{
"@id": "./",
"filename": "isa.investigation.xlsx",
"identifier": "suxManuscript2025",
"title": "A critical role of sux cistron-mediated sucrose uptake for virulence of the rice blight pathogen Xanthomonas oryzae pv. oryzae",
"description": "Characterization of sux cistron in Xanthomonas oryzae pathovar.",
"people": [
{
"@id": "0000-0002-0961-5680",
"firstName": "Nora R.",
"lastName": "Z\u00f6llner",
"email": "nora.zoellner@hhu.de",
"affiliation": "Heinrich Heine University D\u00fcsseldorf, Institute for Molecular Physiology",
"comments": [
{
"name": "ORCID",
"value": "0000-0002-0961-5680"
}
]
},
{
"@id": "0009-0000-1188-6482",
"firstName": "Jacob E.",
"lastName": "Sharkey",
"email": "jacob.sharkey@hhu.de",
"affiliation": "Heinrich Heine University D\u00fcsseldorf, Institute for Molecular Physiology",
"comments": [
{
"name": "ORCID",
"value": "0009-0000-1188-6482"
}
]
},
{
"@id": "0000-0001-6465-0115",
"firstName": "Wolf B.",
"lastName": "Frommer",
"email": "frommew@hhu.de",
"affiliation": "Heinrich-Heine-Universitat D\u00fcsseldorf, Institute for Molecular Physiology;ITbM, ;Carnegie Institution for Science, Plant Biology;Stanford University, Biology;Carnegie Institution for Science, Plant Biology;Stanford University, Biology;Carnegie Institution for Science, Plant Biology;University of T\u00fcbingen, Biology",
"comments": [
{
"name": "ORCID",
"value": "0000-0001-6465-0115"
}
]
}
],
"studies": [
{
"@id": "studies/Bacterial_Resources/",
"filename": "studies/Bacterial Resources/isa.study.xlsx",
"identifier": "Bacterial Resources",
"title": "Bacterial Resources",
"description": "This is a summary of the bacterial strains used in this publication.",
"people": [
{
"@id": "0000-0002-0961-5680",
"firstName": "Nora R.",
"lastName": "Z\u00f6llner",
"email": "nora.zoellner@hhu.de",
"affiliation": "Heinrich Heine University D\u00fcsseldorf, Institute for Molecular Physiology",
"comments": [
{
"name": "performer (ARC:00000168) Growth Curves",
"value": "Growth Curves"
},
{
"name": "ORCID",
"value": "0000-0002-0961-5680"
}
]
}
],
"protocols": [
{
"@id": "#Protocol_2023-08-17-Mutation-in-Xoo-via-Homologous-Recombination.pdf",
"name": "2023-08-17-Mutation-in-Xoo-via-Homologous-Recombination.pdf",
"parameters": [
{
"@id": "#ProtocolParameter/OBI:0100026",
"parameterName": {
"@id": "OBI:0100026",
"annotationValue": "organism",
"termSource": "OBI",
"termAccession": "OBI:0100026"
}
}
]
}
],
"materials": {
"sources": [
{
"@id": "#Source_Xoo_wt",
"name": "Xoo wt"
}
],
"samples": [
{
"@id": "#Sample_Xoo_wt",
"name": "Xoo wt"
},
{
"@id": "#Sample_\u2206sux",
"name": "\u2206sux"
},
{
"@id": "#Sample_\u2206suxA",
"name": "\u2206suxA"
},
{
"@id": "#Sample_\u2206suxB",
"name": "\u2206suxB"
},
{
"@id": "#Sample_\u2206suxC",
"name": "\u2206suxC"
},
{
"@id": "#Sample_\u2206suxR",
"name": "\u2206suxR"
}
]
},
"processSequence": [
{
"@id": "#Process_Strain_generation",
"name": "Strain generation",
"executesProtocol": {
"@id": "#Protocol_2023-08-17-Mutation-in-Xoo-via-Homologous-Recombination.pdf",
"name": "2023-08-17-Mutation-in-Xoo-via-Homologous-Recombination.pdf",
"parameters": [
{
"@id": "#ProtocolParameter/OBI:0100026",
"parameterName": {
"@id": "OBI:0100026",
"annotationValue": "organism",
"termSource": "OBI",
"termAccession": "OBI:0100026"
}
}
]
},
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/OBI:0100026",
"parameterName": {
"@id": "OBI:0100026",
"annotationValue": "organism",
"termSource": "OBI",
"termAccession": "OBI:0100026"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/NCBITAXON_360094",
"annotationValue": "Xanthomonas oryzae pv. oryzae PXO99A",
"termSource": "NCBITAXON",
"termAccession": "http://purl.obolibrary.org/obo/NCBITAXON_360094"
}
}
],
"inputs": [
{
"@id": "#Source_Xoo_wt",
"name": "Xoo wt"
},
{
"@id": "#Source_Xoo_wt",
"name": "Xoo wt"
},
{
"@id": "#Source_Xoo_wt",
"name": "Xoo wt"
},
{
"@id": "#Source_Xoo_wt",
"name": "Xoo wt"
},
{
"@id": "#Source_Xoo_wt",
"name": "Xoo wt"
},
{
"@id": "#Source_Xoo_wt",
"name": "Xoo wt"
}
],
"outputs": [
{
"@id": "#Sample_Xoo_wt",
"name": "Xoo wt"
},
{
"@id": "#Sample_\u2206sux",
"name": "\u2206sux"
},
{
"@id": "#Sample_\u2206suxA",
"name": "\u2206suxA"
},
{
"@id": "#Sample_\u2206suxB",
"name": "\u2206suxB"
},
{
"@id": "#Sample_\u2206suxC",
"name": "\u2206suxC"
},
{
"@id": "#Sample_\u2206suxR",
"name": "\u2206suxR"
}
]
}
],
"assays": [
{
"filename": "assays/Clipping/isa.assay.xlsx",
"@id": "assays/Clipping/",
"measurementType": {
"@id": "https://bioregistry.io/NCIT:C3824",
"annotationValue": "Lesion",
"termSource": "NCIT",
"termAccession": "https://bioregistry.io/NCIT:C3824"
},
"technologyPlatform": "Ruler (NCIT:C138178)",
"dataFiles": [
{
"@id": "assays/Clipping/dataset/Inoculation_data_IR24.xlsx",
"name": "assays/Clipping/dataset/Inoculation data_IR24.xlsx",
"type": "Raw Data File"
},
{
"@id": "assays/Clipping/dataset/Inoculation_data_Kitaake.xlsx",
"name": "assays/Clipping/dataset/Inoculation data_Kitaake.xlsx",
"type": "Raw Data File"
},
{
"@id": "assays/Clipping/dataset/sucrose_gene_on_Nip_V2.xlsx",
"name": "assays/Clipping/dataset/sucrose gene on Nip_V2.xlsx",
"type": "Raw Data File"
}
],
"materials": {
"samples": [
{
"@id": "#Sample_Oryza_sativa_IR24",
"name": "Oryza sativa IR24",
"characteristics": [
{
"@id": "#MaterialAttributeValue/organism=Oryza sativa",
"category": {
"@id": "#MaterialAttribute/OBI:0100026",
"characteristicType": {
"@id": "OBI:0100026",
"annotationValue": "organism",
"termSource": "OBI",
"termAccession": "OBI:0100026"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/C_5438",
"annotationValue": "Oryza sativa",
"termSource": "C",
"termAccession": "http://purl.obolibrary.org/obo/C_5438"
}
},
{
"@id": "#EmptyMaterialAttributeValue",
"category": {
"@id": "#MaterialAttribute/MCO:0000059",
"characteristicType": {
"@id": "MCO:0000059",
"annotationValue": "OD600",
"termSource": "MCO",
"termAccession": "MCO:0000059"
}
}
}
]
},
{
"@id": "#Sample_Xoo_wt",
"name": "Xoo wt",
"characteristics": [
{
"@id": "#MaterialAttributeValue/organism=Xanthomonas oryzae pv. oryzae PXO99A",
"category": {
"@id": "#MaterialAttribute/OBI:0100026",
"characteristicType": {
"@id": "OBI:0100026",
"annotationValue": "organism",
"termSource": "OBI",
"termAccession": "OBI:0100026"
}
},
"value": {
"@id": "#UserTerm_Xanthomonas_oryzae_pv._oryzae_PXO99A",
"annotationValue": "Xanthomonas oryzae pv. oryzae PXO99A"
}
},
{
"@id": "#MaterialAttributeValue/OD600=0,5",
"category": {
"@id": "#MaterialAttribute/MCO:0000059",
"characteristicType": {
"@id": "MCO:0000059",
"annotationValue": "OD600",
"termSource": "MCO",
"termAccession": "MCO:0000059"
}
},
"value": {
"@id": "#UserTerm_0,5",
"annotationValue": "0,5"
}
}
]
},
{
"@id": "#Sample_\u2206sux",
"name": "\u2206sux",
"characteristics": [
{
"@id": "#MaterialAttributeValue/organism=Xanthomonas oryzae pv. oryzae PXO99A",
"category": {
"@id": "#MaterialAttribute/OBI:0100026",
"characteristicType": {
"@id": "OBI:0100026",
"annotationValue": "organism",
"termSource": "OBI",
"termAccession": "OBI:0100026"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/NCBITAXON_360094",
"annotationValue": "Xanthomonas oryzae pv. oryzae PXO99A",
"termSource": "NCBITAXON",
"termAccession": "http://purl.obolibrary.org/obo/NCBITAXON_360094"
}
},
{
"@id": "#MaterialAttributeValue/OD600=0,5",
"category": {
"@id": "#MaterialAttribute/MCO:0000059",
"characteristicType": {
"@id": "MCO:0000059",
"annotationValue": "OD600",
"termSource": "MCO",
"termAccession": "MCO:0000059"
}
},
"value": {
"@id": "#UserTerm_0,5",
"annotationValue": "0,5"
}
}
]
},
{
"@id": "#Sample_\u2206suxC",
"name": "\u2206suxC",
"characteristics": [
{
"@id": "#MaterialAttributeValue/organism=Xanthomonas oryzae pv. oryzae PXO99A",
"category": {
"@id": "#MaterialAttribute/OBI:0100026",
"characteristicType": {
"@id": "OBI:0100026",
"annotationValue": "organism",
"termSource": "OBI",
"termAccession": "OBI:0100026"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/NCBITAXON_360094",
"annotationValue": "Xanthomonas oryzae pv. oryzae PXO99A",
"termSource": "NCBITAXON",
"termAccession": "http://purl.obolibrary.org/obo/NCBITAXON_360094"
}
},
{
"@id": "#MaterialAttributeValue/OD600=0,5",
"category": {
"@id": "#MaterialAttribute/MCO:0000059",
"characteristicType": {
"@id": "MCO:0000059",
"annotationValue": "OD600",
"termSource": "MCO",
"termAccession": "MCO:0000059"
}
},
"value": {
"@id": "#UserTerm_0,5",
"annotationValue": "0,5"
}
}
]
},
{
"@id": "#Sample_\u2206suxA",
"name": "\u2206suxA",
"characteristics": [
{
"@id": "#MaterialAttributeValue/organism=Xanthomonas oryzae pv. oryzae PXO99A",
"category": {
"@id": "#MaterialAttribute/OBI:0100026",
"characteristicType": {
"@id": "OBI:0100026",
"annotationValue": "organism",
"termSource": "OBI",
"termAccession": "OBI:0100026"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/NCBITAXON_360094",
"annotationValue": "Xanthomonas oryzae pv. oryzae PXO99A",
"termSource": "NCBITAXON",
"termAccession": "http://purl.obolibrary.org/obo/NCBITAXON_360094"
}
},
{
"@id": "#MaterialAttributeValue/OD600=0,5",
"category": {
"@id": "#MaterialAttribute/MCO:0000059",
"characteristicType": {
"@id": "MCO:0000059",
"annotationValue": "OD600",
"termSource": "MCO",
"termAccession": "MCO:0000059"
}
},
"value": {
"@id": "#UserTerm_0,5",
"annotationValue": "0,5"
}
}
]
},
{
"@id": "#Sample_\u2206suxB",
"name": "\u2206suxB",
"characteristics": [
{
"@id": "#MaterialAttributeValue/organism=Xanthomonas oryzae pv. oryzae PXO99A",
"category": {
"@id": "#MaterialAttribute/OBI:0100026",
"characteristicType": {
"@id": "OBI:0100026",
"annotationValue": "organism",
"termSource": "OBI",
"termAccession": "OBI:0100026"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/NCBITAXON_360094",
"annotationValue": "Xanthomonas oryzae pv. oryzae PXO99A",
"termSource": "NCBITAXON",
"termAccession": "http://purl.obolibrary.org/obo/NCBITAXON_360094"
}
},
{
"@id": "#MaterialAttributeValue/OD600=0,5",
"category": {
"@id": "#MaterialAttribute/MCO:0000059",
"characteristicType": {
"@id": "MCO:0000059",
"annotationValue": "OD600",
"termSource": "MCO",
"termAccession": "MCO:0000059"
}
},
"value": {
"@id": "#UserTerm_0,5",
"annotationValue": "0,5"
}
}
]
},
{
"@id": "#Sample_Oryza_sativa_Kitaake\t\t",
"name": "Oryza sativa Kitaake\t\t",
"characteristics": [
{
"@id": "#MaterialAttributeValue/organism=Oryza sativa",
"category": {
"@id": "#MaterialAttribute/OBI:0100026",
"characteristicType": {
"@id": "OBI:0100026",
"annotationValue": "organism",
"termSource": "OBI",
"termAccession": "OBI:0100026"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/C_5438",
"annotationValue": "Oryza sativa",
"termSource": "C",
"termAccession": "http://purl.obolibrary.org/obo/C_5438"
}
},
{
"@id": "#EmptyMaterialAttributeValue",
"category": {
"@id": "#MaterialAttribute/MCO:0000059",
"characteristicType": {
"@id": "MCO:0000059",
"annotationValue": "OD600",
"termSource": "MCO",
"termAccession": "MCO:0000059"
}
}
}
]
},
{
"@id": "#Sample_Xoo_wt",
"name": "Xoo wt",
"characteristics": [
{
"@id": "#MaterialAttributeValue/organism=Xanthomonas oryzae pv. oryzae PXO99A",
"category": {
"@id": "#MaterialAttribute/OBI:0100026",
"characteristicType": {
"@id": "OBI:0100026",
"annotationValue": "organism",
"termSource": "OBI",
"termAccession": "OBI:0100026"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/NCBITAXON_360094",
"annotationValue": "Xanthomonas oryzae pv. oryzae PXO99A",
"termSource": "NCBITAXON",
"termAccession": "http://purl.obolibrary.org/obo/NCBITAXON_360094"
}
},
{
"@id": "#MaterialAttributeValue/OD600=0,5",
"category": {
"@id": "#MaterialAttribute/MCO:0000059",
"characteristicType": {
"@id": "MCO:0000059",
"annotationValue": "OD600",
"termSource": "MCO",
"termAccession": "MCO:0000059"
}
},
"value": {
"@id": "#UserTerm_0,5",
"annotationValue": "0,5"
}
}
]
},
{
"@id": "#Sample_Oryzae_sativa_Nipponbare",
"name": "Oryzae sativa Nipponbare",
"characteristics": [
{
"@id": "#MaterialAttributeValue/organism=Oryza sativa",
"category": {
"@id": "#MaterialAttribute/OBI:0100026",
"characteristicType": {
"@id": "OBI:0100026",
"annotationValue": "organism",
"termSource": "OBI",
"termAccession": "OBI:0100026"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/C_5438",
"annotationValue": "Oryza sativa",
"termSource": "C",
"termAccession": "http://purl.obolibrary.org/obo/C_5438"
}
},
{
"@id": "#EmptyMaterialAttributeValue",
"category": {
"@id": "#MaterialAttribute/MCO:0000059",
"characteristicType": {
"@id": "MCO:0000059",
"annotationValue": "OD600",
"termSource": "MCO",
"termAccession": "MCO:0000059"
}
}
}
]
},
{
"@id": "#Sample_\u2206suxC",
"name": "\u2206suxC",
"characteristics": [
{
"@id": "#MaterialAttributeValue/organism=Xanthomonas oryzae pv. oryzae exposure",
"category": {
"@id": "#MaterialAttribute/OBI:0100026",
"characteristicType": {
"@id": "OBI:0100026",
"annotationValue": "organism",
"termSource": "OBI",
"termAccession": "OBI:0100026"
}
},
"value": {
"@id": "https://bioregistry.io/PECO:0007257",
"annotationValue": "Xanthomonas oryzae pv. oryzae exposure",
