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Sample a owl:Class

Subclasses

Annotations

skos:definition Description of the biological sample. Each sequence should define from which sample they are derived.
empusa:propertyDefinitions # An optional name for the sample
name xsd:String?;
#
An optional short description of the sample
description xsd:String?;
# A link to a specific citation related to the sample itself
citation @:Citation
;
# Reference to entries in other databases which also represent the same sample.
xref @:XRef
;
# A note on the sample
note @:Note
;

# Identification of the material in a collection from which the sample is derived. Entries with more than one sampleSource indicates that the sequence was obtained from a sample that was deposited (by the submitter or a collaborator) in more than one collection.
sourceMaterial @:MaterialSource
;

#The primers used to get to get the sample from the collected material. The sample is the PCR product if the property is defined.
PCRPrimers @:PCRPrimerSet?;

# Describes the physical, environmental and/or local geographical source of the biological sample from which the sequence was derived. Use geographicalLocation to denote the geographical location (examples: 'permanent Antarctic sea ice', 'rumen isolates from standard Pelleted ration-fed steer #67', 'denitrifying activated sludge from carbon limited continuous reactor')
isolationSource xsd:String?;
#
This denotes that this sample is the result of a bulk NA extraction method, therefore the organism of the sample and associated sequence(s) are not (exactly) known.
environmentalSample xsd:boolean?;

# Altitude of the location from which the sample was collected in metres above or below nominal sea level
altitude xsd:Double?;

#
The persons or institute who collected the specimen
collectedBy @foaf:Agent;
#
The date and time on which the specimen was collected.
collectionDate xsd:dateTime?;

# The geographical location(country or ocean) from which the sample is collected
geographicalLocation @:GeographicalLocation?;

#
The geographical coordinates(latitude + longtitude) of the location where the specimen was collected
geographicalCoordinate @:GeographicalCoordinate?;

# The developmental stage at which the organism was when the sample was obtained
devStage xsd:String?;
#
The name of the expert who identified the specimen taxonomically
identifiedBy @foaf:Agent?;
# Individual isolate from which the sequence was obtained. For example ('Patient #152','DGGE band PSBAC-13')
isolate xsd:String?;
#
The tissue library from which the sample was obtained
tissueLib xsd:String?;
# The tissue type from which the sample was obtained, use term from the 'BRENDA Tissue and Enzyme Source Ontology' whenever possible
tissueType xsd:String?;
#
Type of membrane-bound intracellular structure from which the sample was obtained. Use a 'cellelar component' term from the GO ontology.
organelle IRI?;

# The serological typing of the species within the sample by its antigenic properties
serotype xsd:String?;

#
The specific name of the host from which the sample has been collected, where the name indicates to which habitat/ecological enviroment the host has adopted to. Example: 'Columbia', which indicate that this Arabidopsis adopted itself with a hairier phenotype to deal with the especially sunny habitat.
ecotype xsd:String?;
# For the host from which the sample was obtained the name for a group of similar haplotypes that share some sequence variation. Haplogroups are often used to track migration of population groups.
haplogroup xsd:String?;
#
For the host from which the sample was obtained the name for a combination of alleles that are linked together on the same physical chromosome. In the absence of recombination, each haplotype is inherited as a unit, and may be used to track gene flow in populations.
haplotype xsd:String?;

# The cultivar (cultivated variety) of plant from which sample was obtained.
cultivar xsd:String?;

#
The cell line from which the sequence was obtained, please use term from 'Cell Line Ontology' (http://www.clo-ontology.org/) where possible
cellLine xsd:String?;
# The cell type from which the sequence was obtained, please use term from 'Cell Ontology' (http://cellontology.org/) where possible
cellType xsd:String?;

#
The host of the organism (from which the sample was obtained), which it lives in, upon or attached to in its natural enviroment.
host @:TaxonomyRef?;
# Scientific name of the laboratory host used to propagate the source organism from which the sample was obtained. The full binomial scientific name of the host organism should be used when known. Extra conditional information relating to the host may also be included. For example '12 year old human with IBD' for a gut bacteria.
labHost xsd:String?;

