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 2023-03-20 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 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 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 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 Hordeolum is a sequelae of infectious and parasitic disease consisting of 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. 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. 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. 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. 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 (feet) 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. 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. 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. soil A significant accumulation of water which is part of a marine biome. 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. 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. sediment Particulate environmental material with diameters less than 500 micrometers. dust Water which contains a significant concentration of dissolved salts. saline water Water which has a low concentration of dissolved solutes, particularly that of sodium chloride. 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. 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. surface layer Airborne solid particles (also called dust or particulate matter (PM)) or liquid droplets. aerosol Anthropogenic material in or on which organisms may live. anthropogenic environmental 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. 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. 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. environmental zone A building part is a construction which is part of a building. 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. 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. 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 building roof Thatch is material composed of dry vegetation such as straw, water reed, sedge (Cladium mariscus), rushes, or heather. 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. 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. toilet fixture A pit latrine is a latrine which is constructed by digging a hole in the ground. 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. 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). 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. 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. 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. 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. metallic material Weather Environmental variability which inheres in an astronomical body part or in outer space. 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. 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. excreta material An environmental material consisting of organic matter from plants and/or animals that is used in agriculture as fertilizer. 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 in India 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 An information content entity about healthcare that is private or public. healthcare information 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 Sample collection location 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</