"termSource": "PECO",
"termAccession": "https://bioregistry.io/PECO:0007257"
}
},
{
"@id": "#MaterialAttributeValue/OD600=0,5",
"category": {
"@id": "#MaterialAttribute/MCO:0000059",
"characteristicType": {
"@id": "MCO:0000059",
"annotationValue": "OD600",
"termSource": "MCO",
"termAccession": "MCO:0000059"
}
},
"value": {
"@id": "#UserTerm_0,5",
"annotationValue": "0,5"
}
}
]
},
{
"@id": "#Sample_Oryza_sativa_IR24_Xoo_wt",
"name": "Oryza sativa IR24_Xoo wt"
},
{
"@id": "#Sample_Oryza_sativa_IR24_\u2206sux",
"name": "Oryza sativa IR24_\u2206sux"
},
{
"@id": "#Sample_Oryza_sativa_IR24_\u2206suxC",
"name": "Oryza sativa IR24_\u2206suxC"
},
{
"@id": "#Sample_Oryza_sativa_IR24_\u2206suxA",
"name": "Oryza sativa IR24_\u2206suxA"
},
{
"@id": "#Sample_Oryza_sativa_IR24_\u2206suxB",
"name": "Oryza sativa IR24_\u2206suxB"
},
{
"@id": "#Sample_Oryza_sativa_Kitaake_Xoo_wt",
"name": "Oryza sativa Kitaake_Xoo wt"
},
{
"@id": "#Sample_Oryza_sativa_Kitaake_\u2206sux",
"name": "Oryza sativa Kitaake_\u2206sux"
},
{
"@id": "#Sample_Oryza_sativa_Kitaake_\u2206suxC",
"name": "Oryza sativa Kitaake_\u2206suxC"
},
{
"@id": "#Sample_Oryza_sativa_Kitaake_\u2206suxA",
"name": "Oryza sativa Kitaake_\u2206suxA"
},
{
"@id": "#Sample_Oryza_sativa_Kitaake_\u2206suxB",
"name": "Oryza sativa Kitaake_\u2206suxB"
},
{
"@id": "#Sample_Oryzae_sativa_Nipponbare_Xoo_wt",
"name": "Oryzae sativa Nipponbare_Xoo wt"
},
{
"@id": "#Sample_Oryzae_sativa_Nipponbare_\u2206sux",
"name": "Oryzae sativa Nipponbare_\u2206sux"
},
{
"@id": "#Sample_Oryzae_sativa_Nipponbare_\u2206suxC",
"name": "Oryzae sativa Nipponbare_\u2206suxC"
},
{
"@id": "#Sample_Oryzae_sativa_Nipponbare_\u2206suxA",
"name": "Oryzae sativa Nipponbare_\u2206suxA"
},
{
"@id": "#Sample_Oryzae_sativa_Nipponbare_\u2206suxB",
"name": "Oryzae sativa Nipponbare_\u2206suxB"
}
]
},
"characteristicCategories": [
{
"@id": "#MaterialAttribute/OBI:0100026",
"characteristicType": {
"@id": "OBI:0100026",
"annotationValue": "organism",
"termSource": "OBI",
"termAccession": "OBI:0100026"
}
},
{
"@id": "#MaterialAttribute/MCO:0000059",
"characteristicType": {
"@id": "MCO:0000059",
"annotationValue": "OD600",
"termSource": "MCO",
"termAccession": "MCO:0000059"
}
}
],
"processSequence": [
{
"@id": "#Process_Inoculation",
"name": "Inoculation",
"inputs": [
{
"@id": "#Sample_Oryza_sativa_IR24",
"name": "Oryza sativa IR24",
"characteristics": [
{
"@id": "#MaterialAttributeValue/organism=Oryza sativa",
"category": {
"@id": "#MaterialAttribute/OBI:0100026",
"characteristicType": {
"@id": "OBI:0100026",
"annotationValue": "organism",
"termSource": "OBI",
"termAccession": "OBI:0100026"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/C_5438",
"annotationValue": "Oryza sativa",
"termSource": "C",
"termAccession": "http://purl.obolibrary.org/obo/C_5438"
}
},
{
"@id": "#EmptyMaterialAttributeValue",
"category": {
"@id": "#MaterialAttribute/MCO:0000059",
"characteristicType": {
"@id": "MCO:0000059",
"annotationValue": "OD600",
"termSource": "MCO",
"termAccession": "MCO:0000059"
}
}
}
]
},
{
"@id": "#Sample_Xoo_wt",
"name": "Xoo wt",
"characteristics": [
{
"@id": "#MaterialAttributeValue/organism=Xanthomonas oryzae pv. oryzae PXO99A",
"category": {
"@id": "#MaterialAttribute/OBI:0100026",
"characteristicType": {
"@id": "OBI:0100026",
"annotationValue": "organism",
"termSource": "OBI",
"termAccession": "OBI:0100026"
}
},
"value": {
"@id": "#UserTerm_Xanthomonas_oryzae_pv._oryzae_PXO99A",
"annotationValue": "Xanthomonas oryzae pv. oryzae PXO99A"
}
},
{
"@id": "#MaterialAttributeValue/OD600=0,5",
"category": {
"@id": "#MaterialAttribute/MCO:0000059",
"characteristicType": {
"@id": "MCO:0000059",
"annotationValue": "OD600",
"termSource": "MCO",
"termAccession": "MCO:0000059"
}
},
"value": {
"@id": "#UserTerm_0,5",
"annotationValue": "0,5"
}
}
]
},
{
"@id": "#Sample_Oryza_sativa_IR24",
"name": "Oryza sativa IR24",
"characteristics": [
{
"@id": "#MaterialAttributeValue/organism=Oryza sativa",
"category": {
"@id": "#MaterialAttribute/OBI:0100026",
"characteristicType": {
"@id": "OBI:0100026",
"annotationValue": "organism",
"termSource": "OBI",
"termAccession": "OBI:0100026"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/C_5438",
"annotationValue": "Oryza sativa",
"termSource": "C",
"termAccession": "http://purl.obolibrary.org/obo/C_5438"
}
},
{
"@id": "#EmptyMaterialAttributeValue",
"category": {
"@id": "#MaterialAttribute/MCO:0000059",
"characteristicType": {
"@id": "MCO:0000059",
"annotationValue": "OD600",
"termSource": "MCO",
"termAccession": "MCO:0000059"
}
}
}
]
},
{
"@id": "#Sample_\u2206sux",
"name": "\u2206sux",
"characteristics": [
{
"@id": "#MaterialAttributeValue/organism=Xanthomonas oryzae pv. oryzae PXO99A",
"category": {
"@id": "#MaterialAttribute/OBI:0100026",
"characteristicType": {
"@id": "OBI:0100026",
"annotationValue": "organism",
"termSource": "OBI",
"termAccession": "OBI:0100026"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/NCBITAXON_360094",
"annotationValue": "Xanthomonas oryzae pv. oryzae PXO99A",
"termSource": "NCBITAXON",
"termAccession": "http://purl.obolibrary.org/obo/NCBITAXON_360094"
}
},
{
"@id": "#MaterialAttributeValue/OD600=0,5",
"category": {
"@id": "#MaterialAttribute/MCO:0000059",
"characteristicType": {
"@id": "MCO:0000059",
"annotationValue": "OD600",
"termSource": "MCO",
"termAccession": "MCO:0000059"
}
},
"value": {
"@id": "#UserTerm_0,5",
"annotationValue": "0,5"
}
}
]
},
{
"@id": "#Sample_Oryza_sativa_IR24",
"name": "Oryza sativa IR24",
"characteristics": [
{
"@id": "#MaterialAttributeValue/organism=Oryza sativa",
"category": {
"@id": "#MaterialAttribute/OBI:0100026",
"characteristicType": {
"@id": "OBI:0100026",
"annotationValue": "organism",
"termSource": "OBI",
"termAccession": "OBI:0100026"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/C_5438",
"annotationValue": "Oryza sativa",
"termSource": "C",
"termAccession": "http://purl.obolibrary.org/obo/C_5438"
}
},
{
"@id": "#EmptyMaterialAttributeValue",
"category": {
"@id": "#MaterialAttribute/MCO:0000059",
"characteristicType": {
"@id": "MCO:0000059",
"annotationValue": "OD600",
"termSource": "MCO",
"termAccession": "MCO:0000059"
}
}
}
]
},
{
"@id": "#Sample_\u2206suxC",
"name": "\u2206suxC",
"characteristics": [
{
"@id": "#MaterialAttributeValue/organism=Xanthomonas oryzae pv. oryzae PXO99A",
"category": {
"@id": "#MaterialAttribute/OBI:0100026",
"characteristicType": {
"@id": "OBI:0100026",
"annotationValue": "organism",
"termSource": "OBI",
"termAccession": "OBI:0100026"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/NCBITAXON_360094",
"annotationValue": "Xanthomonas oryzae pv. oryzae PXO99A",
"termSource": "NCBITAXON",
"termAccession": "http://purl.obolibrary.org/obo/NCBITAXON_360094"
}
},
{
"@id": "#MaterialAttributeValue/OD600=0,5",
"category": {
"@id": "#MaterialAttribute/MCO:0000059",
"characteristicType": {
"@id": "MCO:0000059",
"annotationValue": "OD600",
"termSource": "MCO",
"termAccession": "MCO:0000059"
}
},
"value": {
"@id": "#UserTerm_0,5",
"annotationValue": "0,5"
}
}
]
},
{
"@id": "#Sample_Oryza_sativa_IR24",
"name": "Oryza sativa IR24",
"characteristics": [
{
"@id": "#MaterialAttributeValue/organism=Oryza sativa",
"category": {
"@id": "#MaterialAttribute/OBI:0100026",
"characteristicType": {
"@id": "OBI:0100026",
"annotationValue": "organism",
"termSource": "OBI",
"termAccession": "OBI:0100026"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/C_5438",
"annotationValue": "Oryza sativa",
"termSource": "C",
"termAccession": "http://purl.obolibrary.org/obo/C_5438"
}
},
{
"@id": "#EmptyMaterialAttributeValue",
"category": {
"@id": "#MaterialAttribute/MCO:0000059",
"characteristicType": {
"@id": "MCO:0000059",
"annotationValue": "OD600",
"termSource": "MCO",
"termAccession": "MCO:0000059"
}
}
}
]
},
{
"@id": "#Sample_\u2206suxA",
"name": "\u2206suxA",
"characteristics": [
{
"@id": "#MaterialAttributeValue/organism=Xanthomonas oryzae pv. oryzae PXO99A",
"category": {
"@id": "#MaterialAttribute/OBI:0100026",
"characteristicType": {
"@id": "OBI:0100026",
"annotationValue": "organism",
"termSource": "OBI",
"termAccession": "OBI:0100026"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/NCBITAXON_360094",
"annotationValue": "Xanthomonas oryzae pv. oryzae PXO99A",
"termSource": "NCBITAXON",
"termAccession": "http://purl.obolibrary.org/obo/NCBITAXON_360094"
}
},
{
"@id": "#MaterialAttributeValue/OD600=0,5",
"category": {
"@id": "#MaterialAttribute/MCO:0000059",
"characteristicType": {
"@id": "MCO:0000059",
"annotationValue": "OD600",
"termSource": "MCO",
"termAccession": "MCO:0000059"
}
},
"value": {
"@id": "#UserTerm_0,5",
"annotationValue": "0,5"
}
}
]
},
{
"@id": "#Sample_Oryza_sativa_IR24",
"name": "Oryza sativa IR24",
"characteristics": [
{
"@id": "#MaterialAttributeValue/organism=Oryza sativa",
"category": {
"@id": "#MaterialAttribute/OBI:0100026",
"characteristicType": {
"@id": "OBI:0100026",
"annotationValue": "organism",
"termSource": "OBI",
"termAccession": "OBI:0100026"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/C_5438",
"annotationValue": "Oryza sativa",
"termSource": "C",
"termAccession": "http://purl.obolibrary.org/obo/C_5438"
}
},
{
"@id": "#EmptyMaterialAttributeValue",
"category": {
"@id": "#MaterialAttribute/MCO:0000059",
"characteristicType": {
"@id": "MCO:0000059",
"annotationValue": "OD600",
"termSource": "MCO",
"termAccession": "MCO:0000059"
}
}
}
]
},
{
"@id": "#Sample_\u2206suxB",
"name": "\u2206suxB",
"characteristics": [
{
"@id": "#MaterialAttributeValue/organism=Xanthomonas oryzae pv. oryzae PXO99A",
"category": {
"@id": "#MaterialAttribute/OBI:0100026",
"characteristicType": {
"@id": "OBI:0100026",
"annotationValue": "organism",
"termSource": "OBI",
"termAccession": "OBI:0100026"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/NCBITAXON_360094",
"annotationValue": "Xanthomonas oryzae pv. oryzae PXO99A",
"termSource": "NCBITAXON",
"termAccession": "http://purl.obolibrary.org/obo/NCBITAXON_360094"
}
},
{
"@id": "#MaterialAttributeValue/OD600=0,5",
"category": {
"@id": "#MaterialAttribute/MCO:0000059",
"characteristicType": {
"@id": "MCO:0000059",
"annotationValue": "OD600",
"termSource": "MCO",
"termAccession": "MCO:0000059"
}
},
"value": {
"@id": "#UserTerm_0,5",
"annotationValue": "0,5"
}
}
]
},
{
"@id": "#Sample_Oryza_sativa_Kitaake\t\t",
"name": "Oryza sativa Kitaake\t\t",
"characteristics": [
{
"@id": "#MaterialAttributeValue/organism=Oryza sativa",
"category": {
"@id": "#MaterialAttribute/OBI:0100026",
"characteristicType": {
"@id": "OBI:0100026",
"annotationValue": "organism",
"termSource": "OBI",
"termAccession": "OBI:0100026"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/C_5438",
"annotationValue": "Oryza sativa",
"termSource": "C",
"termAccession": "http://purl.obolibrary.org/obo/C_5438"
}
},
{
"@id": "#EmptyMaterialAttributeValue",
"category": {
"@id": "#MaterialAttribute/MCO:0000059",
"characteristicType": {
"@id": "MCO:0000059",
"annotationValue": "OD600",
"termSource": "MCO",
"termAccession": "MCO:0000059"
}
}
}
]
},
{
"@id": "#Sample_Xoo_wt",
"name": "Xoo wt",
"characteristics": [
{
"@id": "#MaterialAttributeValue/organism=Xanthomonas oryzae pv. oryzae PXO99A",
"category": {
"@id": "#MaterialAttribute/OBI:0100026",
"characteristicType": {
"@id": "OBI:0100026",
"annotationValue": "organism",
"termSource": "OBI",
"termAccession": "OBI:0100026"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/NCBITAXON_360094",
"annotationValue": "Xanthomonas oryzae pv. oryzae PXO99A",
"termSource": "NCBITAXON",
"termAccession": "http://purl.obolibrary.org/obo/NCBITAXON_360094"
}
},
{
"@id": "#MaterialAttributeValue/OD600=0,5",
"category": {
"@id": "#MaterialAttribute/MCO:0000059",
"characteristicType": {
"@id": "MCO:0000059",
"annotationValue": "OD600",
"termSource": "MCO",
"termAccession": "MCO:0000059"
}
},
"value": {
"@id": "#UserTerm_0,5",
"annotationValue": "0,5"
}
}
]
},
{
"@id": "#Sample_Oryza_sativa_Kitaake\t\t",
"name": "Oryza sativa Kitaake\t\t",
"characteristics": [
{
"@id": "#MaterialAttributeValue/organism=Oryza sativa",
"category": {
"@id": "#MaterialAttribute/OBI:0100026",
"characteristicType": {
"@id": "OBI:0100026",
"annotationValue": "organism",
"termSource": "OBI",
"termAccession": "OBI:0100026"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/C_5438",
"annotationValue": "Oryza sativa",
"termSource": "C",
"termAccession": "http://purl.obolibrary.org/obo/C_5438"
}
},
{
"@id": "#EmptyMaterialAttributeValue",
"category": {
"@id": "#MaterialAttribute/MCO:0000059",
"characteristicType": {
"@id": "MCO:0000059",
"annotationValue": "OD600",
"termSource": "MCO",
"termAccession": "MCO:0000059"
}
}
}
]
},
{
"@id": "#Sample_\u2206sux",
"name": "\u2206sux",
"characteristics": [
{
"@id": "#MaterialAttributeValue/organism=Xanthomonas oryzae pv. oryzae PXO99A",
"category": {
"@id": "#MaterialAttribute/OBI:0100026",
"characteristicType": {
"@id": "OBI:0100026",
"annotationValue": "organism",
"termSource": "OBI",
"termAccession": "OBI:0100026"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/NCBITAXON_360094",
