terms.rdf.json

{
    "@context" : {
        "rdfs" : "http://www.w3.org/2000/01/rdf-schema#",
        "xsd" : "http://www.w3.org/2001/XMLSchema#",
        "@base" : "http://w3id.org/poseidon/v1.0/terms.rdf.json"
    },
    "@graph" : [{
        "@id" : "#PackageInfo",
        "@type" : "rdfs:Class",
        "rdfs:comment" : "The class denoting a Poseidon package definition object"
    }, {
        "@id" : "#SitesTableInfo",
        "@type" : "rdfs:Class",
        "rdfs:comment" : "The class denoting the Poseidon Site Table description object"
    }, {
        "@id" : "#siteNote",
        "@type" : "rdfs:Property",
        "rdfs:comment" : "(Optional) note for the site",
        "rdfs:range" : "xsd:string"
    }, {
        "@id" : "#source",
        "@type" : "rdfs:Property",
        "rdfs:comment" : "BibTEX key(s) for bibliographical source(s)",
        "rdfs:range" : "xsd:string"
    }, {
        "@id" : "#IndividualsTableInfo",
        "@type" : "rdfs:Class",
        "rdfs:comment" : "The class denoting the Poseidon Individual Table description object"
    }, {
        "@id" : "#siteReference",
        "@type" : "rdfs:Property",
        "rdfs:comment" : "A foreign key into the Sites table",
        "rdfs:range" : "xsd:string"
    }, {
        "@id" : "#collectionID",
        "@type" : "rdfs:Property",
        "rdfs:comment" : "The class denoting an Identifier for a individual used in the museum or archaeological/anthropological collection that the individual is from.",
        "rdfs:range" : "xsd:string"
    }, {
        "@id" : "#tissueType",
        "@type" : "rdfs:Property",
        "rdfs:comment" : "Name of the tissue used for analysing the individual.",
        "rdfs:range" : "xsd:string"
    }, {
        "@id" : "#contextualDateLower",
        "@type" : "rdfs:Property",
        "rdfs:comment" : "Lower bound of contextual date of the individual, in BP",
        "rdfs:range" : "xsd:nonNegativeInteger"
    }, {
        "@id" : "#contextualDateUpper",
        "@type" : "rdfs:Property",
        "rdfs:comment" : "Upper bound of contextual date of the individual, in BP",
        "rdfs:range" : "xsd:nonNegativeInteger"
    }, {
        "@id" : "#archaeologicalCulture",
        "@type" : "rdfs:Property",
        "rdfs:comment" : "Terms that describe the archaeological culture",
        "rdfs:range" : "xsd:string"
    }, {
        "@id" : "#groupLabel",
        "@type" : "rdfs:Property",
        "rdfs:comment" : "A label used to group this individual with other individuals",
        "rdfs:range" : "xsd:string"
    }, {
        "@id" : "#individualNote",
        "@type" : "rdfs:Property",
        "rdfs:comment" : "(Optional) note for the individual",
        "rdfs:range" : "xsd:string"
    }, {
        "@id" : "#DateTableInfo",
        "@type" : "rdfs:Class",
        "rdfs:comment" : "The class denoting the Poseidon C14 Table description object"
    }, {
        "@id" : "#individualReference",
        "@type" : "rdfs:Property",
        "rdfs:comment" : "A foreign key into the Individuals table",
        "rdfs:range" : "xsd:string"
    }, {
        "@id" : "#C14labName",
        "@type" : "rdfs:Property",
        "rdfs:comment" : "Name of the lab performing the C14 dating",
        "rdfs:range" : "xsd:string"
    }, {
        "@id" : "#C14uncalDateBP",
        "@type" : "rdfs:Property",
        "rdfs:comment" : "Uncalibrated C14 date in years before 1950 (BP)",
        "rdfs:range" : "xsd:nonNegativeInteger"
    }, {
        "@id" : "#C14uncalDateErrBP",
        "@type" : "rdfs:Property",
        "rdfs:comment" : "Uncalibrated C14 date error in years before 1950 (BP)",
        "rdfs:range" : "xsd:nonNegativeInteger"
