at death 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 parasitemia measurement A condition or physical state produced by the ingestion, injection, inhalation of or exposure to a deleterious agent. poisoning Genitourinary condition A disease that involves the genitourinary system. [database_cross_reference: MONDO:patterns/location] disease of genitourinary system Abnormal diagnostic imaging Abnormal result of a diagnostic imaging test. abnormal result of diagnostic imaging Abortion type the ending of pregnancy by removing a fetus or embryo before it can survive outside the uterus. abortion A categorical household wealth index representing the bottom third of values for the numerical household wealth index. Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey PRISM Penn Group obsolete bottom household wealth index true A categorical household wealth index representing the middle third of values for the numerical household wealth index. Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey PRISM Penn Group obsolete middle household wealth index true A categorical household wealth index representing the top third of values for the numerical household wealth index. Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey PRISM Penn Group obsolete top household wealth index true A information content entity created to indicate the lack of air bricks in the dwelling. Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey PRISM Penn Group obsolete no airbrick true A information content entity indicating that the household eats in restaurants. Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey PRISM Penn Group obsolete record of eating in restaurants true A information content entity indicating that the household does not cook in the dwelling. Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey PRISM Penn Group obsolete record of no cooking at home true An information content entity indicates no toilet facility in the dwelling. Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey PRISM Penn Group obsolete record of no toilet facility true An information content entity indicating that a household uses a neighbours' toilet facility. Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey PRISM Penn Group obsolete record of using neighbours' toilet true A time of screening occurring during the initial human subject enrollment period. Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey PRISM Penn Group obsolete time of screening during initial enrollment true A time of screening occuring after the initial enrollment period had ended and the study had begun. Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey PRISM Penn Group obsolete time of screenng after initial enrollment true PRISM obsolete unknown withdrawal reason true PRISM obsolete withdrew due to death true PRISM obsolete inability to comply with protocol true PRISM obsolete moved out of area true PRISM obsolete reached 11 years of age true PRISM obsolete unable to be located for over 120 days true PRISM obsolete withdrawal of all children under care true PRISM obsolete withdrawal of informed consent true PRISM obsolete unknown cause of death true PRISM obsolete complications of HIV true PRISM obsolete diarrheal illness true PRISM obsolete suicide true PRISM obsolete Bwindi Hospital true PRISM obsolete Jinja Hospital true PRISM obsolete Kauka Health Centre true PRISM obsolete Kihihi Health Centre IV true PRISM obsolete Nagongera Health Centre IV true PRISM obsolete Tororo District Hospital true PRISM obsolete record of unknown death location true the growth of a child during three years after birth A unit that represents a change in length of one centimeter in one year. John Judkins ORCID:0000-0001-6595-0902 cm/year VEuPathDB https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/522 ClinEpiDB Danica Helb Jie Zheng 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. John Judkins ORCID:0000-0001-6595-0902 kg/year VEuPathDB https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/523 ClinEpiDB Danica Helb Jie Zheng kilogram per year An organization that manufactures mosquito traps and other mosquito control products. obsolete BioGents true 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. Person: John Judkins VBcv:0001116 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. Person: John Judkins VBcv:0001124 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. Person: John Judkins VBcv:0001111 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. Uganda example to be eventually removed 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 Person:Alan Ruttenberg failed exploratory term 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. metadata complete organizational term Term created to ease viewing/sort terms for development purpose, and will not be included in a release organizational term 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." 