"annotationValue": "Xanthomonas oryzae pv. oryzae PXO99A",
"termSource": "NCBITAXON",
"termAccession": "http://purl.obolibrary.org/obo/NCBITAXON_360094"
}
},
{
"@id": "#MaterialAttributeValue/OD600=0,5",
"category": {
"@id": "#MaterialAttribute/MCO:0000059",
"characteristicType": {
"@id": "MCO:0000059",
"annotationValue": "OD600",
"termSource": "MCO",
"termAccession": "MCO:0000059"
}
},
"value": {
"@id": "#UserTerm_0,5",
"annotationValue": "0,5"
}
}
]
},
{
"@id": "#Sample_Oryza_sativa_Kitaake\t\t",
"name": "Oryza sativa Kitaake\t\t",
"characteristics": [
{
"@id": "#MaterialAttributeValue/organism=Oryza sativa",
"category": {
"@id": "#MaterialAttribute/OBI:0100026",
"characteristicType": {
"@id": "OBI:0100026",
"annotationValue": "organism",
"termSource": "OBI",
"termAccession": "OBI:0100026"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/C_5438",
"annotationValue": "Oryza sativa",
"termSource": "C",
"termAccession": "http://purl.obolibrary.org/obo/C_5438"
}
},
{
"@id": "#EmptyMaterialAttributeValue",
"category": {
"@id": "#MaterialAttribute/MCO:0000059",
"characteristicType": {
"@id": "MCO:0000059",
"annotationValue": "OD600",
"termSource": "MCO",
"termAccession": "MCO:0000059"
}
}
}
]
},
{
"@id": "#Sample_\u2206suxC",
"name": "\u2206suxC",
"characteristics": [
{
"@id": "#MaterialAttributeValue/organism=Xanthomonas oryzae pv. oryzae PXO99A",
"category": {
"@id": "#MaterialAttribute/OBI:0100026",
"characteristicType": {
"@id": "OBI:0100026",
"annotationValue": "organism",
"termSource": "OBI",
"termAccession": "OBI:0100026"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/NCBITAXON_360094",
"annotationValue": "Xanthomonas oryzae pv. oryzae PXO99A",
"termSource": "NCBITAXON",
"termAccession": "http://purl.obolibrary.org/obo/NCBITAXON_360094"
}
},
{
"@id": "#MaterialAttributeValue/OD600=0,5",
"category": {
"@id": "#MaterialAttribute/MCO:0000059",
"characteristicType": {
"@id": "MCO:0000059",
"annotationValue": "OD600",
"termSource": "MCO",
"termAccession": "MCO:0000059"
}
},
"value": {
"@id": "#UserTerm_0,5",
"annotationValue": "0,5"
}
}
]
},
{
"@id": "#Sample_Oryza_sativa_Kitaake\t\t",
"name": "Oryza sativa Kitaake\t\t",
"characteristics": [
{
"@id": "#MaterialAttributeValue/organism=Oryza sativa",
"category": {
"@id": "#MaterialAttribute/OBI:0100026",
"characteristicType": {
"@id": "OBI:0100026",
"annotationValue": "organism",
"termSource": "OBI",
"termAccession": "OBI:0100026"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/C_5438",
"annotationValue": "Oryza sativa",
"termSource": "C",
"termAccession": "http://purl.obolibrary.org/obo/C_5438"
}
},
{
"@id": "#EmptyMaterialAttributeValue",
"category": {
"@id": "#MaterialAttribute/MCO:0000059",
"characteristicType": {
"@id": "MCO:0000059",
"annotationValue": "OD600",
"termSource": "MCO",
"termAccession": "MCO:0000059"
}
}
}
]
},
{
"@id": "#Sample_\u2206suxA",
"name": "\u2206suxA",
"characteristics": [
{
"@id": "#MaterialAttributeValue/organism=Xanthomonas oryzae pv. oryzae PXO99A",
"category": {
"@id": "#MaterialAttribute/OBI:0100026",
"characteristicType": {
"@id": "OBI:0100026",
"annotationValue": "organism",
"termSource": "OBI",
"termAccession": "OBI:0100026"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/NCBITAXON_360094",
"annotationValue": "Xanthomonas oryzae pv. oryzae PXO99A",
"termSource": "NCBITAXON",
"termAccession": "http://purl.obolibrary.org/obo/NCBITAXON_360094"
}
},
{
"@id": "#MaterialAttributeValue/OD600=0,5",
"category": {
"@id": "#MaterialAttribute/MCO:0000059",
"characteristicType": {
"@id": "MCO:0000059",
"annotationValue": "OD600",
"termSource": "MCO",
"termAccession": "MCO:0000059"
}
},
"value": {
"@id": "#UserTerm_0,5",
"annotationValue": "0,5"
}
}
]
},
{
"@id": "#Sample_Oryza_sativa_Kitaake\t\t",
"name": "Oryza sativa Kitaake\t\t",
"characteristics": [
{
"@id": "#MaterialAttributeValue/organism=Oryza sativa",
"category": {
"@id": "#MaterialAttribute/OBI:0100026",
"characteristicType": {
"@id": "OBI:0100026",
"annotationValue": "organism",
"termSource": "OBI",
"termAccession": "OBI:0100026"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/C_5438",
"annotationValue": "Oryza sativa",
"termSource": "C",
"termAccession": "http://purl.obolibrary.org/obo/C_5438"
}
},
{
"@id": "#EmptyMaterialAttributeValue",
"category": {
"@id": "#MaterialAttribute/MCO:0000059",
"characteristicType": {
"@id": "MCO:0000059",
"annotationValue": "OD600",
"termSource": "MCO",
"termAccession": "MCO:0000059"
}
}
}
]
},
{
"@id": "#Sample_\u2206suxB",
"name": "\u2206suxB",
"characteristics": [
{
"@id": "#MaterialAttributeValue/organism=Xanthomonas oryzae pv. oryzae PXO99A",
"category": {
"@id": "#MaterialAttribute/OBI:0100026",
"characteristicType": {
"@id": "OBI:0100026",
"annotationValue": "organism",
"termSource": "OBI",
"termAccession": "OBI:0100026"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/NCBITAXON_360094",
"annotationValue": "Xanthomonas oryzae pv. oryzae PXO99A",
"termSource": "NCBITAXON",
"termAccession": "http://purl.obolibrary.org/obo/NCBITAXON_360094"
}
},
{
"@id": "#MaterialAttributeValue/OD600=0,5",
"category": {
"@id": "#MaterialAttribute/MCO:0000059",
"characteristicType": {
"@id": "MCO:0000059",
"annotationValue": "OD600",
"termSource": "MCO",
"termAccession": "MCO:0000059"
}
},
"value": {
"@id": "#UserTerm_0,5",
"annotationValue": "0,5"
}
}
]
},
{
"@id": "#Sample_Oryzae_sativa_Nipponbare",
"name": "Oryzae sativa Nipponbare",
"characteristics": [
{
"@id": "#MaterialAttributeValue/organism=Oryza sativa",
"category": {
"@id": "#MaterialAttribute/OBI:0100026",
"characteristicType": {
"@id": "OBI:0100026",
"annotationValue": "organism",
"termSource": "OBI",
"termAccession": "OBI:0100026"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/C_5438",
"annotationValue": "Oryza sativa",
"termSource": "C",
"termAccession": "http://purl.obolibrary.org/obo/C_5438"
}
},
{
"@id": "#EmptyMaterialAttributeValue",
"category": {
"@id": "#MaterialAttribute/MCO:0000059",
"characteristicType": {
"@id": "MCO:0000059",
"annotationValue": "OD600",
"termSource": "MCO",
"termAccession": "MCO:0000059"
}
}
}
]
},
{
"@id": "#Sample_Xoo_wt",
"name": "Xoo wt",
"characteristics": [
{
"@id": "#MaterialAttributeValue/organism=Xanthomonas oryzae pv. oryzae PXO99A",
"category": {
"@id": "#MaterialAttribute/OBI:0100026",
"characteristicType": {
"@id": "OBI:0100026",
"annotationValue": "organism",
"termSource": "OBI",
"termAccession": "OBI:0100026"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/NCBITAXON_360094",
"annotationValue": "Xanthomonas oryzae pv. oryzae PXO99A",
"termSource": "NCBITAXON",
"termAccession": "http://purl.obolibrary.org/obo/NCBITAXON_360094"
}
},
{
"@id": "#MaterialAttributeValue/OD600=0,5",
"category": {
"@id": "#MaterialAttribute/MCO:0000059",
"characteristicType": {
"@id": "MCO:0000059",
"annotationValue": "OD600",
"termSource": "MCO",
"termAccession": "MCO:0000059"
}
},
"value": {
"@id": "#UserTerm_0,5",
"annotationValue": "0,5"
}
}
]
},
{
"@id": "#Sample_Oryzae_sativa_Nipponbare",
"name": "Oryzae sativa Nipponbare",
"characteristics": [
{
"@id": "#MaterialAttributeValue/organism=Oryza sativa",
"category": {
"@id": "#MaterialAttribute/OBI:0100026",
"characteristicType": {
"@id": "OBI:0100026",
"annotationValue": "organism",
"termSource": "OBI",
"termAccession": "OBI:0100026"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/C_5438",
"annotationValue": "Oryza sativa",
"termSource": "C",
"termAccession": "http://purl.obolibrary.org/obo/C_5438"
}
},
{
"@id": "#EmptyMaterialAttributeValue",
"category": {
"@id": "#MaterialAttribute/MCO:0000059",
"characteristicType": {
"@id": "MCO:0000059",
"annotationValue": "OD600",
"termSource": "MCO",
"termAccession": "MCO:0000059"
}
}
}
]
},
{
"@id": "#Sample_\u2206sux",
"name": "\u2206sux",
"characteristics": [
{
"@id": "#MaterialAttributeValue/organism=Xanthomonas oryzae pv. oryzae PXO99A",
"category": {
"@id": "#MaterialAttribute/OBI:0100026",
"characteristicType": {
"@id": "OBI:0100026",
"annotationValue": "organism",
"termSource": "OBI",
"termAccession": "OBI:0100026"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/NCBITAXON_360094",
"annotationValue": "Xanthomonas oryzae pv. oryzae PXO99A",
"termSource": "NCBITAXON",
"termAccession": "http://purl.obolibrary.org/obo/NCBITAXON_360094"
}
},
{
"@id": "#MaterialAttributeValue/OD600=0,5",
"category": {
"@id": "#MaterialAttribute/MCO:0000059",
"characteristicType": {
"@id": "MCO:0000059",
"annotationValue": "OD600",
"termSource": "MCO",
"termAccession": "MCO:0000059"
}
},
"value": {
"@id": "#UserTerm_0,5",
"annotationValue": "0,5"
}
}
]
},
{
"@id": "#Sample_Oryzae_sativa_Nipponbare",
"name": "Oryzae sativa Nipponbare",
"characteristics": [
{
"@id": "#MaterialAttributeValue/organism=Oryza sativa",
"category": {
"@id": "#MaterialAttribute/OBI:0100026",
"characteristicType": {
"@id": "OBI:0100026",
"annotationValue": "organism",
"termSource": "OBI",
"termAccession": "OBI:0100026"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/C_5438",
"annotationValue": "Oryza sativa",
"termSource": "C",
"termAccession": "http://purl.obolibrary.org/obo/C_5438"
}
},
{
"@id": "#EmptyMaterialAttributeValue",
"category": {
"@id": "#MaterialAttribute/MCO:0000059",
"characteristicType": {
"@id": "MCO:0000059",
"annotationValue": "OD600",
"termSource": "MCO",
"termAccession": "MCO:0000059"
}
}
}
]
},
{
"@id": "#Sample_\u2206suxC",
"name": "\u2206suxC",
"characteristics": [
{
"@id": "#MaterialAttributeValue/organism=Xanthomonas oryzae pv. oryzae exposure",
"category": {
"@id": "#MaterialAttribute/OBI:0100026",
"characteristicType": {
"@id": "OBI:0100026",
"annotationValue": "organism",
"termSource": "OBI",
"termAccession": "OBI:0100026"
}
},
"value": {
"@id": "https://bioregistry.io/PECO:0007257",
"annotationValue": "Xanthomonas oryzae pv. oryzae exposure",
"termSource": "PECO",
"termAccession": "https://bioregistry.io/PECO:0007257"
}
},
{
"@id": "#MaterialAttributeValue/OD600=0,5",
"category": {
"@id": "#MaterialAttribute/MCO:0000059",
"characteristicType": {
"@id": "MCO:0000059",
"annotationValue": "OD600",
"termSource": "MCO",
"termAccession": "MCO:0000059"
}
},
"value": {
"@id": "#UserTerm_0,5",
"annotationValue": "0,5"
}
}
]
},
{
"@id": "#Sample_Oryzae_sativa_Nipponbare",
"name": "Oryzae sativa Nipponbare",
"characteristics": [
{
"@id": "#MaterialAttributeValue/organism=Oryza sativa",
"category": {
"@id": "#MaterialAttribute/OBI:0100026",
"characteristicType": {
"@id": "OBI:0100026",
"annotationValue": "organism",
"termSource": "OBI",
"termAccession": "OBI:0100026"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/C_5438",
"annotationValue": "Oryza sativa",
"termSource": "C",
"termAccession": "http://purl.obolibrary.org/obo/C_5438"
}
},
{
"@id": "#EmptyMaterialAttributeValue",
"category": {
"@id": "#MaterialAttribute/MCO:0000059",
"characteristicType": {
"@id": "MCO:0000059",
"annotationValue": "OD600",
"termSource": "MCO",
"termAccession": "MCO:0000059"
}
}
}
]
},
{
"@id": "#Sample_\u2206suxA",
"name": "\u2206suxA",
"characteristics": [
{
"@id": "#MaterialAttributeValue/organism=Xanthomonas oryzae pv. oryzae PXO99A",
"category": {
"@id": "#MaterialAttribute/OBI:0100026",
"characteristicType": {
"@id": "OBI:0100026",
"annotationValue": "organism",
"termSource": "OBI",
"termAccession": "OBI:0100026"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/NCBITAXON_360094",
"annotationValue": "Xanthomonas oryzae pv. oryzae PXO99A",
"termSource": "NCBITAXON",
"termAccession": "http://purl.obolibrary.org/obo/NCBITAXON_360094"
}
},
{
"@id": "#MaterialAttributeValue/OD600=0,5",
"category": {
"@id": "#MaterialAttribute/MCO:0000059",
"characteristicType": {
"@id": "MCO:0000059",
"annotationValue": "OD600",
"termSource": "MCO",
"termAccession": "MCO:0000059"
}
},
"value": {
"@id": "#UserTerm_0,5",
"annotationValue": "0,5"
}
}
]
},
{
"@id": "#Sample_Oryzae_sativa_Nipponbare",
"name": "Oryzae sativa Nipponbare",
"characteristics": [
{
"@id": "#MaterialAttributeValue/organism=Oryza sativa",
"category": {
"@id": "#MaterialAttribute/OBI:0100026",
"characteristicType": {
"@id": "OBI:0100026",
"annotationValue": "organism",
"termSource": "OBI",
"termAccession": "OBI:0100026"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/C_5438",
"annotationValue": "Oryza sativa",
"termSource": "C",
"termAccession": "http://purl.obolibrary.org/obo/C_5438"
}
},
{
"@id": "#EmptyMaterialAttributeValue",
"category": {
"@id": "#MaterialAttribute/MCO:0000059",
"characteristicType": {
"@id": "MCO:0000059",
"annotationValue": "OD600",
"termSource": "MCO",
"termAccession": "MCO:0000059"
}
}
}
]
},
{
"@id": "#Sample_\u2206suxB",
"name": "\u2206suxB",
"characteristics": [
{
"@id": "#MaterialAttributeValue/organism=Xanthomonas oryzae pv. oryzae PXO99A",
"category": {
"@id": "#MaterialAttribute/OBI:0100026",
"characteristicType": {
"@id": "OBI:0100026",
"annotationValue": "organism",
"termSource": "OBI",
"termAccession": "OBI:0100026"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/NCBITAXON_360094",
