EVORAO

Class: Pathogen identification (PathogenIdentification)

A collection of distinguishing information that enables the differentiation of a pathogen from another.

 classDiagram
    class PathogenIdentification
    click PathogenIdentification href "../PathogenIdentification"
      Resource <|-- PathogenIdentification
        click Resource href "../Resource"
      
      PathogenIdentification : dateIssued
        
      PathogenIdentification : dateModified
        
      PathogenIdentification : genotype
        
      PathogenIdentification : hostType
        
      PathogenIdentification : identifier
        
      PathogenIdentification : iri
        
      PathogenIdentification : isolate
        
      PathogenIdentification : keyword
        
      PathogenIdentification : pathogenName
        
          
    
    
    PathogenIdentification --> "1" CommonName : pathogenName
    click CommonName href "../CommonName"

        
      PathogenIdentification : pathogenType
        
      PathogenIdentification : publisher
        
          
    
    
    PathogenIdentification --> "0..1" PersonOrOrganization : publisher
    click PersonOrOrganization href "../PersonOrOrganization"

        
      PathogenIdentification : serotype
        
      PathogenIdentification : strain
        
      PathogenIdentification : subspecies
        
      PathogenIdentification : taxon
        
          
    
    
    PathogenIdentification --> "1" Taxon : taxon
    click Taxon href "../Taxon"

        
      PathogenIdentification : variant
        
          
    
    
    PathogenIdentification --> "0..1" Variant : variant
    click Variant href "../Variant"

Inheritance

Resource
- PathogenIdentification

Slots

Name	Cardinality and Range	Description	Inheritance
taxon	1 Taxon	Scientifically classified group or entity within the reference taxonomy	direct
pathogenName	1 CommonName	A pathogen common name or a name that describes a group of pathogens	direct
pathogenType	1 String	Identification of the specific type of pathogen among the listed categories e	direct
hostType	* recommended String	Indication of the possible host(s) for the identified pathogens among the lis…	direct
subspecies	0..1 String	Taxonomic subdivision below species used to differentiates closely related pa…	direct
strain	0..1 recommended String	Identifier given to a genetic variant within a single species	direct
isolate	0..1 String	Identifier given to a pathogen that has been isolated from an infected host a…	direct
genotype	0..1 String	Genotype information that identifies organisms that cluster in phylogenetic t…	direct
serotype	0..1 String	Genetically related pathogens that group together based on serological relati…	direct
variant	0..1 Variant	An organism with one or more new mutations is referred to as a “variant” of t…	direct
keyword	* String	A keyword or tag describing the resource	Resource
dateIssued	0..1 Datetime	Date of formal issuance (e	Resource
dateModified	0..1 Datetime	Most recent date on which the resource was changed, updated or modified	Resource
identifier	* String	A unique identifier of the resource being described or cataloged	Resource
iri	* Uri	International Resource Identifier (IRI) that uniquely identifies or refers to…	Resource
publisher	0..1 PersonOrOrganization	The entity responsible for making the resource available	Resource

Usages

used by	used in	type	used
ProductOrService	pathogenIdentification	range	PathogenIdentification
Service	pathogenIdentification	range	PathogenIdentification
Product	pathogenIdentification	range	PathogenIdentification
Antibody	pathogenIdentification	range	PathogenIdentification
Hybridoma	pathogenIdentification	range	PathogenIdentification
Protein	pathogenIdentification	range	PathogenIdentification
NucleicAcid	pathogenIdentification	range	PathogenIdentification
DetectionKit	pathogenIdentification	range	PathogenIdentification
Bundle	pathogenIdentification	range	PathogenIdentification
Pathogen	pathogenIdentification	range	PathogenIdentification
Virus	pathogenIdentification	range	PathogenIdentification
Bacterium	pathogenIdentification	range	PathogenIdentification
Fungus	pathogenIdentification	range	PathogenIdentification
Protozoan	pathogenIdentification	range	PathogenIdentification
Viroid	pathogenIdentification	range	PathogenIdentification
Prion	pathogenIdentification	range	PathogenIdentification

Identifier and Mapping Information

Schema Source

from schema: https://w3id.org/evorao/

Mappings

Mapping Type	Mapped Value
self	EVORAO:PathogenIdentification
native	EVORAO:PathogenIdentification
broad	dwc:Identification, dwc:Identification