    }, {
        "@id" : "#C14calDateMedianBP",
        "@type" : "rdfs:Property",
        "rdfs:comment" : "Calbibrated C14 date median value in years before 1950 (BP)",
        "rdfs:range" : "xsd:nonNegativeInteger"
    }, {
        "@id" : "#C14calDateLower2SigmaBP",
        "@type" : "rdfs:Property",
        "rdfs:comment" : "Lower end of 2-sigma range of calbibrated C14 date in years before 1950 (BP)",
        "rdfs:range" : "xsd:nonNegativeInteger"
    }, {
        "@id" : "#C14calDateUpper2SigmaBP",
        "@type" : "rdfs:Property",
        "rdfs:comment" : "Upper end of 2-sigma range of calbibrated C14 date in years before 1950 (BP)",
        "rdfs:range" : "xsd:nonNegativeInteger"
    }, {
        "@id" : "#C14dateType",
        "@type" : "rdfs:Property",
        "rdfs:comment" : "Can be either \"direct\" or \"indirect\" (e.g. through charcoal at the site)",
        "rdfs:range" : "xsd:string"
    }, {
        "@id" : "#C14note",
        "@type" : "rdfs:Property",
        "rdfs:comment" : "Optional note for the C14 date",
        "rdfs:range" : "xsd:string"
    }, {
        "@id" : "#SeqTableInfo",
        "@type" : "rdfs:Class",
        "rdfs:comment" : "The class denoting the Poseidon Sequencing Table description object"
    }, {
        "@id" : "#seqLabName",
        "@type" : "rdfs:Property",
        "rdfs:comment" : "Name of the lab performing the Sequencing",
        "rdfs:range": "xsd:string"
    }, {
        "@id" : "#libraryType",
        "@type" : "rdfs:Property",
        "rdfs:comment" : "DNA Library construction (Non-UDG, UDG-half, UDG-full, Single-Stranded-Non-UDG, Multiple)",
        "rdfs:range": "xsd:string"
    }, {
        "@id" : "#captureType",
        "@type" : "rdfs:Property",
        "rdfs:comment" : "Type of Capture (NoCapture, 1240Kcapture, MTcapture, OtherCapture). If not given, assume NoCapture",
        "rdfs:range": "xsd:string"
    }, {
        "@id" : "#captureNote",
        "@type" : "rdfs:Property",
        "rdfs:comment" : "Note describing the capture, in particular of CaptureType was \"OtherCapture\"",
        "rdfs:range": "xsd:string"
    }, {
        "@id" : "#nrReadsSequenced",
        "@type" : "rdfs:Property",
        "rdfs:comment" : "Number of raw read or read-pairs sequenced",
        "rdfs:range": "xsd:string"
    }, {
        "@id" : "#referenceGenome",
        "@type" : "rdfs:Property",
        "rdfs:comment" : "Name of reference genome. If Human, use HG19 or HG38.",
        "rdfs:range": "xsd:string"
    }, {
        "@id" : "#nrReadsMapped",
        "@type" : "rdfs:Property",
        "rdfs:comment" : "Number of reads mapped to the reference genome.",
        "rdfs:range": "xsd:string"
    }, {
        "@id" : "#nrReadsMappedQF30",
        "@type" : "rdfs:Property",
        "rdfs:comment" : "Number of reads mapped to the reference genome, filtered for mapping quality <=30",
        "rdfs:range": "xsd:string"
    }, {
        "@id" : "#nrReadsMappedUnique",
        "@type" : "rdfs:Property",
        "rdfs:comment" : "Number of unique reads mapped to the reference genome.",
        "rdfs:range": "xsd:string"
    }, {
        "@id" : "#nrReadsMappedUniqueQF30",
        "@type" : "rdfs:Property",
        "rdfs:comment" : "Number of unique reads mapped to the reference genome, filtered for mapping quality >= 30",
        "rdfs:range": "xsd:string"
    }, {
        "@id" : "#rawReadsRepository",
        "@type" : "rdfs:Property",
        "rdfs:comment" : "Repository for sequencing data. Can be \"ENA\" or \"SRA\"",
        "rdfs:range": "xsd:string"
    }, {
        "@id" : "#rawReadsAccessionNr",
        "@type" : "rdfs:Property",