"annotationValue": "Xanthomonas oryzae pv. oryzae PXO99A",
"termSource": "NCBITAXON",
"termAccession": "http://purl.obolibrary.org/obo/NCBITAXON_360094"
}
},
{
"@id": "#MaterialAttributeValue/OD600=0,5",
"category": {
"@id": "#MaterialAttribute/MCO:0000059",
"characteristicType": {
"@id": "MCO:0000059",
"annotationValue": "OD600",
"termSource": "MCO",
"termAccession": "MCO:0000059"
}
},
"value": {
"@id": "#UserTerm_0,5",
"annotationValue": "0,5"
}
}
]
}
],
"outputs": [
{
"@id": "#Sample_Oryza_sativa_IR24_Xoo_wt",
"name": "Oryza sativa IR24_Xoo wt"
},
{
"@id": "#Sample_Oryza_sativa_IR24_Xoo_wt",
"name": "Oryza sativa IR24_Xoo wt"
},
{
"@id": "#Sample_Oryza_sativa_IR24_\u2206sux",
"name": "Oryza sativa IR24_\u2206sux"
},
{
"@id": "#Sample_Oryza_sativa_IR24_\u2206sux",
"name": "Oryza sativa IR24_\u2206sux"
},
{
"@id": "#Sample_Oryza_sativa_IR24_\u2206suxC",
"name": "Oryza sativa IR24_\u2206suxC"
},
{
"@id": "#Sample_Oryza_sativa_IR24_\u2206suxC",
"name": "Oryza sativa IR24_\u2206suxC"
},
{
"@id": "#Sample_Oryza_sativa_IR24_\u2206suxA",
"name": "Oryza sativa IR24_\u2206suxA"
},
{
"@id": "#Sample_Oryza_sativa_IR24_\u2206suxA",
"name": "Oryza sativa IR24_\u2206suxA"
},
{
"@id": "#Sample_Oryza_sativa_IR24_\u2206suxB",
"name": "Oryza sativa IR24_\u2206suxB"
},
{
"@id": "#Sample_Oryza_sativa_IR24_\u2206suxB",
"name": "Oryza sativa IR24_\u2206suxB"
},
{
"@id": "#Sample_Oryza_sativa_Kitaake_Xoo_wt",
"name": "Oryza sativa Kitaake_Xoo wt"
},
{
"@id": "#Sample_Oryza_sativa_Kitaake_Xoo_wt",
"name": "Oryza sativa Kitaake_Xoo wt"
},
{
"@id": "#Sample_Oryza_sativa_Kitaake_\u2206sux",
"name": "Oryza sativa Kitaake_\u2206sux"
},
{
"@id": "#Sample_Oryza_sativa_Kitaake_\u2206sux",
"name": "Oryza sativa Kitaake_\u2206sux"
},
{
"@id": "#Sample_Oryza_sativa_Kitaake_\u2206suxC",
"name": "Oryza sativa Kitaake_\u2206suxC"
},
{
"@id": "#Sample_Oryza_sativa_Kitaake_\u2206suxC",
"name": "Oryza sativa Kitaake_\u2206suxC"
},
{
"@id": "#Sample_Oryza_sativa_Kitaake_\u2206suxA",
"name": "Oryza sativa Kitaake_\u2206suxA"
},
{
"@id": "#Sample_Oryza_sativa_Kitaake_\u2206suxA",
"name": "Oryza sativa Kitaake_\u2206suxA"
},
{
"@id": "#Sample_Oryza_sativa_Kitaake_\u2206suxB",
"name": "Oryza sativa Kitaake_\u2206suxB"
},
{
"@id": "#Sample_Oryza_sativa_Kitaake_\u2206suxB",
"name": "Oryza sativa Kitaake_\u2206suxB"
},
{
"@id": "#Sample_Oryzae_sativa_Nipponbare_Xoo_wt",
"name": "Oryzae sativa Nipponbare_Xoo wt"
},
{
"@id": "#Sample_Oryzae_sativa_Nipponbare_Xoo_wt",
"name": "Oryzae sativa Nipponbare_Xoo wt"
},
{
"@id": "#Sample_Oryzae_sativa_Nipponbare_\u2206sux",
"name": "Oryzae sativa Nipponbare_\u2206sux"
},
{
"@id": "#Sample_Oryzae_sativa_Nipponbare_\u2206sux",
"name": "Oryzae sativa Nipponbare_\u2206sux"
},
{
"@id": "#Sample_Oryzae_sativa_Nipponbare_\u2206suxC",
"name": "Oryzae sativa Nipponbare_\u2206suxC"
},
{
"@id": "#Sample_Oryzae_sativa_Nipponbare_\u2206suxC",
"name": "Oryzae sativa Nipponbare_\u2206suxC"
},
{
"@id": "#Sample_Oryzae_sativa_Nipponbare_\u2206suxA",
"name": "Oryzae sativa Nipponbare_\u2206suxA"
},
{
"@id": "#Sample_Oryzae_sativa_Nipponbare_\u2206suxA",
"name": "Oryzae sativa Nipponbare_\u2206suxA"
},
{
"@id": "#Sample_Oryzae_sativa_Nipponbare_\u2206suxB",
"name": "Oryzae sativa Nipponbare_\u2206suxB"
},
{
"@id": "#Sample_Oryzae_sativa_Nipponbare_\u2206suxB",
"name": "Oryzae sativa Nipponbare_\u2206suxB"
}
]
},
{
"@id": "#Process_lesion_measurement",
"name": "lesion measurement",
"executesProtocol": {
"@id": "#Protocol_clippingassay.docx",
"name": "clippingassay.docx",
"parameters": [
{
"@id": "#ProtocolParameter/NCIT:C25207",
"parameterName": {
"@id": "NCIT:C25207",
"annotationValue": "Time",
"termSource": "NCIT",
"termAccession": "NCIT:C25207"
}
}
]
},
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NCIT:C25207",
"parameterName": {
"@id": "NCIT:C25207",
"annotationValue": "Time",
"termSource": "NCIT",
"termAccession": "NCIT:C25207"
}
},
"value": {
"@id": "#UserTerm_12_DAI",
"annotationValue": "12 DAI"
}
}
],
"inputs": [
{
"@id": "#Sample_Oryza_sativa_IR24_Xoo_wt",
"name": "Oryza sativa IR24_Xoo wt"
},
{
"@id": "#Sample_Oryza_sativa_IR24_\u2206sux",
"name": "Oryza sativa IR24_\u2206sux"
},
{
"@id": "#Sample_Oryza_sativa_IR24_\u2206suxC",
"name": "Oryza sativa IR24_\u2206suxC"
},
{
"@id": "#Sample_Oryza_sativa_IR24_\u2206suxA",
"name": "Oryza sativa IR24_\u2206suxA"
},
{
"@id": "#Sample_Oryza_sativa_IR24_\u2206suxB",
"name": "Oryza sativa IR24_\u2206suxB"
},
{
"@id": "#Sample_Oryza_sativa_IR24_\u2206suxB",
"name": "Oryza sativa IR24_\u2206suxB"
},
{
"@id": "#Sample_Oryza_sativa_Kitaake_Xoo_wt",
"name": "Oryza sativa Kitaake_Xoo wt"
},
{
"@id": "#Sample_Oryza_sativa_Kitaake_\u2206sux",
"name": "Oryza sativa Kitaake_\u2206sux"
},
{
"@id": "#Sample_Oryza_sativa_Kitaake_\u2206suxC",
"name": "Oryza sativa Kitaake_\u2206suxC"
},
{
"@id": "#Sample_Oryza_sativa_Kitaake_\u2206suxA",
"name": "Oryza sativa Kitaake_\u2206suxA"
},
{
"@id": "#Sample_Oryza_sativa_Kitaake_\u2206suxB",
"name": "Oryza sativa Kitaake_\u2206suxB"
},
{
"@id": "#Sample_Oryza_sativa_Kitaake_\u2206suxC",
"name": "Oryza sativa Kitaake_\u2206suxC"
},
{
"@id": "#Sample_Oryzae_sativa_Nipponbare_Xoo_wt",
"name": "Oryzae sativa Nipponbare_Xoo wt"
},
{
"@id": "#Sample_Oryzae_sativa_Nipponbare_\u2206sux",
"name": "Oryzae sativa Nipponbare_\u2206sux"
},
{
"@id": "#Sample_Oryzae_sativa_Nipponbare_\u2206suxC",
"name": "Oryzae sativa Nipponbare_\u2206suxC"
},
{
"@id": "#Sample_Oryzae_sativa_Nipponbare_\u2206suxA",
"name": "Oryzae sativa Nipponbare_\u2206suxA"
},
{
"@id": "#Sample_Oryzae_sativa_Nipponbare_\u2206suxB",
"name": "Oryzae sativa Nipponbare_\u2206suxB"
}
],
"outputs": [
{
"@id": "assays/Clipping/dataset/Inoculation_data_IR24.xlsx",
"name": "assays/Clipping/dataset/Inoculation data_IR24.xlsx",
"type": "Raw Data File"
},
{
"@id": "assays/Clipping/dataset/Inoculation_data_IR24.xlsx",
"name": "assays/Clipping/dataset/Inoculation data_IR24.xlsx",
"type": "Raw Data File"
},
{
"@id": "assays/Clipping/dataset/Inoculation_data_IR24.xlsx",
"name": "assays/Clipping/dataset/Inoculation data_IR24.xlsx",
"type": "Raw Data File"
},
{
"@id": "assays/Clipping/dataset/Inoculation_data_IR24.xlsx",
"name": "assays/Clipping/dataset/Inoculation data_IR24.xlsx",
"type": "Raw Data File"
},
{
"@id": "assays/Clipping/dataset/Inoculation_data_IR24.xlsx",
"name": "assays/Clipping/dataset/Inoculation data_IR24.xlsx",
"type": "Raw Data File"
},
{
"@id": "assays/Clipping/dataset/Inoculation_data_IR24.xlsx",
"name": "assays/Clipping/dataset/Inoculation data_IR24.xlsx",
"type": "Raw Data File"
},
{
"@id": "assays/Clipping/dataset/Inoculation_data_Kitaake.xlsx",
"name": "assays/Clipping/dataset/Inoculation data_Kitaake.xlsx",
"type": "Raw Data File"
},
{
"@id": "assays/Clipping/dataset/Inoculation_data_Kitaake.xlsx",
"name": "assays/Clipping/dataset/Inoculation data_Kitaake.xlsx",
"type": "Raw Data File"
},
{
"@id": "assays/Clipping/dataset/Inoculation_data_Kitaake.xlsx",
"name": "assays/Clipping/dataset/Inoculation data_Kitaake.xlsx",
"type": "Raw Data File"
},
{
"@id": "assays/Clipping/dataset/Inoculation_data_Kitaake.xlsx",
"name": "assays/Clipping/dataset/Inoculation data_Kitaake.xlsx",
"type": "Raw Data File"
},
{
"@id": "assays/Clipping/dataset/Inoculation_data_Kitaake.xlsx",
"name": "assays/Clipping/dataset/Inoculation data_Kitaake.xlsx",
"type": "Raw Data File"
},
{
"@id": "assays/Clipping/dataset/Inoculation_data_Kitaake.xlsx",
"name": "assays/Clipping/dataset/Inoculation data_Kitaake.xlsx",
"type": "Raw Data File"
},
{
"@id": "assays/Clipping/dataset/sucrose_gene_on_Nip_V2.xlsx",
"name": "assays/Clipping/dataset/sucrose gene on Nip_V2.xlsx",
"type": "Raw Data File"
},
{
"@id": "assays/Clipping/dataset/sucrose_gene_on_Nip_V2.xlsx",
"name": "assays/Clipping/dataset/sucrose gene on Nip_V2.xlsx",
"type": "Raw Data File"
},
{
"@id": "assays/Clipping/dataset/sucrose_gene_on_Nip_V2.xlsx",
"name": "assays/Clipping/dataset/sucrose gene on Nip_V2.xlsx",
"type": "Raw Data File"
},
{
"@id": "assays/Clipping/dataset/sucrose_gene_on_Nip_V2.xlsx",
"name": "assays/Clipping/dataset/sucrose gene on Nip_V2.xlsx",
"type": "Raw Data File"
},
{
"@id": "assays/Clipping/dataset/sucrose_gene_on_Nip_V2.xlsx",
"name": "assays/Clipping/dataset/sucrose gene on Nip_V2.xlsx",
"type": "Raw Data File"
}
]
}
]
},
{
"filename": "assays/Growth Curves/isa.assay.xlsx",
"@id": "assays/Growth_Curves/",
"measurementType": {
"@id": "http://purl.obolibrary.org/obo/MCO_0000059",
"annotationValue": "OD600",
"termSource": "MCO",
"termAccession": "http://purl.obolibrary.org/obo/MCO_0000059"
},
"technologyType": {
"@id": "#UserTerm_Photospectrometer",
"annotationValue": "Photospectrometer"
},
"technologyPlatform": "Tecan",
"dataFiles": [
{
"@id": "assays/Growth_Curves/dataset/RawData",
"name": "assays/Growth Curves/dataset/RawData",
"type": "Raw Data File"
},
{
"@id": "assays/Growth_Curves/dataset/RawData/\u2206sux_raw",
"name": "assays/Growth Curves/dataset/RawData/\u2206sux_raw",
"type": "Raw Data File"
},
{
"@id": "assays/Growth_Curves/dataset/RawData/\u2206suxA_raw",
"name": "assays/Growth Curves/dataset/RawData/\u2206suxA_raw",
"type": "Raw Data File"
},
{
"@id": "assays/Growth_Curves/dataset/RawData/\u2206suxB_raw",
"name": "assays/Growth Curves/dataset/RawData/\u2206suxB_raw",
"type": "Raw Data File"
},
{
"@id": "assays/Growth_Curves/dataset/RawData/\u2206suxC_raw",
"name": "assays/Growth Curves/dataset/RawData/\u2206suxC_raw",
"type": "Raw Data File"
},
{
"@id": "assays/Growth_Curves/dataset/RawData/\u2206suxR_raw",
"name": "assays/Growth Curves/dataset/RawData/\u2206suxR_raw",
"type": "Raw Data File"
},
{
"@id": "assays/Growth_Curves/dataset/AnalyzedData/\u2206sux_analyzed/\u2206sux(203-205)_summary.xlsx",
"name": "assays/Growth Curves/dataset/AnalyzedData/\u2206sux_analyzed/\u2206sux(203-205)_summary.xlsx",
"type": "Raw Data File"
},
{
"@id": "assays/Growth_Curves/dataset/AnalyzedData/\u2206suxR_analyzed/suxR.tif",
"name": "assays/Growth Curves/dataset/AnalyzedData/\u2206suxR_analyzed/suxR.tif",
"type": "Raw Data File"
},
{
"@id": "assays/Growth_Curves/dataset/AnalyzedData/\u2206suxC_analyzed/suxC.tif",
"name": "assays/Growth Curves/dataset/AnalyzedData/\u2206suxC_analyzed/suxC.tif",
"type": "Raw Data File"
},
{
"@id": "assays/Growth_Curves/dataset/AnalyzedData/\u2206suxB_analyzed/suxB.tif",
"name": "assays/Growth Curves/dataset/AnalyzedData/\u2206suxB_analyzed/suxB.tif",
"type": "Raw Data File"
},
{
"@id": "assays/Growth_Curves/dataset/AnalyzedData/\u2206suxA_analyzed/suxA.tif",
"name": "assays/Growth Curves/dataset/AnalyzedData/\u2206suxA_analyzed/suxA.tif",
"type": "Raw Data File"
},
{
"@id": "assays/Growth_Curves/dataset/RawData/wt_raw",
"name": "assays/Growth Curves/dataset/RawData/wt_raw",
"type": "Raw Data File"
},
{
"@id": "assays/Growth_Curves/dataset/AnalyzedData/wt_analyzed/wt.tif",
"name": "assays/Growth Curves/dataset/AnalyzedData/wt_analyzed/wt.tif",
"type": "Raw Data File"
}
],
"materials": {},
"unitCategories": [
{
"@id": "https://bioregistry.io/UO:0000027",
"annotationValue": "degree celsius",
"termSource": "UO",
"termAccession": "https://bioregistry.io/UO:0000027"
},
{
"@id": "https://bioregistry.io/NCIT:C28251",
"annotationValue": "Millimeter",
"termSource": "NCIT",
"termAccession": "https://bioregistry.io/NCIT:C28251"
},
{
"@id": "https://bioregistry.io/NCIT:C25529",
"annotationValue": "Hour",
"termSource": "NCIT",
"termAccession": "https://bioregistry.io/NCIT:C25529"
}
],
"processSequence": [
{
"@id": "#Process_Growth_curves",
"name": "Growth curves",
"executesProtocol": {
"@id": "#Protocol_Growth-Assay-in-12-well-plates.pdf",
"name": "Growth-Assay-in-12-well-plates.pdf",
"parameters": [
{
"@id": "#ProtocolParameter/EFO:0001702",
"parameterName": {
"@id": "EFO:0001702",
"annotationValue": "temperature",
"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
{
"@id": "#ProtocolParameter/NCIT:C64646",
"parameterName": {
"@id": "NCIT:C64646",
"annotationValue": "Amplitude",
"termSource": "NCIT",
"termAccession": "NCIT:C64646"
}
},
{
"@id": "#ProtocolParameter/NCIT:C25207",
"parameterName": {
"@id": "NCIT:C25207",
"annotationValue": "Time",
"termSource": "NCIT",
"termAccession": "NCIT:C25207"
}
}
]
},
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/EFO:0001702",
"parameterName": {
"@id": "EFO:0001702",
"annotationValue": "temperature",
"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
"value": 28,
"unit": {
"@id": "https://bioregistry.io/UO:0000027",
"annotationValue": "degree celsius",
"termSource": "UO",
"termAccession": "https://bioregistry.io/UO:0000027"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C64646",
"parameterName": {
"@id": "NCIT:C64646",
"annotationValue": "Amplitude",
"termSource": "NCIT",
"termAccession": "NCIT:C64646"
}
},
"value": 3,
"unit": {
"@id": "https://bioregistry.io/NCIT:C28251",
"annotationValue": "Millimeter",
"termSource": "NCIT",
"termAccession": "https://bioregistry.io/NCIT:C28251"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C25207",
"parameterName": {
"@id": "NCIT:C25207",