#
The mating type of the organism from which the sample was obtained. Mating type is used for prokaryotes, and for eukaryotes that undergo meiosis without sexually dimorphic gametes. For eukaryotic organisms that undergo meiosis with sexually dimorphic gametes please use the sex property.
matingType xsd:String?;
# The sex of the organism from which the sample was obtained. Sex is used for eukaryotic organisms that undergo meiosis with sexually dimorphic gametes. For prokaryotes, and for eukaryotes that undergo meiosis without sexually dimorphic gametes please use the mathingType property.
sex xsd:String?;

#
The name of the subpopulation or phenotype from which the sample was collected.
popVariant xsd:String?;

# The variety of the host from which the sample was derived. Use cultivar if the host is a cultivated plant.
variety xsd:String?;

#
The name or identifier of virus or phage (segment) from which the sample was obtained (using PCR).
segment xsd:String?;
# The name of the chromosome from which the sample was obtained (using PCR).
chromosome xsd:String?;
#
The map location on the chromosome from which the sample was obtained (using PCR).
map xsd:String?;
# The name or identifier of plasmid from which the sample was obtained (using PCR).
plasmid xsd:String?;
#
The name or identifier of the strain from which the sample was obtained (using PCR).
strain xsd:String?;
# The name or identifier of the sub-clone from which the sample was obtained (using PCR).
subClone xsd:String?;
#
The name or identifier of the sub-species from which the sample was obtained (using PCR).
subSpecies xsd:String?;
# The name or identifier of a genetically or otherwise modified strain from which the sample was obtained (using PCR). The parental strain from which it is derived should be annotated with the strain property.
subStrain xsd:String?;

#
Indicate that this sample is an proviral sequence extracted from another organism using PCR.
proviralExtraction xsd:boolean?;
subDomain DocumentCore
skos:editorialNote # removed & moved

#bioMaterial xsd:String?;
#cultureCollection xsd:String?;
#specimenVoucher xsd:String?;
#--> merged to sourceMaterial, use collectionSampleType to identify type
#country type::Country?; -> replaced with geographicalLocation
#latLon-> replaced with geographicalCoordinate
#serovar xsd:String?; -> killed store under seroType
#focus xsd:boolean?; --> replaced with the integratedInto property in the sequence object
#transgenic xsd:boolean?; --> replaced with the integratedInto property in the sequence object
#mol_type --> removed replaced with strandType & NASequence subclasses

#germline xsd:boolean?; --> moved to sequence & removed replace with rearranged = false
#rearranged xsd:boolean?; --> moved to sequence

#clone xsd:String?; --> move to sequence, is a bit outdated now a days
#cloneLib xsd:String?; --> move to sequence, is a bit outdated now a days
#proviral xsd:boolean?; --> moved to sequence & set proviralExtraction = true on sample
#division --> removed information already captures by the taxonomy property
#organism --> replaced with taxonomy in organism object linked to sequence object
#type_material --> replaced with the nomenclaturalType in the TaxonomyRef under the Sequence object