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. metadata incomplete uncurated Nothing done yet beyond assigning a unique class ID and proposing a preferred term. uncurated 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. pending final vetting Core is an instance of a grouping of terms from an ontology or ontologies. It is used by the ontology to identify main classes. PERSON: Alan Ruttenberg PERSON: Melanie Courtot obsolete_core true placeholder removed placeholder removed terms merged An editor note should explain what were the merged terms and the reason for the merge. terms merged 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 imported 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. term split 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. Alan Ruttenberg A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf universal 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. Alan Ruttenberg defined class 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 Alan Ruttenberg named class expression to be replaced with external ontology term Terms with this status should eventually replaced with a term from another ontology. Alan Ruttenberg group:OBI to be replaced with external ontology term 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. Alan Ruttenberg group:OBI requires discussion Illumina Philippe Rocca-Serra Illumina BioGents An organization that manufactures mosquito traps and other mosquito control products. John Judkins WEB:https://eu.biogents.com/about-biogents/ BioGents Abbott A manufacturer of rapid point-of-care assay devices. John Judkins ORCID:0000-0001-6595-0902 WEB:https://www.globalpointofcare.abbott/en/about.html https://github.com/obi-ontology/obi/issues/1456 Abbott J. Mitra A manufacturer of in vitro diagnostic assay kits in India. John Judkins ORCID:0000-0001-6595-0902 WEB:https://jmitra.co.in/about-us/ https://github.com/obi-ontology/obi/issues/1456 J. Mitra InBios A manufacturer that specializes in in vitro diagnostic devices designed to test for infectious diseases. John Judkins ORCID:0000-0001-6595-0902 WEB:https://inbios.com/about/ https://github.com/obi-ontology/obi/issues/1456 InBios 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. https://github.com/information-artifact-ontology/ontology-metadata/issues/77 https://orcid.org/0000-0001-5208-3432 out of scope "A mass unit which is equal to one millionth of a gram or 10^[-6] g." [UOC:GVG] microgram "A mass unit which is equal to one thousandth of one millionth of a gram or 10^[-9] g." [UOC:GVG] nanogram "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] degree Celsius "A time unit which is equal to 60 seconds." [Wikipedia:Wikipedia] minute "A time unit which is equal to 3600 seconds or 60 minutes." [Wikipedia:Wikipedia] hour "A time unit which is equal to 24 hours." [Wikipedia:Wikipedia] day "A time unit which is equal to 12 months which in science is taken to be equal to 365.25 days." [Wikipedia:Wikipedia] year "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] parts per million "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] parts per billion "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] pi "A dimensionless count unit which denotes the number of molecules." [MGED:MGED] molecule count "A dimensionless percent unit which denotes the homogeneity of a biomaterial." [MGED:MGED] purity percentage "A dimensionless percent unit which denotes the density of an attached or monolayer culture (e.g., cell culture)." [MGED:MGED] confluence percentage "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] degree Fahrenheit "A dimensionless concentration notation which denotes the acidity of a solution in terms of activity of hydrogen ions (H+)." [Wikipedia:Wikipedia] pH "A specific volume unit which is equal to one liter volume occupied by one kilogram of a particular substance." [NIST:NIST] liter per kilogram "A specific volume unit which is equal to a thousandth of a liter per kilogram or 10^[-3] l/kg." [NIST:NIST] milliliter per kilogram "A specific volume unit which is equal to one millionth of a liter per kilogram or 10^[-6] l/kg." [NIST:NIST] microliter per kilogram "A unit of cell concentration which is equal to one cell in a volume of 1 milliliter." [Bioedonline:Bioedonline] cells per milliliter "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] katal per cubic meter "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] katal per liter "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] milliliter per cubic meter "A volume per unit volume unit which is equal to one millionth of a liter of solute in one liter of solution." [NIST:NIST] milliliter per liter "A mass density unit which is equal to mass of an object in grams divided by the volume in deciliters." [UOC:GVG] gram per deciliter "A mass unit density which is equal to mass of an object in milligrams divided by the volume in liters." [UOC:GVG] milligram per liter "A mass unit density which is equal to mass of an object in micrograms divided by the volume in millliters." [UOC:GVG] microgram per milliliter "A mass unit density which is equal to mass of an object in micrograms divided by the volume in liters." [UOC:GVG] microgram per liter "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] milligram per square meter "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] acre "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] gram per square meter "A unit of mass concentration defined as the number of micrograms of a substance per 250 ml Wheaton bottle." [UOB:LTS] micrograms per wheaton bottle