"annotationValue": "Time",
"termSource": "NCIT",
"termAccession": "NCIT:C25207"
}
},
"value": 24,
"unit": {
"@id": "https://bioregistry.io/NCIT:C25529",
"annotationValue": "Hour",
"termSource": "NCIT",
"termAccession": "https://bioregistry.io/NCIT:C25529"
}
}
],
"inputs": [
{
"@id": "#Source_Xoo_wt",
"name": "Xoo wt"
},
{
"@id": "#Source_\u2206sux",
"name": "\u2206sux"
},
{
"@id": "#Source_\u2206suxA",
"name": "\u2206suxA"
},
{
"@id": "#Source_\u2206suxB",
"name": "\u2206suxB"
},
{
"@id": "#Source_\u2206suxC",
"name": "\u2206suxC"
},
{
"@id": "#Source_\u2206suxR",
"name": "\u2206suxR"
}
],
"outputs": [
{
"@id": "assays/Growth_Curves/dataset/RawData",
"name": "assays/Growth Curves/dataset/RawData",
"type": "Raw Data File"
},
{
"@id": "assays/Growth_Curves/dataset/RawData/\u2206sux_raw",
"name": "assays/Growth Curves/dataset/RawData/\u2206sux_raw",
"type": "Raw Data File"
},
{
"@id": "assays/Growth_Curves/dataset/RawData/\u2206suxA_raw",
"name": "assays/Growth Curves/dataset/RawData/\u2206suxA_raw",
"type": "Raw Data File"
},
{
"@id": "assays/Growth_Curves/dataset/RawData/\u2206suxB_raw",
"name": "assays/Growth Curves/dataset/RawData/\u2206suxB_raw",
"type": "Raw Data File"
},
{
"@id": "assays/Growth_Curves/dataset/RawData/\u2206suxC_raw",
"name": "assays/Growth Curves/dataset/RawData/\u2206suxC_raw",
"type": "Raw Data File"
},
{
"@id": "assays/Growth_Curves/dataset/RawData/\u2206suxR_raw",
"name": "assays/Growth Curves/dataset/RawData/\u2206suxR_raw",
"type": "Raw Data File"
}
]
},
{
"@id": "#Process_Growth_curves_analysis_0",
"name": "Growth curves analysis_0",
"executesProtocol": {
"@id": "#Protocol_AnalyzedData/\u2206sux_analyzed",
"name": "AnalyzedData/\u2206sux_analyzed"
},
"inputs": [
{
"@id": "assays/Growth_Curves/dataset/RawData/\u2206sux_raw",
"name": "assays/Growth Curves/dataset/RawData/\u2206sux_raw",
"type": "Raw Data File"
}
],
"outputs": [
{
"@id": "assays/Growth_Curves/dataset/AnalyzedData/\u2206sux_analyzed/\u2206sux(203-205)_summary.xlsx",
"name": "assays/Growth Curves/dataset/AnalyzedData/\u2206sux_analyzed/\u2206sux(203-205)_summary.xlsx",
"type": "Raw Data File"
}
]
},
{
"@id": "#Process_Growth_curves_analysis_1",
"name": "Growth curves analysis_1",
"executesProtocol": {
"@id": "#Protocol_AnalyzedData/\u2206suxR_analyzed",
"name": "AnalyzedData/\u2206suxR_analyzed"
},
"inputs": [
{
"@id": "assays/Growth_Curves/dataset/RawData/\u2206suxR_raw",
"name": "assays/Growth Curves/dataset/RawData/\u2206suxR_raw",
"type": "Raw Data File"
}
],
"outputs": [
{
"@id": "assays/Growth_Curves/dataset/AnalyzedData/\u2206suxR_analyzed/suxR.tif",
"name": "assays/Growth Curves/dataset/AnalyzedData/\u2206suxR_analyzed/suxR.tif",
"type": "Raw Data File"
}
]
},
{
"@id": "#Process_Growth_curves_analysis_2",
"name": "Growth curves analysis_2",
"executesProtocol": {
"@id": "#Protocol_AnalyzedData/\u2206suxC_analyzed",
"name": "AnalyzedData/\u2206suxC_analyzed"
},
"inputs": [
{
"@id": "assays/Growth_Curves/dataset/RawData/\u2206suxC_raw",
"name": "assays/Growth Curves/dataset/RawData/\u2206suxC_raw",
"type": "Raw Data File"
}
],
"outputs": [
{
"@id": "assays/Growth_Curves/dataset/AnalyzedData/\u2206suxC_analyzed/suxC.tif",
"name": "assays/Growth Curves/dataset/AnalyzedData/\u2206suxC_analyzed/suxC.tif",
"type": "Raw Data File"
}
]
},
{
"@id": "#Process_Growth_curves_analysis_3",
"name": "Growth curves analysis_3",
"executesProtocol": {
"@id": "#Protocol_AnalyzedData/\u2206suxB_analyzed",
"name": "AnalyzedData/\u2206suxB_analyzed"
},
"inputs": [
{
"@id": "assays/Growth_Curves/dataset/RawData/\u2206suxB_raw",
"name": "assays/Growth Curves/dataset/RawData/\u2206suxB_raw",
"type": "Raw Data File"
}
],
"outputs": [
{
"@id": "assays/Growth_Curves/dataset/AnalyzedData/\u2206suxB_analyzed/suxB.tif",
"name": "assays/Growth Curves/dataset/AnalyzedData/\u2206suxB_analyzed/suxB.tif",
"type": "Raw Data File"
}
]
},
{
"@id": "#Process_Growth_curves_analysis_4",
"name": "Growth curves analysis_4",
"executesProtocol": {
"@id": "#Protocol_AnalyzedData/\u2206suxA_analyzed",
"name": "AnalyzedData/\u2206suxA_analyzed"
},
"inputs": [
{
"@id": "assays/Growth_Curves/dataset/RawData/\u2206suxA_raw",
"name": "assays/Growth Curves/dataset/RawData/\u2206suxA_raw",
"type": "Raw Data File"
}
],
"outputs": [
{
"@id": "assays/Growth_Curves/dataset/AnalyzedData/\u2206suxA_analyzed/suxA.tif",
"name": "assays/Growth Curves/dataset/AnalyzedData/\u2206suxA_analyzed/suxA.tif",
"type": "Raw Data File"
}
]
},
{
"@id": "#Process_Growth_curves_analysis_5",
"name": "Growth curves analysis_5",
"executesProtocol": {
"@id": "#Protocol_AnalyzedData/wt_analyzed",
"name": "AnalyzedData/wt_analyzed"
},
"inputs": [
{
"@id": "assays/Growth_Curves/dataset/RawData/wt_raw",
"name": "assays/Growth Curves/dataset/RawData/wt_raw",
"type": "Raw Data File"
}
],
"outputs": [
{
"@id": "assays/Growth_Curves/dataset/AnalyzedData/wt_analyzed/wt.tif",
"name": "assays/Growth Curves/dataset/AnalyzedData/wt_analyzed/wt.tif",
"type": "Raw Data File"
}
]
}
]
},
{
"filename": "assays/Motility/isa.assay.xlsx",
"@id": "assays/Motility/",
"measurementType": {
"@id": "https://bioregistry.io/EFO:0002908",
"annotationValue": "motility assay",
"termSource": "EFO",
"termAccession": "https://bioregistry.io/EFO:0002908"
},
"technologyType": {
"@id": "https://bioregistry.io/NCIT:C16215",
"annotationValue": "Soft Agar Assay",
"termSource": "NCIT",
"termAccession": "https://bioregistry.io/NCIT:C16215"
},
"dataFiles": [
{
"@id": "assays/Motility/dataset/RawData/Swimming/Swimming_wt.xlsx",
"name": "assays/Motility/dataset/RawData/Swimming/Swimming_wt.xlsx",
"type": "Raw Data File"
},
{
"@id": "assays/Motility/dataset/RawData/Swimming/Swimming_\u2206sux.xlsx",
"name": "assays/Motility/dataset/RawData/Swimming/Swimming_\u2206sux.xlsx",
"type": "Raw Data File"
},
{
"@id": "assays/Motility/dataset/RawData/Swarming",
"name": "assays/Motility/dataset/RawData/Swarming",
"type": "Raw Data File"
},
{
"@id": "assays/Motility/dataset/AnalyzedData/Swimming_summary.xlsx",
"name": "assays/Motility/dataset/AnalyzedData/Swimming_summary.xlsx",
"type": "Raw Data File"
},
{
"@id": "assays/Motility/dataset/RawData/Swarming/Swarming_\u2206sux.xlsx",
"name": "assays/Motility/dataset/RawData/Swarming/Swarming_\u2206sux.xlsx",
"type": "Raw Data File"
},
{
"@id": "assays/Motility/dataset/RawData/Swarming/Swarming_wt.xlsx",
"name": "assays/Motility/dataset/RawData/Swarming/Swarming_wt.xlsx",
"type": "Raw Data File"
},
{
"@id": "assays/Motility/dataset/AnalyzedData/Swarming_summary.xlsx",
"name": "assays/Motility/dataset/AnalyzedData/Swarming_summary.xlsx",
"type": "Raw Data File"
}
],
"materials": {},
"processSequence": [
{
"@id": "#Process_Motility_0",
"name": "Motility_0",
"executesProtocol": {
"@id": "#Protocol_Protocol_Swimming-Assay-for-Xoo.pdf",
"name": "Protocol_Swimming-Assay-for-Xoo.pdf",
"parameters": [
{
"@id": "#ProtocolParameter/NCIT:C60819",
"parameterName": {
"@id": "NCIT:C60819",
"annotationValue": "Assay",
"termSource": "NCIT",
"termAccession": "NCIT:C60819"
}
}
]
},
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NCIT:C60819",
"parameterName": {
"@id": "NCIT:C60819",
"annotationValue": "Assay",
"termSource": "NCIT",
"termAccession": "NCIT:C60819"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/C_1E56D0A8",
"annotationValue": "swimming",
"termSource": "C",
"termAccession": "http://purl.obolibrary.org/obo/C_1E56D0A8"
}
}
],
"inputs": [
{
"@id": "#Source_Xoo_wt",
"name": "Xoo wt"
},
{
"@id": "#Source_\u2206sux",
"name": "\u2206sux"
}
],
"outputs": [
{
"@id": "assays/Motility/dataset/RawData/Swimming/Swimming_wt.xlsx",
"name": "assays/Motility/dataset/RawData/Swimming/Swimming_wt.xlsx",
"type": "Raw Data File"
},
{
"@id": "assays/Motility/dataset/RawData/Swimming/Swimming_\u2206sux.xlsx",
"name": "assays/Motility/dataset/RawData/Swimming/Swimming_\u2206sux.xlsx",
"type": "Raw Data File"
}
]
},
{
"@id": "#Process_Motility_1",
"name": "Motility_1",
"executesProtocol": {
"@id": "#Protocol_Protocol_Swarming-Assay-for-Xoo.pdf",
"name": "Protocol_Swarming-Assay-for-Xoo.pdf",
"parameters": [
{
"@id": "#ProtocolParameter/NCIT:C60819",
"parameterName": {
"@id": "NCIT:C60819",
"annotationValue": "Assay",
"termSource": "NCIT",
"termAccession": "NCIT:C60819"
}
}
]
},
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NCIT:C60819",
"parameterName": {
"@id": "NCIT:C60819",
"annotationValue": "Assay",
"termSource": "NCIT",
"termAccession": "NCIT:C60819"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/C_7546",
"annotationValue": "swarming",
"termSource": "C",
"termAccession": "http://purl.obolibrary.org/obo/C_7546"
}
}
],
"inputs": [
{
"@id": "#Source_Xoo_wt",
"name": "Xoo wt"
},
{
"@id": "#Source_\u2206sux",
"name": "\u2206sux"
}
],
"outputs": [
{
"@id": "assays/Motility/dataset/RawData/Swarming",
"name": "assays/Motility/dataset/RawData/Swarming",
"type": "Raw Data File"
},
{
"@id": "assays/Motility/dataset/RawData/Swarming",
"name": "assays/Motility/dataset/RawData/Swarming",
"type": "Raw Data File"
}
]
},
{
"@id": "#Process_Motility_Analysis_0",
"name": "Motility Analysis_0",
"executesProtocol": {
"@id": "#Protocol_Protocol_Swimming-Assay-for-Xoo.pdf",
"name": "Protocol_Swimming-Assay-for-Xoo.pdf"
},
"inputs": [
{
"@id": "assays/Motility/dataset/RawData/Swimming/Swimming_\u2206sux.xlsx",
"name": "assays/Motility/dataset/RawData/Swimming/Swimming_\u2206sux.xlsx",
"type": "Raw Data File"
},
{
"@id": "assays/Motility/dataset/RawData/Swimming/Swimming_wt.xlsx",
"name": "assays/Motility/dataset/RawData/Swimming/Swimming_wt.xlsx",
"type": "Raw Data File"
}
],
"outputs": [
{
"@id": "assays/Motility/dataset/AnalyzedData/Swimming_summary.xlsx",
"name": "assays/Motility/dataset/AnalyzedData/Swimming_summary.xlsx",
"type": "Raw Data File"
},
{
"@id": "assays/Motility/dataset/AnalyzedData/Swimming_summary.xlsx",
"name": "assays/Motility/dataset/AnalyzedData/Swimming_summary.xlsx",
"type": "Raw Data File"
}
]
},
{
"@id": "#Process_Motility_Analysis_1",
"name": "Motility Analysis_1",
"executesProtocol": {
"@id": "#Protocol_Protocol_Swarming-Assay-for-Xoo.pdf",
"name": "Protocol_Swarming-Assay-for-Xoo.pdf"
},
"inputs": [
{
"@id": "assays/Motility/dataset/RawData/Swarming/Swarming_\u2206sux.xlsx",
"name": "assays/Motility/dataset/RawData/Swarming/Swarming_\u2206sux.xlsx",
"type": "Raw Data File"
},
{
"@id": "assays/Motility/dataset/RawData/Swarming/Swarming_wt.xlsx",
"name": "assays/Motility/dataset/RawData/Swarming/Swarming_wt.xlsx",
"type": "Raw Data File"
}
],
"outputs": [
{
"@id": "assays/Motility/dataset/AnalyzedData/Swarming_summary.xlsx",
"name": "assays/Motility/dataset/AnalyzedData/Swarming_summary.xlsx",
"type": "Raw Data File"
},
{
"@id": "assays/Motility/dataset/AnalyzedData/Swarming_summary.xlsx",
"name": "assays/Motility/dataset/AnalyzedData/Swarming_summary.xlsx",
"type": "Raw Data File"
}
]
}
]
},
{
"filename": "assays/qRT-PCR/isa.assay.xlsx",
"@id": "assays/qRT-PCR/",
"measurementType": {
"@id": "https://bioregistry.io/NCIT:C185299",
"annotationValue": "Transcript Variant",
"termSource": "NCIT",
"termAccession": "https://bioregistry.io/NCIT:C185299"
},
"technologyType": {
"@id": "http://purl.obolibrary.org/obo/GENEPIO_0001959",
"annotationValue": "RT-PCR method",
"termSource": "GENEPIO",
"termAccession": "http://purl.obolibrary.org/obo/GENEPIO_0001959"
},
"dataFiles": [
{
"@id": "assays/qRT-PCR/dataset/qRT-PCR_14022024/raw_data/suxA",
"name": "assays/qRT-PCR/dataset/qRT-PCR_14022024/raw data/suxA",
"type": "Raw Data File"
},
{
"@id": "assays/qRT-PCR/dataset/qRT-PCR_14022024/raw_data/suxB",
"name": "assays/qRT-PCR/dataset/qRT-PCR_14022024/raw data/suxB",
"type": "Raw Data File"
},
{
"@id": "assays/qRT-PCR/dataset/qRT-PCR_14022024/raw_data/suxC",
"name": "assays/qRT-PCR/dataset/qRT-PCR_14022024/raw data/suxC",
"type": "Raw Data File"
},
{
"@id": "assays/qRT-PCR/dataset/qRT-PCR_14022024/raw_data/suxR",
"name": "assays/qRT-PCR/dataset/qRT-PCR_14022024/raw data/suxR",
"type": "Raw Data File"
},
{
"@id": "assays/qRT-PCR/dataset/qRT-PCR_07082023/raw_data/suxA",
"name": "assays/qRT-PCR/dataset/qRT-PCR_07082023/raw data/suxA",
"type": "Raw Data File"
},
{
"@id": "assays/qRT-PCR/dataset/qRT-PCR_07082023/raw_data/suxB",
"name": "assays/qRT-PCR/dataset/qRT-PCR_07082023/raw data/suxB",
"type": "Raw Data File"
},
{
"@id": "assays/qRT-PCR/dataset/qRT-PCR_07082023/raw_data/suxC",
"name": "assays/qRT-PCR/dataset/qRT-PCR_07082023/raw data/suxC",
"type": "Raw Data File"
},
{
"@id": "assays/qRT-PCR/dataset/qRT-PCR_07082023/raw_data/suxR",
"name": "assays/qRT-PCR/dataset/qRT-PCR_07082023/raw data/suxR",
"type": "Raw Data File"
},
{
"@id": "assays/qRT-PCR/dataset/qRT-PCR_07082023/\u2206ct_sux_genes",
"name": "assays/qRT-PCR/dataset/qRT-PCR_07082023/\u2206ct sux genes",
"type": "Raw Data File"
},
{
"@id": "assays/qRT-PCR/dataset/qRT-PCR_14022024/14022024_\u2206ct_sux_genes",
"name": "assays/qRT-PCR/dataset/qRT-PCR_14022024/14022024_\u2206ct sux genes",
"type": "Raw Data File"
}
],
"materials": {},
"processSequence": [
{
"@id": "#Process_qRT-PCR_0",