LinkML Source

Direct

Induced

```yaml name: PathogenIdentification description: A collection of distinguishing information that enables the differentiation of a pathogen from another. title: Pathogen identification from_schema: https://w3id.org/evorao/ broad_mappings: - dwc:Identification - dwc:Identification is_a: Resource slot_usage: taxon: name: taxon description: Scientifically classified group or entity within the reference taxonomy. title: taxon comments: - The taxon of the highest rank known that can be used to classify a pathogen or group of pathogens (e.g viruses) in the reference taxonomy. close_mappings: - schema:taxonomicRange - dwc:taxonID - dwc:toTaxon related_mappings: - dwc:Taxon domain_of: - PathogenIdentification - Taxonomy - ClinicalGroup range: Taxon required: true multivalued: false pathogenName: name: pathogenName description: A pathogen common name or a name that describes a group of pathogens. title: pathogen name exact_mappings: - dwc:organismName domain_of: - PathogenIdentification range: CommonName required: true multivalued: false pathogenType: name: pathogenType description: Identification of the specific type of pathogen among the listed categories e.g. 'Virus','Viroid','Bacterium'... title: pathogen type exact_mappings: - schema:infectiousAgentClass close_mappings: - dwc:organismScope domain_of: - PathogenIdentification range: string required: true multivalued: false hostType: name: hostType description: Indication of the possible host(s) for the identified pathogens among the listed main categories. title: host type domain_of: - PathogenIdentification range: string required: false recommended: true multivalued: true subspecies: name: subspecies description: Taxonomic subdivision below species used to differentiates closely related pathogen populations within a single species. title: subspecies domain_of: - PathogenIdentification range: string required: false multivalued: false strain: name: strain description: Identifier given to a genetic variant within a single species. title: strain domain_of: - PathogenIdentification range: string required: false recommended: true multivalued: false isolate: name: isolate description: Identifier given to a pathogen that has been isolated from an infected host and propagated in a laboratory culture. The isolate information may include an internal reference code from the laboratory that took the sample or performed the isolation, as well as details about the specific conditions of isolation, such as the name of the town, hospital, and type of host. title: isolate domain_of: - PathogenIdentification range: string required: false multivalued: false genotype: name: genotype description: Genotype information that identifies organisms that cluster in phylogenetic trees, thus different clusters are distinct genotypes. title: genotype close_mappings: - geno:0000222 domain_of: - PathogenIdentification range: string required: false multivalued: false serotype: name: serotype description: Genetically related pathogens that group together based on serological relationships. title: serotype domain_of: - PathogenIdentification range: string required: false multivalued: false variant: name: variant description: An organism with one or more new mutations is referred to as a “variant” of the original organism if not sufficiently different to be termed a distinct strain. title: variant domain_of: - PathogenIdentification range: Variant required: false multivalued: false attributes: taxon: name: taxon description: Scientifically classified group or entity within the reference taxonomy. title: taxon comments: - The taxon of the highest rank known that can be used to classify a pathogen or group of pathogens (e.g viruses) in the reference taxonomy. from_schema: https://w3id.org/evorao/ close_mappings: - schema:taxonomicRange - dwc:taxonID - dwc:toTaxon related_mappings: - dwc:Taxon rank: 1000 alias: taxon owner: PathogenIdentification domain_of: - PathogenIdentification - Taxonomy - ClinicalGroup range: Taxon required: true multivalued: false pathogenName: name: pathogenName description: A pathogen common name or a name that describes a group of pathogens. title: pathogen name from_schema: https://w3id.org/evorao/ exact_mappings: - dwc:organismName rank: 1000 alias: pathogenName owner: PathogenIdentification domain_of: - PathogenIdentification range: CommonName required: true multivalued: false pathogenType: name: pathogenType description: Identification of the specific type of pathogen among the listed categories e.g. 