Description of the biological sample. Each sequence should define from which sample they are derived. DocumentCore #* A name for the sample name xsd:string; #* An optional short description description xsd:string?; #* Any publication associated to feature annotation citation @:Citation*; #* Reference to other entries holding entries with related information in other databases xref @:XRef*; #* A set off some additional notes 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?; #* Barcode sequence set barcodes @:BarcodeSet?; #* ASV sequence set asv @:ASVSet*; #* 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 meters 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 + longitude) 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 'cellular 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 environment 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 environment. 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. segment xsd:string?; #* The chromosome name or number 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 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?; #* Additional sample metadata metadata IRI*;

http://gbol.life/0.1/Sample

DocumentCore

#* A name for the sample name xsd:string; #* An optional short description description xsd:string?; #* Any publication associated to feature annotation citation @:Citation*; #* Reference to other entries holding entries with related information in other databases xref @:XRef*; #* A set off some additional notes 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?; #* Barcode sequence set barcodes @:BarcodeSet?; #* ASV sequence set asv @:ASVSet*; #* 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 meters 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 + longitude) 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 'cellular 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 environment 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 environment. 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. segment xsd:string?; #* The chromosome name or number 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 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?; #* Additional sample metadata metadata IRI*;

Description of the biological sample. Each sequence should define from which sample they are derived.

DocumentCore

#* A name for the sample name xsd:string; #* An optional short description description xsd:string?; #* Any publication associated to feature annotation citation @:Citation*; #* Reference to other entries holding entries with related information in other databases xref @:XRef*; #* A set off some additional notes 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?; #* Barcode sequence set barcodes @:BarcodeSet?; #* ASV sequence set asv @:ASVSet*; #* 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 meters 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 + longitude) 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 'cellular 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 environment 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 environment. 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. segment xsd:string?; #* The chromosome name or number 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 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?; #* Additional sample metadata metadata IRI*;

# 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

Sample

Sample

#* A name for the sample name xsd:string; #* An optional short description description xsd:string?; #* Any publication associated to feature annotation citation @:Citation*; #* Reference to other entries holding entries with related information in other databases xref @:XRef*; #* A set off some additional notes 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?; #* Barcode sequence set barcodes @:BarcodeSet?; #* ASV sequence set asv @:ASVSet*; #* 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 meters 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 + longitude) 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 'cellular 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 environment 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 environment. 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. segment xsd:string?; #* The chromosome name or number 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 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?; #* Additional sample metadata metadata IRI*;

DocumentCore

http://www.w3.org/2002/07/owl#Thing