"name": "qRT-PCR_0",
"executesProtocol": {
"@id": "#Protocol_qRT-PCR_07082023/2023-07-17-qPCR-of-suxA.pdf",
"name": "qRT-PCR_07082023/2023-07-17-qPCR-of-suxA.pdf",
"parameters": [
{
"@id": "#ProtocolParameter/SO:0000704",
"parameterName": {
"@id": "SO:0000704",
"annotationValue": "gene",
"termSource": "SO",
"termAccession": "SO:0000704"
}
}
]
},
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/SO:0000704",
"parameterName": {
"@id": "SO:0000704",
"annotationValue": "gene",
"termSource": "SO",
"termAccession": "SO:0000704"
}
},
"value": {
"@id": "#UserTerm_suxA",
"annotationValue": "suxA"
}
}
],
"inputs": [
{
"@id": "#Source_Xoo_wt",
"name": "Xoo wt"
}
],
"outputs": [
{
"@id": "assays/qRT-PCR/dataset/qRT-PCR_14022024/raw_data/suxA",
"name": "assays/qRT-PCR/dataset/qRT-PCR_14022024/raw data/suxA",
"type": "Raw Data File"
}
]
},
{
"@id": "#Process_qRT-PCR_1",
"name": "qRT-PCR_1",
"executesProtocol": {
"@id": "#Protocol_qRT-PCR_07082023/2023-07-19-qPCR-of-suxB.pdf",
"name": "qRT-PCR_07082023/2023-07-19-qPCR-of-suxB.pdf",
"parameters": [
{
"@id": "#ProtocolParameter/SO:0000704",
"parameterName": {
"@id": "SO:0000704",
"annotationValue": "gene",
"termSource": "SO",
"termAccession": "SO:0000704"
}
}
]
},
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/SO:0000704",
"parameterName": {
"@id": "SO:0000704",
"annotationValue": "gene",
"termSource": "SO",
"termAccession": "SO:0000704"
}
},
"value": {
"@id": "#UserTerm_suxB",
"annotationValue": "suxB"
}
}
],
"inputs": [
{
"@id": "#Source_Xoo_wt",
"name": "Xoo wt"
}
],
"outputs": [
{
"@id": "assays/qRT-PCR/dataset/qRT-PCR_14022024/raw_data/suxB",
"name": "assays/qRT-PCR/dataset/qRT-PCR_14022024/raw data/suxB",
"type": "Raw Data File"
}
]
},
{
"@id": "#Process_qRT-PCR_2",
"name": "qRT-PCR_2",
"executesProtocol": {
"@id": "#Protocol_qRT-PCR_07082023/2023-08-03-qPCR-of-suxC.pdf",
"name": "qRT-PCR_07082023/2023-08-03-qPCR-of-suxC.pdf",
"parameters": [
{
"@id": "#ProtocolParameter/SO:0000704",
"parameterName": {
"@id": "SO:0000704",
"annotationValue": "gene",
"termSource": "SO",
"termAccession": "SO:0000704"
}
}
]
},
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/SO:0000704",
"parameterName": {
"@id": "SO:0000704",
"annotationValue": "gene",
"termSource": "SO",
"termAccession": "SO:0000704"
}
},
"value": {
"@id": "#UserTerm_suxC",
"annotationValue": "suxC"
}
}
],
"inputs": [
{
"@id": "#Source_Xoo_wt",
"name": "Xoo wt"
}
],
"outputs": [
{
"@id": "assays/qRT-PCR/dataset/qRT-PCR_14022024/raw_data/suxC",
"name": "assays/qRT-PCR/dataset/qRT-PCR_14022024/raw data/suxC",
"type": "Raw Data File"
}
]
},
{
"@id": "#Process_qRT-PCR_3",
"name": "qRT-PCR_3",
"executesProtocol": {
"@id": "#Protocol_qRT-PCR_07082023/2023-08-07-qPCR-of-suxR.pdf",
"name": "qRT-PCR_07082023/2023-08-07-qPCR-of-suxR.pdf",
"parameters": [
{
"@id": "#ProtocolParameter/SO:0000704",
"parameterName": {
"@id": "SO:0000704",
"annotationValue": "gene",
"termSource": "SO",
"termAccession": "SO:0000704"
}
}
]
},
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/SO:0000704",
"parameterName": {
"@id": "SO:0000704",
"annotationValue": "gene",
"termSource": "SO",
"termAccession": "SO:0000704"
}
},
"value": {
"@id": "#UserTerm_suxR",
"annotationValue": "suxR"
}
}
],
"inputs": [
{
"@id": "#Source_Xoo_wt",
"name": "Xoo wt"
}
],
"outputs": [
{
"@id": "assays/qRT-PCR/dataset/qRT-PCR_14022024/raw_data/suxR",
"name": "assays/qRT-PCR/dataset/qRT-PCR_14022024/raw data/suxR",
"type": "Raw Data File"
}
]
},
{
"@id": "#Process_qRT-PCR_4",
"name": "qRT-PCR_4",
"executesProtocol": {
"@id": "#Protocol_qRT-PCR_14022024/qPCR_14.02.2024_I_Analysis.xlsx",
"name": "qRT-PCR_14022024/qPCR_14.02.2024_I_Analysis.xlsx",
"parameters": [
{
"@id": "#ProtocolParameter/SO:0000704",
"parameterName": {
"@id": "SO:0000704",
"annotationValue": "gene",
"termSource": "SO",
"termAccession": "SO:0000704"
}
}
]
},
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/SO:0000704",
"parameterName": {
"@id": "SO:0000704",
"annotationValue": "gene",
"termSource": "SO",
"termAccession": "SO:0000704"
}
},
"value": {
"@id": "#UserTerm_suxA",
"annotationValue": "suxA"
}
}
],
"inputs": [
{
"@id": "#Source_Xoo_wt",
"name": "Xoo wt"
}
],
"outputs": [
{
"@id": "assays/qRT-PCR/dataset/qRT-PCR_14022024/raw_data/suxA",
"name": "assays/qRT-PCR/dataset/qRT-PCR_14022024/raw data/suxA",
"type": "Raw Data File"
}
]
},
{
"@id": "#Process_qRT-PCR_5",
"name": "qRT-PCR_5",
"executesProtocol": {
"@id": "#Protocol_qRT-PCR_14022024/qPCR_14.02.2024_I_Analysis.xlsx",
"name": "qRT-PCR_14022024/qPCR_14.02.2024_I_Analysis.xlsx",
"parameters": [
{
"@id": "#ProtocolParameter/SO:0000704",
"parameterName": {
"@id": "SO:0000704",
"annotationValue": "gene",
"termSource": "SO",
"termAccession": "SO:0000704"
}
}
]
},
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/SO:0000704",
"parameterName": {
"@id": "SO:0000704",
"annotationValue": "gene",
"termSource": "SO",
"termAccession": "SO:0000704"
}
},
"value": {
"@id": "#UserTerm_suxB",
"annotationValue": "suxB"
}
}
],
"inputs": [
{
"@id": "#Source_Xoo_wt",
"name": "Xoo wt"
}
],
"outputs": [
{
"@id": "assays/qRT-PCR/dataset/qRT-PCR_14022024/raw_data/suxB",
"name": "assays/qRT-PCR/dataset/qRT-PCR_14022024/raw data/suxB",
"type": "Raw Data File"
}
]
},
{
"@id": "#Process_qRT-PCR_6",
"name": "qRT-PCR_6",
"executesProtocol": {
"@id": "#Protocol_qRT-PCR_14022024/qPCR_14.02.2024_I_Analysis.xlsx",
"name": "qRT-PCR_14022024/qPCR_14.02.2024_I_Analysis.xlsx",
"parameters": [
{
"@id": "#ProtocolParameter/SO:0000704",
"parameterName": {
"@id": "SO:0000704",
"annotationValue": "gene",
"termSource": "SO",
"termAccession": "SO:0000704"
}
}
]
},
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/SO:0000704",
"parameterName": {
"@id": "SO:0000704",
"annotationValue": "gene",
"termSource": "SO",
"termAccession": "SO:0000704"
}
},
"value": {
"@id": "#UserTerm_suxC",
"annotationValue": "suxC"
}
}
],
"inputs": [
{
"@id": "#Source_Xoo_wt",
"name": "Xoo wt"
}
],
"outputs": [
{
"@id": "assays/qRT-PCR/dataset/qRT-PCR_14022024/raw_data/suxC",
"name": "assays/qRT-PCR/dataset/qRT-PCR_14022024/raw data/suxC",
"type": "Raw Data File"
}
]
},
{
"@id": "#Process_qRT-PCR_7",
"name": "qRT-PCR_7",
"executesProtocol": {
"@id": "#Protocol_qRT-PCR_14022024/qPCR_14.02.2024_I_Analysis.xlsx",
"name": "qRT-PCR_14022024/qPCR_14.02.2024_I_Analysis.xlsx",
"parameters": [
{
"@id": "#ProtocolParameter/SO:0000704",
"parameterName": {
"@id": "SO:0000704",
"annotationValue": "gene",
"termSource": "SO",
"termAccession": "SO:0000704"
}
}
]
},
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/SO:0000704",
"parameterName": {
"@id": "SO:0000704",
"annotationValue": "gene",
"termSource": "SO",
"termAccession": "SO:0000704"
}
},
"value": {
"@id": "#UserTerm_suxR",
"annotationValue": "suxR"
}
}
],
"inputs": [
{
"@id": "#Source_Xoo_wt",
"name": "Xoo wt"
}
],
"outputs": [
{
"@id": "assays/qRT-PCR/dataset/qRT-PCR_14022024/raw_data/suxR",
"name": "assays/qRT-PCR/dataset/qRT-PCR_14022024/raw data/suxR",
"type": "Raw Data File"
}
]
},
{
"@id": "#Process_qRT-PCR_analysis_0",
"name": "qRT-PCR analysis_0",
"executesProtocol": {
"@id": "#Protocol_qRT-PCR_07082023/\u2206ct_sux_genes/sucrase_summary.xlsx",
"name": "qRT-PCR_07082023/\u2206ct sux genes/sucrase_summary.xlsx"
},
"inputs": [
{
"@id": "assays/qRT-PCR/dataset/qRT-PCR_07082023/raw_data/suxA",
"name": "assays/qRT-PCR/dataset/qRT-PCR_07082023/raw data/suxA",
"type": "Raw Data File"
},
{
"@id": "assays/qRT-PCR/dataset/qRT-PCR_07082023/raw_data/suxB",
"name": "assays/qRT-PCR/dataset/qRT-PCR_07082023/raw data/suxB",
"type": "Raw Data File"
},
{
"@id": "assays/qRT-PCR/dataset/qRT-PCR_07082023/raw_data/suxC",
"name": "assays/qRT-PCR/dataset/qRT-PCR_07082023/raw data/suxC",
"type": "Raw Data File"
},
{
"@id": "assays/qRT-PCR/dataset/qRT-PCR_07082023/raw_data/suxR",
"name": "assays/qRT-PCR/dataset/qRT-PCR_07082023/raw data/suxR",
"type": "Raw Data File"
}
],
"outputs": [
{
"@id": "assays/qRT-PCR/dataset/qRT-PCR_07082023/\u2206ct_sux_genes",
"name": "assays/qRT-PCR/dataset/qRT-PCR_07082023/\u2206ct sux genes",
"type": "Raw Data File"
},
{
"@id": "assays/qRT-PCR/dataset/qRT-PCR_07082023/\u2206ct_sux_genes",
"name": "assays/qRT-PCR/dataset/qRT-PCR_07082023/\u2206ct sux genes",
"type": "Raw Data File"
},
{
"@id": "assays/qRT-PCR/dataset/qRT-PCR_07082023/\u2206ct_sux_genes",
"name": "assays/qRT-PCR/dataset/qRT-PCR_07082023/\u2206ct sux genes",
"type": "Raw Data File"
},
{
"@id": "assays/qRT-PCR/dataset/qRT-PCR_07082023/\u2206ct_sux_genes",
"name": "assays/qRT-PCR/dataset/qRT-PCR_07082023/\u2206ct sux genes",
"type": "Raw Data File"
}
]
},
{
"@id": "#Process_qRT-PCR_analysis_1",
"name": "qRT-PCR analysis_1",
"executesProtocol": {
"@id": "#Protocol_qRT-PCR_14022024/14022024_\u2206ct_sux_genes/dct_2_4_6_8hours.pptx",
"name": "qRT-PCR_14022024/14022024_\u2206ct sux genes/dct_2_4_6_8hours.pptx"
},
"inputs": [
{
"@id": "assays/qRT-PCR/dataset/qRT-PCR_14022024/raw_data/suxA",
"name": "assays/qRT-PCR/dataset/qRT-PCR_14022024/raw data/suxA",
"type": "Raw Data File"
},
{
"@id": "assays/qRT-PCR/dataset/qRT-PCR_14022024/raw_data/suxB",
"name": "assays/qRT-PCR/dataset/qRT-PCR_14022024/raw data/suxB",
"type": "Raw Data File"
},
{
"@id": "assays/qRT-PCR/dataset/qRT-PCR_14022024/raw_data/suxC",
"name": "assays/qRT-PCR/dataset/qRT-PCR_14022024/raw data/suxC",
"type": "Raw Data File"
},
{
"@id": "assays/qRT-PCR/dataset/qRT-PCR_14022024/raw_data/suxR",
"name": "assays/qRT-PCR/dataset/qRT-PCR_14022024/raw data/suxR",
"type": "Raw Data File"
}
],
"outputs": [
{
"@id": "assays/qRT-PCR/dataset/qRT-PCR_14022024/14022024_\u2206ct_sux_genes",
"name": "assays/qRT-PCR/dataset/qRT-PCR_14022024/14022024_\u2206ct sux genes",
"type": "Raw Data File"
},
{
"@id": "assays/qRT-PCR/dataset/qRT-PCR_14022024/14022024_\u2206ct_sux_genes",
"name": "assays/qRT-PCR/dataset/qRT-PCR_14022024/14022024_\u2206ct sux genes",
"type": "Raw Data File"
},
{
"@id": "assays/qRT-PCR/dataset/qRT-PCR_14022024/14022024_\u2206ct_sux_genes",
"name": "assays/qRT-PCR/dataset/qRT-PCR_14022024/14022024_\u2206ct sux genes",
"type": "Raw Data File"
},
{
"@id": "assays/qRT-PCR/dataset/qRT-PCR_14022024/14022024_\u2206ct_sux_genes",
"name": "assays/qRT-PCR/dataset/qRT-PCR_14022024/14022024_\u2206ct sux genes",
"type": "Raw Data File"
}
]
}
]
}
]
},
{
"@id": "studies/Media/",
"filename": "studies/Media/isa.study.xlsx",
"identifier": "Media",
"title": "Media",
"description": "This is a summary of the media used in this study",
"protocols": [
{
"@id": "#EmptyProtocol",
"components": [
{
"componentName": "0 percent (UO:0000187)",
"componentType": {
"@id": "CHEBI:2509",
"annotationValue": "agar",
"termSource": "CHEBI",
"termAccession": "CHEBI:2509"
}
}
]
},
{
"@id": "#EmptyProtocol",
"components": [
{
"componentName": "15 percent (UO:0000187)",
"componentType": {
"@id": "CHEBI:2509",
"annotationValue": "agar",
"termSource": "CHEBI",
"termAccession": "CHEBI:2509"
}
}
]
},
{
"@id": "#EmptyProtocol",
"components": [
{
"componentName": "3 percent (UO:0000187)",
"componentType": {
"@id": "CHEBI:2509",
"annotationValue": "agar",
"termSource": "CHEBI",
"termAccession": "CHEBI:2509"
}
}
]
},
{
"@id": "#EmptyProtocol",
"components": [
{
"componentName": "6 percent (UO:0000187)",
"componentType": {
"@id": "CHEBI:2509",
"annotationValue": "agar",
"termSource": "CHEBI",
"termAccession": "CHEBI:2509"
}
}
]
}
],
"materials": {
"samples": [
{
"@id": "#Sample_NB",
"name": "NB"
},
{
"@id": "#Sample_NB",
"name": "NB",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Assay=Liquid Culture",
"category": {
"@id": "#MaterialAttribute/NCIT:C60819",
"characteristicType": {
"@id": "NCIT:C60819",
"annotationValue": "Assay",
"termSource": "NCIT",
"termAccession": "NCIT:C60819"
}
},
"value": {
"@id": "#UserTerm_Liquid_Culture",
"annotationValue": "Liquid Culture"
}
}
]
},
{
"@id": "#Sample_NB",
"name": "NB",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Assay=Agar plate",
"category": {
"@id": "#MaterialAttribute/NCIT:C60819",
"characteristicType": {
"@id": "NCIT:C60819",
"annotationValue": "Assay",
"termSource": "NCIT",
"termAccession": "NCIT:C60819"
}
},
"value": {
"@id": "#UserTerm_Agar_plate",
"annotationValue": "Agar plate"
}
}
]
},
{
"@id": "#Sample_NB",
"name": "NB",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Assay=Swimming",
"category": {
"@id": "#MaterialAttribute/NCIT:C60819",
"characteristicType": {
"@id": "NCIT:C60819",
"annotationValue": "Assay",
"termSource": "NCIT",
"termAccession": "NCIT:C60819"
}
},
"value": {
"@id": "https://bioregistry.io/NCIT:C94738",
"annotationValue": "Swimming",
"termSource": "NCIT",
"termAccession": "https://bioregistry.io/NCIT:C94738"
}
}
]
},
{
"@id": "#Sample_NB",
"name": "NB",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Assay=swarming",
"category": {
"@id": "#MaterialAttribute/NCIT:C60819",
"characteristicType": {
"@id": "NCIT:C60819",
"annotationValue": "Assay",
"termSource": "NCIT",
"termAccession": "NCIT:C60819"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/C_7546",
"annotationValue": "swarming",
"termSource": "C",