'Virus','Viroid','Bacterium'... title: pathogen type from_schema: https://w3id.org/evorao/ exact_mappings: - schema:infectiousAgentClass close_mappings: - dwc:organismScope rank: 1000 alias: pathogenType owner: PathogenIdentification domain_of: - PathogenIdentification range: string required: true multivalued: false equals_string_in: - Virus - Bacterium - Fungus - Protozoan - Viroid - Prion hostType: name: hostType description: Indication of the possible host(s) for the identified pathogens among the listed main categories. title: host type from_schema: https://w3id.org/evorao/ rank: 1000 alias: hostType owner: PathogenIdentification domain_of: - PathogenIdentification range: string required: false recommended: true multivalued: true equals_string_in: - Animal - Human - Plant subspecies: name: subspecies description: Taxonomic subdivision below species used to differentiates closely related pathogen populations within a single species. title: subspecies from_schema: https://w3id.org/evorao/ rank: 1000 alias: subspecies owner: PathogenIdentification domain_of: - PathogenIdentification range: string required: false multivalued: false strain: name: strain description: Identifier given to a genetic variant within a single species. title: strain from_schema: https://w3id.org/evorao/ rank: 1000 alias: strain owner: PathogenIdentification domain_of: - PathogenIdentification range: string required: false recommended: true multivalued: false isolate: name: isolate description: Identifier given to a pathogen that has been isolated from an infected host and propagated in a laboratory culture. The isolate information may include an internal reference code from the laboratory that took the sample or performed the isolation, as well as details about the specific conditions of isolation, such as the name of the town, hospital, and type of host. title: isolate from_schema: https://w3id.org/evorao/ rank: 1000 alias: isolate owner: PathogenIdentification domain_of: - PathogenIdentification range: string required: false multivalued: false genotype: name: genotype description: Genotype information that identifies organisms that cluster in phylogenetic trees, thus different clusters are distinct genotypes. title: genotype from_schema: https://w3id.org/evorao/ close_mappings: - geno:0000222 rank: 1000 alias: genotype owner: PathogenIdentification domain_of: - PathogenIdentification range: string required: false multivalued: false serotype: name: serotype description: Genetically related pathogens that group together based on serological relationships. title: serotype from_schema: https://w3id.org/evorao/ rank: 1000 alias: serotype owner: PathogenIdentification domain_of: - PathogenIdentification range: string required: false multivalued: false variant: name: variant description: An organism with one or more new mutations is referred to as a “variant” of the original organism if not sufficiently different to be termed a distinct strain. title: variant from_schema: https://w3id.org/evorao/ rank: 1000 alias: variant owner: PathogenIdentification domain_of: - PathogenIdentification range: Variant required: false multivalued: false keyword: name: keyword description: A keyword or tag describing the resource. title: keyword from_schema: https://w3id.org/evorao/ rank: 1000 slot_uri: dcat:keyword alias: keyword owner: PathogenIdentification domain_of: - Resource range: string required: false multivalued: true dateIssued: name: dateIssued description: Date of formal issuance (e.g., publication) of the resource. title: date issued comments: - encoded using the relevant ISO 8601 Date and Time compliant string [DATETIME]. from_schema: https://w3id.org/evorao/ exact_mappings: - sepio:0000051 close_mappings: - schema:datePublished - schema:dateCreated rank: 1000 slot_uri: dct:issued alias: dateIssued owner: PathogenIdentification domain_of: - Resource range: datetime required: false multivalued: false dateModified: name: dateModified description: Most recent date on which the resource was changed, updated or modified. title: date modified comments: - encoded using the relevant ISO 8601 Date and Time compliant string [DATETIME]. from_schema: https://w3id.org/evorao/ exact_mappings: - sepio:0000036 close_mappings: - schema:dateModified rank: 1000 slot_uri: dct:modified alias: dateModified owner: PathogenIdentification domain_of: - Resource range: datetime required: false multivalued: false identifier: name: identifier description: A unique identifier of the resource being described or cataloged. title: identifier comments: - The identifier is a text string which is assigned to the resource to provide an unambiguous reference within a particular context. Persistent identifiers should be provided as HTTP URIs. from_schema: https://w3id.org/evorao/ exact_mappings: - schema:identifier rank: 1000 slot_uri: dct:identifier alias: identifier owner: PathogenIdentification domain_of: - Resource range: string required: false multivalued: true iri: name: iri description: International Resource Identifier (IRI) that uniquely identifies or refers to the resource. IRIs include URIs, and URIs include URLs. title: IRI comments: - An IRI is a global identifier standardized by IETF RFC 3987. It may or may not be resolvable on the web. IRIs include URIs, and URIs include URLs. from_schema: https://w3id.org/evorao/ close_mappings: - biolink:iri related_mappings: - mi:url narrow_mappings: - schema:url rank: 1000 is_a: identifier alias: iri owner: PathogenIdentification domain_of: - Resource range: uri required: false multivalued: true publisher: name: publisher description: The entity responsible for making the resource available. title: publisher comments: - Resources of type foaf:Agent like EVORAO:PersonOrOrganization are recommended as values for this property. from_schema: https://w3id.org/evorao/ rank: 1000 slot_uri: dct:publisher alias: publisher owner: PathogenIdentification domain_of: - Resource range: PersonOrOrganization required: false multivalued: false ```

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