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Update platforms and other tidying #74

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merged 7 commits into from
Sep 28, 2023
Merged

Update platforms and other tidying #74

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751ca59
Add platforms and sort
anngvu Sep 28, 2023
da5d45f
Add enum
anngvu Sep 28, 2023
8f7df74
Pretty format
anngvu Sep 28, 2023
deac86b
Swap in BoolEnum
anngvu Sep 28, 2023
bfe70d6
Lint
anngvu Sep 28, 2023
f49b0fe
Lint
anngvu Sep 28, 2023
29b0381
Build jsonld
invalid-email-address Sep 28, 2023
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204 changes: 128 additions & 76 deletions GF.jsonld
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Original file line number Diff line number Diff line change
Expand Up @@ -2763,7 +2763,11 @@
"@id" : "http://schema.biothings.io/"
},
"sms:required" : "sms:true",
"schema:rangeIncludes" : [ ],
"schema:rangeIncludes" : [ {
"@id" : "bts:Yes"
}, {
"@id" : "bts:No"
} ],
"rdfs:label" : "CryopreservedCellsinSample",
"rdfs:comment" : "Indicate if library preparation was based on revived frozen cells.",
"@type" : "rdfs:Class",
Expand Down Expand Up @@ -3892,6 +3896,8 @@
"@id" : "bts:R2"
}, {
"@id" : "bts:R1&R2"
}, {
"@id" : "bts:R3"
}, {
"@id" : "bts:NotApplicable"
} ],
Expand Down Expand Up @@ -6635,69 +6641,71 @@
},
"sms:required" : "sms:true",
"schema:rangeIncludes" : [ {
"@id" : "bts:PromethION"
"@id" : "bts:454GSFLXTitanium"
}, {
"@id" : "bts:IlluminaNovaSeq6000"
"@id" : "bts:ABSOLiD3"
}, {
"@id" : "bts:PacBioRS"
"@id" : "bts:ABSOLiD4ABSOLiD2"
}, {
"@id" : "bts:NotReported"
"@id" : "bts:CompleteGenomics"
}, {
"@id" : "bts:IlluminaNextSeq500"
"@id" : "bts:GridION"
}, {
"@id" : "bts:NovaSeq6000"
"@id" : "bts:IlluminaGenomeAnalyzerII"
}, {
"@id" : "bts:IlluminaNextSeq2500"
"@id" : "bts:IlluminaGenomeAnalyzerIIx"
}, {
"@id" : "bts:IlluminaHiSeq4000"
"@id" : "bts:IlluminaHiSeq2000"
}, {
"@id" : "bts:unknown"
"@id" : "bts:IlluminaHiSeq2500"
}, {
"@id" : "bts:CompleteGenomics"
"@id" : "bts:IlluminaHiSeq4000"
}, {
"@id" : "bts:UltimaGenomicsUG100"
"@id" : "bts:IlluminaHiSeqXFive"
}, {
"@id" : "bts:IlluminaHiSeqXTen"
}, {
"@id" : "bts:IlluminaMiSeq"
}, {
"@id" : "bts:IlluminaHiSeqXTen"
"@id" : "bts:IlluminaNextSeq1000"
}, {
"@id" : "bts:IlluminaGenomeAnalyzerIIx"
"@id" : "bts:IlluminaNextSeq2000"
}, {
"@id" : "bts:IonTorrentProton"
"@id" : "bts:IlluminaNextSeq2500"
}, {
"@id" : "bts:ABSOLiD4ABSOLiD2"
"@id" : "bts:IlluminaNextSeq500"
}, {
"@id" : "bts:IlluminaGenomeAnalyzerII"
"@id" : "bts:IlluminaNextSeq550"
}, {
"@id" : "bts:NovaSeqS4"
"@id" : "bts:IlluminaNovaSeq6000"
}, {
"@id" : "bts:Revio"
"@id" : "bts:IonTorrentPGM"
}, {
"@id" : "bts:IlluminaHiSeq2500"
"@id" : "bts:IonTorrentProton"
}, {
"@id" : "bts:454GSFLXTitanium"
"@id" : "bts:IonTorrentS5"
}, {
"@id" : "bts:IlluminaNextSeq550"
"@id" : "bts:NotReported"
}, {
"@id" : "bts:GridION"
"@id" : "bts:NovaSeq6000"
}, {
"@id" : "bts:Other"
"@id" : "bts:NovaSeqS4"
}, {
"@id" : "bts:IlluminaHiSeq2000"
"@id" : "bts:Other"
}, {
"@id" : "bts:IlluminaHiSeqXFive"