"termAccession": "http://purl.obolibrary.org/obo/C_7546"
}
}
]
}
],
"otherMaterials": [
{
"@id": "#Material_Yeast_Extract",
"name": "Yeast Extract"
},
{
"@id": "#Material_Meat_Extract",
"name": "Meat Extract"
},
{
"@id": "#Material_Peptone",
"name": "Peptone"
},
{
"@id": "#Material_NB",
"name": "NB"
},
{
"@id": "#Material_NB_liquid",
"name": "NB_liquid"
},
{
"@id": "#Material_NB_plate",
"name": "NB_plate"
},
{
"@id": "#Material_NB_swimming",
"name": "NB_swimming"
},
{
"@id": "#Material_NB_swarming",
"name": "NB_swarming"
}
]
},
"processSequence": [
{
"@id": "#Process_NB_composition_0",
"name": "NB composition_0",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/PATO:0000070",
"parameterName": {
"@id": "PATO:0000070",
"annotationValue": "amount",
"termSource": "PATO",
"termAccession": "PATO:0000070"
}
},
"unit": {
"@id": "#UserTerm_1",
"annotationValue": "1"
}
},
{
"category": {
"@id": "#ProtocolParameter/C:50324",
"parameterName": {
"@id": "C:50324",
"annotationValue": "units",
"termSource": "C",
"termAccession": "C:50324"
}
},
"unit": {
"@id": "#UserTerm_gramm_per_liter",
"annotationValue": "gramm per liter"
}
},
{
"category": {
"@id": "#ProtocolParameter/NMR:1002011",
"parameterName": {
"@id": "NMR:1002011",
"annotationValue": "pH",
"termSource": "NMR",
"termAccession": "NMR:1002011"
}
},
"value": {
"@id": "#UserTerm_7",
"annotationValue": "7"
}
}
],
"inputs": [
{
"@id": "#Material_Yeast_Extract",
"name": "Yeast Extract"
}
],
"outputs": [
{
"@id": "#Sample_NB",
"name": "NB"
}
]
},
{
"@id": "#Process_NB_composition_1",
"name": "NB composition_1",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/PATO:0000070",
"parameterName": {
"@id": "PATO:0000070",
"annotationValue": "amount",
"termSource": "PATO",
"termAccession": "PATO:0000070"
}
},
"value": 3
},
{
"category": {
"@id": "#ProtocolParameter/C:50324",
"parameterName": {
"@id": "C:50324",
"annotationValue": "units",
"termSource": "C",
"termAccession": "C:50324"
}
},
"unit": {
"@id": "#UserTerm_gramm_per_liter",
"annotationValue": "gramm per liter"
}
},
{
"category": {
"@id": "#ProtocolParameter/NMR:1002011",
"parameterName": {
"@id": "NMR:1002011",
"annotationValue": "pH",
"termSource": "NMR",
"termAccession": "NMR:1002011"
}
},
"value": {
"@id": "#UserTerm_7",
"annotationValue": "7"
}
}
],
"inputs": [
{
"@id": "#Material_Meat_Extract",
"name": "Meat Extract"
}
],
"outputs": [
{
"@id": "#Sample_NB",
"name": "NB"
}
]
},
{
"@id": "#Process_NB_composition_2",
"name": "NB composition_2",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/PATO:0000070",
"parameterName": {
"@id": "PATO:0000070",
"annotationValue": "amount",
"termSource": "PATO",
"termAccession": "PATO:0000070"
}
},
"value": 5
},
{
"category": {
"@id": "#ProtocolParameter/C:50324",
"parameterName": {
"@id": "C:50324",
"annotationValue": "units",
"termSource": "C",
"termAccession": "C:50324"
}
},
"unit": {
"@id": "#UserTerm_gramm_per_liter",
"annotationValue": "gramm per liter"
}
},
{
"category": {
"@id": "#ProtocolParameter/NMR:1002011",
"parameterName": {
"@id": "NMR:1002011",
"annotationValue": "pH",
"termSource": "NMR",
"termAccession": "NMR:1002011"
}
},
"value": {
"@id": "#UserTerm_7",
"annotationValue": "7"
}
}
],
"inputs": [
{
"@id": "#Material_Peptone",
"name": "Peptone"
}
],
"outputs": [
{
"@id": "#Sample_NB",
"name": "NB"
}
]
},
{
"@id": "#Process_NB_usage_0",
"name": "NB usage_0",
"executesProtocol": {
"@id": "#Protocol_Media_NB_usage_0",
"components": [
{
"componentName": "0 percent (UO:0000187)",
"componentType": {
"@id": "CHEBI:2509",
"annotationValue": "agar",
"termSource": "CHEBI",
"termAccession": "CHEBI:2509"
}
}
]
},
"inputs": [
{
"@id": "#Material_NB",
"name": "NB"
},
{
"@id": "#Sample_NB",
"name": "NB",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Assay=Liquid Culture",
"category": {
"@id": "#MaterialAttribute/NCIT:C60819",
"characteristicType": {
"@id": "NCIT:C60819",
"annotationValue": "Assay",
"termSource": "NCIT",
"termAccession": "NCIT:C60819"
}
},
"value": {
"@id": "#UserTerm_Liquid_Culture",
"annotationValue": "Liquid Culture"
}
}
]
}
],
"outputs": [
{
"@id": "#Material_NB_liquid",
"name": "NB_liquid"
},
{
"@id": "#Material_NB_liquid",
"name": "NB_liquid"
}
]
},
{
"@id": "#Process_NB_usage_1",
"name": "NB usage_1",
"executesProtocol": {
"@id": "#Protocol_Media_NB_usage_1",
"components": [
{
"componentName": "15 percent (UO:0000187)",
"componentType": {
"@id": "CHEBI:2509",
"annotationValue": "agar",
"termSource": "CHEBI",
"termAccession": "CHEBI:2509"
}
}
]
},
"inputs": [
{
"@id": "#Material_NB",
"name": "NB"
},
{
"@id": "#Sample_NB",
"name": "NB",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Assay=Agar plate",
"category": {
"@id": "#MaterialAttribute/NCIT:C60819",
"characteristicType": {
"@id": "NCIT:C60819",
"annotationValue": "Assay",
"termSource": "NCIT",
"termAccession": "NCIT:C60819"
}
},
"value": {
"@id": "#UserTerm_Agar_plate",
"annotationValue": "Agar plate"
}
}
]
}
],
"outputs": [
{
"@id": "#Material_NB_plate",
"name": "NB_plate"
},
{
"@id": "#Material_NB_plate",
"name": "NB_plate"
}
]
},
{
"@id": "#Process_NB_usage_2",
"name": "NB usage_2",
"executesProtocol": {
"@id": "#Protocol_Media_NB_usage_2",
"components": [
{
"componentName": "3 percent (UO:0000187)",
"componentType": {
"@id": "CHEBI:2509",
"annotationValue": "agar",
"termSource": "CHEBI",
"termAccession": "CHEBI:2509"
}
}
]
},
"inputs": [
{
"@id": "#Material_NB",
"name": "NB"
},
{
"@id": "#Sample_NB",
"name": "NB",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Assay=Swimming",
"category": {
"@id": "#MaterialAttribute/NCIT:C60819",
"characteristicType": {
"@id": "NCIT:C60819",
"annotationValue": "Assay",
"termSource": "NCIT",
"termAccession": "NCIT:C60819"
}
},
"value": {
"@id": "https://bioregistry.io/NCIT:C94738",
"annotationValue": "Swimming",
"termSource": "NCIT",
"termAccession": "https://bioregistry.io/NCIT:C94738"
}
}
]
}
],
"outputs": [
{
"@id": "#Material_NB_swimming",
"name": "NB_swimming"
},
{
"@id": "#Material_NB_swimming",
"name": "NB_swimming"
}
]
},
{
"@id": "#Process_NB_usage_3",
"name": "NB usage_3",
"executesProtocol": {
"@id": "#Protocol_Media_NB_usage_3",
"components": [
{
"componentName": "6 percent (UO:0000187)",
"componentType": {
"@id": "CHEBI:2509",
"annotationValue": "agar",
"termSource": "CHEBI",
"termAccession": "CHEBI:2509"
}
}
]
},
"inputs": [
{
"@id": "#Material_NB",
"name": "NB"
},
{
"@id": "#Sample_NB",
"name": "NB",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Assay=swarming",
"category": {
"@id": "#MaterialAttribute/NCIT:C60819",
"characteristicType": {
"@id": "NCIT:C60819",
"annotationValue": "Assay",
"termSource": "NCIT",
"termAccession": "NCIT:C60819"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/C_7546",
"annotationValue": "swarming",
"termSource": "C",
"termAccession": "http://purl.obolibrary.org/obo/C_7546"
}
}
]
}
],
"outputs": [
{
"@id": "#Material_NB_swarming",
"name": "NB_swarming"
},
{
"@id": "#Material_NB_swarming",
"name": "NB_swarming"
}
]
}
],
"characteristicCategories": [
{
"@id": "#MaterialAttribute/NCIT:C60819",
"characteristicType": {
"@id": "NCIT:C60819",
"annotationValue": "Assay",
"termSource": "NCIT",
"termAccession": "NCIT:C60819"
}
}
],
"unitCategories": [
{
"@id": "#UserTerm_1",
"annotationValue": "1"
},
{
"@id": "#UserTerm_gramm_per_liter",
"annotationValue": "gramm per liter"
}
]
},
{
"@id": "studies/Plant_Resources/",
"filename": "studies/Plant Resources/isa.study.xlsx",
"identifier": "Plant Resources",
"title": "Plant Resources",
"description": "This is an overview of all plants used in this study.",
"materials": {
"sources": [
{
"@id": "#Source_Oryza_sativa_IR24",
"name": "Oryza sativa IR24"
},
{
"@id": "#Source_Oryza_sativa_Kitaake",
"name": "Oryza sativa Kitaake"
},
{
"@id": "#Source_Oryza_sativa_Nipponbare",
"name": "Oryza sativa Nipponbare"
}
],
"samples": [
{
"@id": "#Sample_Oryza_sativa_IR24",
"name": "Oryza sativa IR24"
},
{
"@id": "#Sample_Oryza_sativa_Kitaake",
"name": "Oryza sativa Kitaake"
},
{
"@id": "#Sample_Oryza_sativa_Nipponbare",
"name": "Oryza sativa Nipponbare"
}
]
},
"processSequence": [
{
"@id": "#Process_Plant_cultivation",
"name": "Plant_cultivation",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NCIT:C64650",
"parameterName": {
"@id": "NCIT:C64650",
"annotationValue": "Light",
"termSource": "NCIT",
"termAccession": "NCIT:C64650"
}
},
"value": {
"@id": "#UserTerm_12h_on",
"annotationValue": "12h on"
}
},
{
"category": {
"@id": "#ProtocolParameter/EFO:0001702",
"parameterName": {
"@id": "EFO:0001702",
"annotationValue": "temperature",
"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
"value": {
"@id": "#UserTerm_28_\u00b0C",
"annotationValue": "28 \u00b0C"
}
},
{
"category": {
"@id": "#ProtocolParameter/PATO:0015009",
"parameterName": {
"@id": "PATO:0015009",
"annotationValue": "humidity",
"termSource": "PATO",
"termAccession": "PATO:0015009"
}
},
"value": {
"@id": "#UserTerm_80_%",
"annotationValue": "80 %"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C25207",
"parameterName": {
"@id": "NCIT:C25207",
"annotationValue": "Time",
"termSource": "NCIT",
"termAccession": "NCIT:C25207"
}
},
"value": {
"@id": "#UserTerm_four_weeks",
"annotationValue": "four weeks"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C64650",
"parameterName": {
"@id": "NCIT:C64650",
"annotationValue": "Light",
"termSource": "NCIT",
"termAccession": "NCIT:C64650"
}
},
"value": {
"@id": "#UserTerm_12_off",
"annotationValue": "12 off"
}
},
{
"category": {
"@id": "#ProtocolParameter/EFO:0001702",
"parameterName": {
"@id": "EFO:0001702",
"annotationValue": "temperature",
"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
"value": {
"@id": "#UserTerm_25_\u00b0C",
"annotationValue": "25 \u00b0C"
}
}
],
"inputs": [
{
"@id": "#Source_Oryza_sativa_IR24",
"name": "Oryza sativa IR24"
},
{
"@id": "#Source_Oryza_sativa_Kitaake",
"name": "Oryza sativa Kitaake"
},
{
"@id": "#Source_Oryza_sativa_Nipponbare",
"name": "Oryza sativa Nipponbare"
}
],
"outputs": [
{
"@id": "#Sample_Oryza_sativa_IR24",
"name": "Oryza sativa IR24"
},
{
"@id": "#Sample_Oryza_sativa_Kitaake",
"name": "Oryza sativa Kitaake"
},
{
"@id": "#Sample_Oryza_sativa_Nipponbare",
"name": "Oryza sativa Nipponbare"
}
]
}
],
"assays": [
{
"filename": "assays/Clipping/isa.assay.xlsx",
"@id": "assays/Clipping/",
"measurementType": {
"@id": "https://bioregistry.io/NCIT:C3824",
"annotationValue": "Lesion",
"termSource": "NCIT",
"termAccession": "https://bioregistry.io/NCIT:C3824"
},
"technologyPlatform": "Ruler (NCIT:C138178)",
"dataFiles": [
{
"@id": "assays/Clipping/dataset/Inoculation_data_IR24.xlsx",
"name": "assays/Clipping/dataset/Inoculation data_IR24.xlsx",
"type": "Raw Data File"
},
{
"@id": "assays/Clipping/dataset/Inoculation_data_Kitaake.xlsx",
"name": "assays/Clipping/dataset/Inoculation data_Kitaake.xlsx",
"type": "Raw Data File"
},
{
"@id": "assays/Clipping/dataset/sucrose_gene_on_Nip_V2.xlsx",
"name": "assays/Clipping/dataset/sucrose gene on Nip_V2.xlsx",
"type": "Raw Data File"
}
],
"materials": {
"samples": [
{
"@id": "#Sample_Oryza_sativa_IR24",
"name": "Oryza sativa IR24",
"characteristics": [
{
"@id": "#MaterialAttributeValue/organism=Oryza sativa",
"category": {
"@id": "#MaterialAttribute/OBI:0100026",
"characteristicType": {
"@id": "OBI:0100026",
"annotationValue": "organism",
"termSource": "OBI",
"termAccession": "OBI:0100026"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/C_5438",
"annotationValue": "Oryza sativa",
"termSource": "C",
"termAccession": "http://purl.obolibrary.org/obo/C_5438"
}
},
{
"@id": "#EmptyMaterialAttributeValue",
"category": {
"@id": "#MaterialAttribute/MCO:0000059",
"characteristicType": {
"@id": "MCO:0000059",
"annotationValue": "OD600",
"termSource": "MCO",
"termAccession": "MCO:0000059"
}
}
}
]
},
{
"@id": "#Sample_Xoo_wt",
"name": "Xoo wt",
"characteristics": [
{
"@id": "#MaterialAttributeValue/organism=Xanthomonas oryzae pv. oryzae PXO99A",
"category": {
"@id": "#MaterialAttribute/OBI:0100026",
"characteristicType": {
"@id": "OBI:0100026",
"annotationValue": "organism",
"termSource": "OBI",
"termAccession": "OBI:0100026"
}
},
"value": {
"@id": "#UserTerm_Xanthomonas_oryzae_pv._oryzae_PXO99A",
"annotationValue": "Xanthomonas oryzae pv. oryzae PXO99A"
}
},
{
"@id": "#MaterialAttributeValue/OD600=0,5",
"category": {
"@id": "#MaterialAttribute/MCO:0000059",
"characteristicType": {
"@id": "MCO:0000059",
"annotationValue": "OD600",
"termSource": "MCO",
"termAccession": "MCO:0000059"
}
},
"value": {
"@id": "#UserTerm_0,5",
"annotationValue": "0,5"
}
}
]
},
{
"@id": "#Sample_\u2206sux",
"name": "\u2206sux",
"characteristics": [
{
"@id": "#MaterialAttributeValue/organism=Xanthomonas oryzae pv. oryzae PXO99A",
"category": {
"@id": "#MaterialAttribute/OBI:0100026",
"characteristicType": {
"@id": "OBI:0100026",
"annotationValue": "organism",
"termSource": "OBI",
"termAccession": "OBI:0100026"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/NCBITAXON_360094",
"annotationValue": "Xanthomonas oryzae pv. oryzae PXO99A",