        "rdfs:comment" : "Accession number to raw read files and/or alignments",
        "rdfs:range": "xsd:string"
    }, {
        "@id" : "#frac5pCT",
        "@type" : "rdfs:Property",
        "rdfs:comment" : "Fraction of reads with C->T substitutions at the 5p end of the read. Used as a proxy for post-mortem DNA damage",
        "rdfs:range": "xsd:string"
    }, {
        "@id" : "#frac3pGA",
        "@type" : "rdfs:Property",
        "rdfs:comment" : "Fraction of reads with G->A substitutions at the 3p end of the read. Used as a proxy for post-mortem DNA damage",
        "rdfs:range": "xsd:string"
    }, {
        "@id" : "#fracContam",
        "@type" : "rdfs:Property",
        "rdfs:comment" : "Estimate for the library contamination",
        "rdfs:range": "xsd:string"
    }, {
        "@id" : "#contamNote",
        "@type" : "rdfs:Property",
        "rdfs:comment" : "Optional note for how the contamination was estimated",
        "rdfs:range": "xsd:string"
    }, {
        "@id" : "#geneticSex",
        "@type" : "rdfs:Property",
        "rdfs:comment" : "Inferred sex genotype (XX, XY, Other)",
        "rdfs:range": "xsd:string"
    }, {
        "@id" : "#mtHaplotype",
        "@type" : "rdfs:Property",
        "rdfs:comment" : "Mitochondrial haplotype",
        "rdfs:range": "xsd:string"
    }, {
        "@id" : "#yHaplotype",
        "@type" : "rdfs:Property",
        "rdfs:comment" : "Y chromosome haplotype",
        "rdfs:range": "xsd:string"
    }, {
        "@id" : "#seqNote",
        "@type" : "rdfs:Property",
        "rdfs:comment" : "Optional general note for the sequencing data",
        "rdfs:range": "xsd:string"
    }, {
        "@id" : "#seqReference",
        "@type" : "rdfs:Property",
        "rdfs:comment" : "Foreigen key into the sequencing table.",
        "rdfs:range": "xsd:string"
    }, {
        "@id" : "#genotypingSnpSetName",
        "@type" : "rdfs:Property",
        "rdfs:comment" : "Standardized Name of the SNP set (can be \"1240K\", \"1000_Genomes\" or \"Other\"",
        "rdfs:range": "xsd:string"
    }, {
        "@id" : "#GenoTableInfo",
        "@type" : "rdfs:Class",
        "rdfs:comment" : "The class denoting the Poseidon Genotyping Table description object"
    }, {
        "@id@" : "#genotypingPositionsFile",
        "@type" : "rdfs:Property",
        "rdfs:comment" : "URL to the eigenstrat positions file for the specific genotyping pulldown",
        "rdfs:range" : "xsd:anyURI"
    }, {
        "@id" : "#genotypingGenotypeFile",
        "@type" : "rdfs:Property",
        "rdfs:comment" : "URL or filename of the genotype matrix file",
        "rdfs:range": "xsd:string"
    }, {
        "@id" : "#genotypingFileFormat",
        "@type" : "rdfs:Property",
        "rdfs:comment" : "URL or filename of the genotype matrix file",
        "rdfs:range": "xsd:string"
    }, {
        "@id" : "#genotypingColumnPosition",
        "@type" : "rdfs:Property",
        "rdfs:comment" : "1-based Column position of the individual in the genotype matrix.",
        "rdfs:range": "xsd:string"
    }, {
        "@id" : "#genotypingMethod",
        "@type" : "rdfs:Property",
        "rdfs:comment" : "Method of the genotyping. Can be \"RandomReadSampling\", \"MajorityReadSampling\", \"DiploidModelBased\" or \"Other\"",
        "rdfs:range": "xsd:string"
    }, {
        "@id" : "#genotypingTool",
        "@type" : "rdfs:Property",
        "rdfs:comment" : "Tool used for genotyping, such as \"pileupCaller\" or \"GATK\"",
        "rdfs:range": "xsd:string"
    }, {
        "@id" : "#genotypingNote",
        "@type" : "rdfs:Property",
        "rdfs:comment" : "Optional Note for genotyping",
        "rdfs:range": "xsd:string"
    }]
}