"@id" : "bts:OxfordNanoporeminION"
}, {
"@id" : "bts:IlluminaNextSeq"
"@id" : "bts:PacBioRS"
}, {
"@id" : "bts:IonTorrentS5"
"@id" : "bts:PacBioSequel2"
}, {
"@id" : "bts:IonTorrentPGM"
"@id" : "bts:PromethION"
}, {
"@id" : "bts:OxfordNanoporeminION"
"@id" : "bts:Revio"
}, {
"@id" : "bts:ABSOLiD3"
"@id" : "bts:UltimaGenomicsUG100"
}, {
"@id" : "bts:PacBioSequel2"
"@id" : "bts:Unknown"
} ],
"rdfs:label" : "SequencingPlatform",
"rdfs:comment" : "A platform is an object aggregate that is the set of instruments and software needed to perform a process [OBI_0000050]. Specific model of the sequencing instrument.",
Expand Down Expand Up @@ -11015,6 +11023,17 @@
},
"sms:displayName" : "TotalVolumeUnitEnum",
"sms:required" : "sms:false"
}, {
"@id" : "bts:BooleanEnum",
"@type" : "rdfs:Class",
"rdfs:comment" : "TBD",
"rdfs:label" : "BooleanEnum",
"rdfs:subClassOf" : [ ],
"schema:isPartOf" : {
"@id" : "http://schema.biothings.io/"
},
"sms:displayName" : "BooleanEnum",
"sms:required" : "sms:false"
}, {
"@id" : "bts:MolecularAnalysisMethodEnum",
"@type" : "rdfs:Class",
Expand Down Expand Up @@ -12676,6 +12695,17 @@
},
"sms:displayName" : "Uruguay",
"sms:required" : "sms:false"
}, {
"@id" : "bts:IlluminaNextSeq2000",
"@type" : "rdfs:Class",
"rdfs:comment" : "TBD",
"rdfs:label" : "IlluminaNextSeq2000",
"rdfs:subClassOf" : [ ],
"schema:isPartOf" : {
"@id" : "http://schema.biothings.io/"
},
"sms:displayName" : "Illumina NextSeq 2000",
"sms:required" : "sms:false"
}, {
"@id" : "bts:Mixedsmallcellcarcinoma",
"@type" : "rdfs:Class",
Expand Down Expand Up @@ -13809,6 +13839,17 @@
},
"sms:displayName" : "rmd",
"sms:required" : "sms:false"
}, {
"@id" : "bts:R3",
"@type" : "rdfs:Class",
"rdfs:comment" : "TBD",
"rdfs:label" : "R3",
"rdfs:subClassOf" : [ ],
"schema:isPartOf" : {
"@id" : "http://schema.biothings.io/"
},
"sms:displayName" : "R3",
"sms:required" : "sms:false"
}, {
"@id" : "bts:Signature20",
"@type" : "rdfs:Class",
Expand Down Expand Up @@ -16229,17 +16270,6 @@
},
"sms:displayName" : "bed narrowPeak",
"sms:required" : "sms:false"
}, {
"@id" : "bts:IlluminaNextSeq550",
"@type" : "rdfs:Class",
"rdfs:comment" : "TBD",
"rdfs:label" : "IlluminaNextSeq550",
"rdfs:subClassOf" : [ ],
"schema:isPartOf" : {
"@id" : "http://schema.biothings.io/"
},
"sms:displayName" : "Illumina Next Seq 550",
"sms:required" : "sms:false"
}, {
"@id" : "bts:CyCIF",
"@type" : "rdfs:Class",
Expand Down Expand Up @@ -18066,6 +18096,17 @@
},
"sms:displayName" : "BRAF sequencing",
"sms:required" : "sms:false"
}, {
"@id" : "bts:IlluminaNextSeq550",
"@type" : "rdfs:Class",
"rdfs:comment" : "TBD",
"rdfs:label" : "IlluminaNextSeq550",
"rdfs:subClassOf" : [ ],
"schema:isPartOf" : {
"@id" : "http://schema.biothings.io/"
},
"sms:displayName" : "Illumina NextSeq 550",
"sms:required" : "sms:false"
}, {
"@id" : "bts:Carcinomainpleomorphicadenoma",
"@type" : "rdfs:Class",
Expand Down Expand Up @@ -20068,6 +20109,17 @@
},
"sms:displayName" : "FLCN mutation",
"sms:required" : "sms:false"
}, {
"@id" : "bts:IlluminaNextSeq1000",
"@type" : "rdfs:Class",