Properties

property description cardinality type
proviralExtraction Indicate that this sample is an proviral sequence extracted from another organism using PCR. 0:1 xsd:Boolean
map The map location on the chromosome from which the sample was obtained (using PCR). 0:1 xsd:String
strain The name or identifier of the strain from which the sample was obtained (using PCR). 0:1 xsd:String
ecotype The specific name of the host from which the sample has been collected, where the name indicates to which habitat/ecological enviroment the host has adopted to. Example: 'Columbia', which indicate that this Arabidopsis adopted itself with a hairier phenotype to deal with the especially sunny habitat. 0:1 xsd:String
subClone The name or identifier of the sub-clone from which the sample was obtained (using PCR). 0:1 xsd:String
isolate Individual isolate from which the sequence was obtained. For example ('Patient #152','DGGE band PSBAC-13') 0:1 xsd:String
haplogroup For the host from which the sample was obtained the name for a group of similar haplotypes that share some sequence variation. Haplogroups are often used to track migration of population groups. 0:1 xsd:String
devStage The developmental stage at which the organism was when the sample was obtained 0:1 xsd:String
sex The sex of the organism from which the sample was obtained. Sex is used for eukaryotic organisms that undergo meiosis with sexually dimorphic gametes. For prokaryotes, and for eukaryotes that undergo meiosis without sexually dimorphic gametes please use the mathingType property. 0:1 xsd:String
plasmid The name or identifier of plasmid from which the sample was obtained (using PCR). 0:1 xsd:String
popVariant The name of the subpopulation or phenotype from which the sample was collected. 0:1 xsd:String
haplotype For the host from which the sample was obtained the name for a combination of alleles that are linked together on the same physical chromosome. In the absence of recombination, each haplotype is inherited as a unit, and may be used to track gene flow in populations. 0:1 xsd:String
name An optional name for the sample 0:1 xsd:String
isolationSource Describes the physical, environmental and/or local geographical source of the biological sample from which the sequence was derived. Use geographicalLocation to denote the geographical location (examples: 'permanent Antarctic sea ice', 'rumen isolates from standard Pelleted ration-fed steer #67', 'denitrifying activated sludge from carbon limited continuous reactor') 0:1 xsd:String
labHost Scientific name of the laboratory host used to propagate the source organism from which the sample was obtained. The full binomial scientific name of the host organism should be used when known. Extra conditional information relating to the host may also be included. For example '12 year old human with IBD' for a gut bacteria. 0:1 xsd:String
geographicalCoordinate The geographical coordinates(latitude + longtitude) of the location where the specimen was collected 0:1 GeographicalCoordinate
tissueLib The tissue library from which the sample was obtained 0:1 xsd:String
organelle Type of membrane-bound intracellular structure from which the sample was obtained. Use a 'cellelar component' term from the GO ontology. 0:1 IRI
cellType The cell type from which the sequence was obtained, please use term from 'Cell Ontology' (http://cellontology.org/) where possible 0:1 xsd:String
subSpecies The name or identifier of the sub-species from which the sample was obtained (using PCR). 0:1 xsd:String
altitude Altitude of the location from which the sample was collected in metres above or below nominal sea level 0:1 xsd:Double
cellLine The cell line from which the sequence was obtained, please use term from 'Cell Line Ontology' (http://www.clo-ontology.org/) where possible 0:1 xsd:String
tissueType The tissue type from which the sample was obtained, use term from the 'BRENDA Tissue and Enzyme Source Ontology' whenever possible 0:1 xsd:String
cultivar The cultivar (cultivated variety) of plant from which sample was obtained. 0:1 xsd:String
matingType The mating type of the organism from which the sample was obtained. Mating type is used for prokaryotes, and for eukaryotes that undergo meiosis without sexually dimorphic gametes. For eukaryotic organisms that undergo meiosis with sexually dimorphic gametes please use the sex property. 0:1 xsd:String
citation A link to a specific citation related to the sample itself 0:N Citation
sourceMaterial Identification of the material in a collection from which the sample is derived. Entries with more than one sampleSource indicates that the sequence was obtained from a sample that was deposited (by the submitter or a collaborator) in more than one collection. 0:N MaterialSource
subStrain The name or identifier of a genetically or otherwise modified strain from which the sample was obtained (using PCR). The parental strain from which it is derived should be annotated with the strain property. 0:1 xsd:String
description An optional short description of the sample 0:1 xsd:String
chromosome The name of the chromosome from which the sample was obtained (using PCR). 0:1 xsd:String
collectedBy The persons or institute who collected the specimen 0:N foaf:Agent
identifiedBy The name of the expert who identified the specimen taxonomically 0:1 foaf:Agent
xref Reference to entries in other databases which also represent the same sample. 0:N XRef
variety The variety of the host from which the sample was derived. Use cultivar if the host is a cultivated plant. 0:1 xsd:String
host The host of the organism (from which the sample was obtained), which it lives in, upon or attached to in its natural enviroment. 0:1 TaxonomyRef
PCRPrimers 0:1 PCRPrimerSet
collectionDate The date and time on which the specimen was collected. 0:1 xsd:DateTime
geographicalLocation The geographical location(country or ocean) from which the sample is collected 0:1 GeographicalLocation
segment The name or identifier of virus or phage (segment) from which the sample was obtained (using PCR). 0:1 xsd:String
environmentalSample This denotes that this sample is the result of a bulk NA extraction method, therefore the organism of the sample and associated sequence(s) are not (exactly) known. 0:1 xsd:Boolean
serotype The serological typing of the species within the sample by its antigenic properties 0:1 xsd:String
note A note on the sample 0:N Note