"rdfs:comment" : "TBD",
"rdfs:label" : "IlluminaNextSeq1000",
"rdfs:subClassOf" : [ ],
"schema:isPartOf" : {
"@id" : "http://schema.biothings.io/"
},
"sms:displayName" : "Illumina NextSeq 1000",
"sms:required" : "sms:false"
}, {
"@id" : "bts:Carneycomplex",
"@type" : "rdfs:Class",
Expand Down Expand Up @@ -20849,6 +20901,17 @@
},
"sms:displayName" : "Rearrangement",
"sms:required" : "sms:false"
}, {
"@id" : "bts:Unknown",
"@type" : "rdfs:Class",
"rdfs:comment" : "TBD",
"rdfs:label" : "Unknown",
"rdfs:subClassOf" : [ ],
"schema:isPartOf" : {
"@id" : "http://schema.biothings.io/"
},
"sms:displayName" : "Unknown",
"sms:required" : "sms:false"
}, {
"@id" : "bts:CENP-A",
"@type" : "rdfs:Class",
Expand Down Expand Up @@ -25183,6 +25246,17 @@
},
"sms:displayName" : "Slovakia",
"sms:required" : "sms:false"
}, {
"@id" : "bts:IlluminaNextSeq2500",
"@type" : "rdfs:Class",
"rdfs:comment" : "TBD",
"rdfs:label" : "IlluminaNextSeq2500",
"rdfs:subClassOf" : [ ],
"schema:isPartOf" : {
"@id" : "http://schema.biothings.io/"
},
"sms:displayName" : "Illumina NextSeq 2500",
"sms:required" : "sms:false"
}, {
"@id" : "bts:Somalia",
"@type" : "rdfs:Class",
Expand Down Expand Up @@ -25480,17 +25554,6 @@
},
"sms:displayName" : "Hepatocellular carcinoma NOS",
"sms:required" : "sms:false"
}, {
"@id" : "bts:IlluminaNextSeq2500",
"@type" : "rdfs:Class",
"rdfs:comment" : "TBD",
"rdfs:label" : "IlluminaNextSeq2500",
"rdfs:subClassOf" : [ ],
"schema:isPartOf" : {
"@id" : "http://schema.biothings.io/"
},
"sms:displayName" : "Illumina Next Seq 2500",
"sms:required" : "sms:false"
}, {
"@id" : "bts:PAX5mutation",
"@type" : "rdfs:Class",
Expand Down Expand Up @@ -30342,6 +30405,17 @@
},
"sms:displayName" : "Total RNA Analyte",
"sms:required" : "sms:false"
}, {
"@id" : "bts:IlluminaNextSeq500",
"@type" : "rdfs:Class",
"rdfs:comment" : "TBD",
"rdfs:label" : "IlluminaNextSeq500",
"rdfs:subClassOf" : [ ],
"schema:isPartOf" : {
"@id" : "http://schema.biothings.io/"
},
"sms:displayName" : "Illumina NextSeq 500",
"sms:required" : "sms:false"
}, {
"@id" : "bts:GumNOS",
"@type" : "rdfs:Class",
Expand Down Expand Up @@ -32883,17 +32957,6 @@
},
"sms:displayName" : "Dermatofibroma NOS",
"sms:required" : "sms:false"
}, {
"@id" : "bts:IlluminaNextSeq",
"@type" : "rdfs:Class",
"rdfs:comment" : "TBD",
"rdfs:label" : "IlluminaNextSeq",
"rdfs:subClassOf" : [ ],
"schema:isPartOf" : {
"@id" : "http://schema.biothings.io/"
},
"sms:displayName" : "Illumina NextSeq",
"sms:required" : "sms:false"
}, {
"@id" : "bts:Benign",
"@type" : "rdfs:Class",
Expand Down Expand Up @@ -33059,17 +33122,6 @@
},
"sms:displayName" : "Clear cell",
"sms:required" : "sms:false"
}, {
"@id" : "bts:IlluminaNextSeq500",
"@type" : "rdfs:Class",
"rdfs:comment" : "TBD",
"rdfs:label" : "IlluminaNextSeq500",
"rdfs:subClassOf" : [ ],
"schema:isPartOf" : {
"@id" : "http://schema.biothings.io/"
},
"sms:displayName" : "Illumina Next Seq 500",
"sms:required" : "sms:false"
}, {
"@id" : "bts:Hereditarydiffusegastriccancer",
"@type" : "rdfs:Class",
Expand Down
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