"termSource": "NCBITAXON",
"termAccession": "http://purl.obolibrary.org/obo/NCBITAXON_360094"
}
},
{
"@id": "#MaterialAttributeValue/OD600=0,5",
"category": {
"@id": "#MaterialAttribute/MCO:0000059",
"characteristicType": {
"@id": "MCO:0000059",
"annotationValue": "OD600",
"termSource": "MCO",
"termAccession": "MCO:0000059"
}
},
"value": {
"@id": "#UserTerm_0,5",
"annotationValue": "0,5"
}
}
]
},
{
"@id": "#Sample_\u2206suxC",
"name": "\u2206suxC",
"characteristics": [
{
"@id": "#MaterialAttributeValue/organism=Xanthomonas oryzae pv. oryzae PXO99A",
"category": {
"@id": "#MaterialAttribute/OBI:0100026",
"characteristicType": {
"@id": "OBI:0100026",
"annotationValue": "organism",
"termSource": "OBI",
"termAccession": "OBI:0100026"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/NCBITAXON_360094",
"annotationValue": "Xanthomonas oryzae pv. oryzae PXO99A",
"termSource": "NCBITAXON",
"termAccession": "http://purl.obolibrary.org/obo/NCBITAXON_360094"
}
},
{
"@id": "#MaterialAttributeValue/OD600=0,5",
"category": {
"@id": "#MaterialAttribute/MCO:0000059",
"characteristicType": {
"@id": "MCO:0000059",
"annotationValue": "OD600",
"termSource": "MCO",
"termAccession": "MCO:0000059"
}
},
"value": {
"@id": "#UserTerm_0,5",
"annotationValue": "0,5"
}
}
]
},
{
"@id": "#Sample_\u2206suxA",
"name": "\u2206suxA",
"characteristics": [
{
"@id": "#MaterialAttributeValue/organism=Xanthomonas oryzae pv. oryzae PXO99A",
"category": {
"@id": "#MaterialAttribute/OBI:0100026",
"characteristicType": {
"@id": "OBI:0100026",
"annotationValue": "organism",
"termSource": "OBI",
"termAccession": "OBI:0100026"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/NCBITAXON_360094",
"annotationValue": "Xanthomonas oryzae pv. oryzae PXO99A",
"termSource": "NCBITAXON",
"termAccession": "http://purl.obolibrary.org/obo/NCBITAXON_360094"
}
},
{
"@id": "#MaterialAttributeValue/OD600=0,5",
"category": {
"@id": "#MaterialAttribute/MCO:0000059",
"characteristicType": {
"@id": "MCO:0000059",
"annotationValue": "OD600",
"termSource": "MCO",
"termAccession": "MCO:0000059"
}
},
"value": {
"@id": "#UserTerm_0,5",
"annotationValue": "0,5"
}
}
]
},
{
"@id": "#Sample_\u2206suxB",
"name": "\u2206suxB",
"characteristics": [
{
"@id": "#MaterialAttributeValue/organism=Xanthomonas oryzae pv. oryzae PXO99A",
"category": {
"@id": "#MaterialAttribute/OBI:0100026",
"characteristicType": {
"@id": "OBI:0100026",
"annotationValue": "organism",
"termSource": "OBI",
"termAccession": "OBI:0100026"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/NCBITAXON_360094",
"annotationValue": "Xanthomonas oryzae pv. oryzae PXO99A",
"termSource": "NCBITAXON",
"termAccession": "http://purl.obolibrary.org/obo/NCBITAXON_360094"
}
},
{
"@id": "#MaterialAttributeValue/OD600=0,5",
"category": {
"@id": "#MaterialAttribute/MCO:0000059",
"characteristicType": {
"@id": "MCO:0000059",
"annotationValue": "OD600",
"termSource": "MCO",
"termAccession": "MCO:0000059"
}
},
"value": {
"@id": "#UserTerm_0,5",
"annotationValue": "0,5"
}
}
]
},
{
"@id": "#Sample_Oryza_sativa_Kitaake\t\t",
"name": "Oryza sativa Kitaake\t\t",
"characteristics": [
{
"@id": "#MaterialAttributeValue/organism=Oryza sativa",
"category": {
"@id": "#MaterialAttribute/OBI:0100026",
"characteristicType": {
"@id": "OBI:0100026",
"annotationValue": "organism",
"termSource": "OBI",
"termAccession": "OBI:0100026"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/C_5438",
"annotationValue": "Oryza sativa",
"termSource": "C",
"termAccession": "http://purl.obolibrary.org/obo/C_5438"
}
},
{
"@id": "#EmptyMaterialAttributeValue",
"category": {
"@id": "#MaterialAttribute/MCO:0000059",
"characteristicType": {
"@id": "MCO:0000059",
"annotationValue": "OD600",
"termSource": "MCO",
"termAccession": "MCO:0000059"
}
}
}
]
},
{
"@id": "#Sample_Xoo_wt",
"name": "Xoo wt",
"characteristics": [
{
"@id": "#MaterialAttributeValue/organism=Xanthomonas oryzae pv. oryzae PXO99A",
"category": {
"@id": "#MaterialAttribute/OBI:0100026",
"characteristicType": {
"@id": "OBI:0100026",
"annotationValue": "organism",
"termSource": "OBI",
"termAccession": "OBI:0100026"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/NCBITAXON_360094",
"annotationValue": "Xanthomonas oryzae pv. oryzae PXO99A",
"termSource": "NCBITAXON",
"termAccession": "http://purl.obolibrary.org/obo/NCBITAXON_360094"
}
},
{
"@id": "#MaterialAttributeValue/OD600=0,5",
"category": {
"@id": "#MaterialAttribute/MCO:0000059",
"characteristicType": {
"@id": "MCO:0000059",
"annotationValue": "OD600",
"termSource": "MCO",
"termAccession": "MCO:0000059"
}
},
"value": {
"@id": "#UserTerm_0,5",
"annotationValue": "0,5"
}
}
]
},
{
"@id": "#Sample_Oryzae_sativa_Nipponbare",
"name": "Oryzae sativa Nipponbare",
"characteristics": [
{
"@id": "#MaterialAttributeValue/organism=Oryza sativa",
"category": {
"@id": "#MaterialAttribute/OBI:0100026",
"characteristicType": {
"@id": "OBI:0100026",
"annotationValue": "organism",
"termSource": "OBI",
"termAccession": "OBI:0100026"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/C_5438",
"annotationValue": "Oryza sativa",
"termSource": "C",
"termAccession": "http://purl.obolibrary.org/obo/C_5438"
}
},
{
"@id": "#EmptyMaterialAttributeValue",
"category": {
"@id": "#MaterialAttribute/MCO:0000059",
"characteristicType": {
"@id": "MCO:0000059",
"annotationValue": "OD600",
"termSource": "MCO",
"termAccession": "MCO:0000059"
}
}
}
]
},
{
"@id": "#Sample_\u2206suxC",
"name": "\u2206suxC",
"characteristics": [
{
"@id": "#MaterialAttributeValue/organism=Xanthomonas oryzae pv. oryzae exposure",
"category": {
"@id": "#MaterialAttribute/OBI:0100026",
"characteristicType": {
"@id": "OBI:0100026",
"annotationValue": "organism",
"termSource": "OBI",
"termAccession": "OBI:0100026"
}
},
"value": {
"@id": "https://bioregistry.io/PECO:0007257",
"annotationValue": "Xanthomonas oryzae pv. oryzae exposure",
"termSource": "PECO",
"termAccession": "https://bioregistry.io/PECO:0007257"
}
},
{
"@id": "#MaterialAttributeValue/OD600=0,5",
"category": {
"@id": "#MaterialAttribute/MCO:0000059",
"characteristicType": {
"@id": "MCO:0000059",
"annotationValue": "OD600",
"termSource": "MCO",
"termAccession": "MCO:0000059"
}
},
"value": {
"@id": "#UserTerm_0,5",
"annotationValue": "0,5"
}
}
]
},
{
"@id": "#Sample_Oryza_sativa_IR24_Xoo_wt",
"name": "Oryza sativa IR24_Xoo wt"
},
{
"@id": "#Sample_Oryza_sativa_IR24_\u2206sux",
"name": "Oryza sativa IR24_\u2206sux"
},
{
"@id": "#Sample_Oryza_sativa_IR24_\u2206suxC",
"name": "Oryza sativa IR24_\u2206suxC"
},
{
"@id": "#Sample_Oryza_sativa_IR24_\u2206suxA",
"name": "Oryza sativa IR24_\u2206suxA"
},
{
"@id": "#Sample_Oryza_sativa_IR24_\u2206suxB",
"name": "Oryza sativa IR24_\u2206suxB"
},
{
"@id": "#Sample_Oryza_sativa_Kitaake_Xoo_wt",
"name": "Oryza sativa Kitaake_Xoo wt"
},
{
"@id": "#Sample_Oryza_sativa_Kitaake_\u2206sux",
"name": "Oryza sativa Kitaake_\u2206sux"
},
{
"@id": "#Sample_Oryza_sativa_Kitaake_\u2206suxC",
"name": "Oryza sativa Kitaake_\u2206suxC"
},
{
"@id": "#Sample_Oryza_sativa_Kitaake_\u2206suxA",
"name": "Oryza sativa Kitaake_\u2206suxA"
},
{
"@id": "#Sample_Oryza_sativa_Kitaake_\u2206suxB",
"name": "Oryza sativa Kitaake_\u2206suxB"
},
{
"@id": "#Sample_Oryzae_sativa_Nipponbare_Xoo_wt",
"name": "Oryzae sativa Nipponbare_Xoo wt"
},
{
"@id": "#Sample_Oryzae_sativa_Nipponbare_\u2206sux",
"name": "Oryzae sativa Nipponbare_\u2206sux"
},
{
"@id": "#Sample_Oryzae_sativa_Nipponbare_\u2206suxC",
"name": "Oryzae sativa Nipponbare_\u2206suxC"
},
{
"@id": "#Sample_Oryzae_sativa_Nipponbare_\u2206suxA",
"name": "Oryzae sativa Nipponbare_\u2206suxA"
},
{
"@id": "#Sample_Oryzae_sativa_Nipponbare_\u2206suxB",
"name": "Oryzae sativa Nipponbare_\u2206suxB"
}
]
},
"characteristicCategories": [
{
"@id": "#MaterialAttribute/OBI:0100026",
"characteristicType": {
"@id": "OBI:0100026",
"annotationValue": "organism",
"termSource": "OBI",
"termAccession": "OBI:0100026"
}
},
{
"@id": "#MaterialAttribute/MCO:0000059",
"characteristicType": {
"@id": "MCO:0000059",
"annotationValue": "OD600",
"termSource": "MCO",
"termAccession": "MCO:0000059"
}
}
],
"processSequence": [
{
"@id": "#Process_Inoculation",
"name": "Inoculation",
"inputs": [
{
"@id": "#Sample_Oryza_sativa_IR24",
"name": "Oryza sativa IR24",
"characteristics": [
{
"@id": "#MaterialAttributeValue/organism=Oryza sativa",
"category": {
"@id": "#MaterialAttribute/OBI:0100026",
"characteristicType": {
"@id": "OBI:0100026",
"annotationValue": "organism",
"termSource": "OBI",
"termAccession": "OBI:0100026"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/C_5438",
"annotationValue": "Oryza sativa",
"termSource": "C",
"termAccession": "http://purl.obolibrary.org/obo/C_5438"
}
},
{
"@id": "#EmptyMaterialAttributeValue",
"category": {
"@id": "#MaterialAttribute/MCO:0000059",
"characteristicType": {
"@id": "MCO:0000059",
"annotationValue": "OD600",
"termSource": "MCO",
"termAccession": "MCO:0000059"
}
}
}
]
},
{
"@id": "#Sample_Xoo_wt",
"name": "Xoo wt",
"characteristics": [
{
"@id": "#MaterialAttributeValue/organism=Xanthomonas oryzae pv. oryzae PXO99A",
"category": {
"@id": "#MaterialAttribute/OBI:0100026",
"characteristicType": {
"@id": "OBI:0100026",
"annotationValue": "organism",
"termSource": "OBI",
"termAccession": "OBI:0100026"
}
},
"value": {
"@id": "#UserTerm_Xanthomonas_oryzae_pv._oryzae_PXO99A",
"annotationValue": "Xanthomonas oryzae pv. oryzae PXO99A"
}
},
{
"@id": "#MaterialAttributeValue/OD600=0,5",
"category": {
"@id": "#MaterialAttribute/MCO:0000059",
"characteristicType": {
"@id": "MCO:0000059",
"annotationValue": "OD600",
"termSource": "MCO",
"termAccession": "MCO:0000059"
}
},
"value": {
"@id": "#UserTerm_0,5",
"annotationValue": "0,5"
}
}
]
},
{
"@id": "#Sample_Oryza_sativa_IR24",
"name": "Oryza sativa IR24",
"characteristics": [
{
"@id": "#MaterialAttributeValue/organism=Oryza sativa",
"category": {
"@id": "#MaterialAttribute/OBI:0100026",
"characteristicType": {
"@id": "OBI:0100026",
"annotationValue": "organism",
"termSource": "OBI",
"termAccession": "OBI:0100026"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/C_5438",
"annotationValue": "Oryza sativa",
"termSource": "C",
"termAccession": "http://purl.obolibrary.org/obo/C_5438"
}
},
{
"@id": "#EmptyMaterialAttributeValue",
"category": {
"@id": "#MaterialAttribute/MCO:0000059",
"characteristicType": {
"@id": "MCO:0000059",
"annotationValue": "OD600",
"termSource": "MCO",
"termAccession": "MCO:0000059"
}
}
}
]
},
{
"@id": "#Sample_\u2206sux",
"name": "\u2206sux",
"characteristics": [
{
"@id": "#MaterialAttributeValue/organism=Xanthomonas oryzae pv. oryzae PXO99A",
"category": {
"@id": "#MaterialAttribute/OBI:0100026",
"characteristicType": {
"@id": "OBI:0100026",
"annotationValue": "organism",
"termSource": "OBI",
"termAccession": "OBI:0100026"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/NCBITAXON_360094",
"annotationValue": "Xanthomonas oryzae pv. oryzae PXO99A",
"termSource": "NCBITAXON",
"termAccession": "http://purl.obolibrary.org/obo/NCBITAXON_360094"
}
},
{
"@id": "#MaterialAttributeValue/OD600=0,5",
"category": {
"@id": "#MaterialAttribute/MCO:0000059",
"characteristicType": {
"@id": "MCO:0000059",
"annotationValue": "OD600",
"termSource": "MCO",
"termAccession": "MCO:0000059"
}
},
"value": {
"@id": "#UserTerm_0,5",
"annotationValue": "0,5"
}
}
]
},
{
"@id": "#Sample_Oryza_sativa_IR24",
"name": "Oryza sativa IR24",
"characteristics": [
{
"@id": "#MaterialAttributeValue/organism=Oryza sativa",
"category": {
"@id": "#MaterialAttribute/OBI:0100026",
"characteristicType": {
"@id": "OBI:0100026",
"annotationValue": "organism",
"termSource": "OBI",
"termAccession": "OBI:0100026"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/C_5438",
"annotationValue": "Oryza sativa",
"termSource": "C",
"termAccession": "http://purl.obolibrary.org/obo/C_5438"
}
},
{
"@id": "#EmptyMaterialAttributeValue",
"category": {
"@id": "#MaterialAttribute/MCO:0000059",
"characteristicType": {
"@id": "MCO:0000059",
"annotationValue": "OD600",
"termSource": "MCO",
"termAccession": "MCO:0000059"
}
}
}
]
},
{
"@id": "#Sample_\u2206suxC",
"name": "\u2206suxC",
"characteristics": [
{
"@id": "#MaterialAttributeValue/organism=Xanthomonas oryzae pv. oryzae PXO99A",
"category": {
"@id": "#MaterialAttribute/OBI:0100026",
"characteristicType": {
"@id": "OBI:0100026",
"annotationValue": "organism",
"termSource": "OBI",
"termAccession": "OBI:0100026"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/NCBITAXON_360094",
"annotationValue": "Xanthomonas oryzae pv. oryzae PXO99A",
"termSource": "NCBITAXON",
"termAccession": "http://purl.obolibrary.org/obo/NCBITAXON_360094"
}
},
{
"@id": "#MaterialAttributeValue/OD600=0,5",
"category": {
"@id": "#MaterialAttribute/MCO:0000059",
"characteristicType": {
"@id": "MCO:0000059",
"annotationValue": "OD600",
"termSource": "MCO",
"termAccession": "MCO:0000059"
}
},
"value": {
"@id": "#UserTerm_0,5",
"annotationValue": "0,5"
}
}
]
},
{
"@id": "#Sample_Oryza_sativa_IR24",
"name": "Oryza sativa IR24",
"characteristics": [
{
"@id": "#MaterialAttributeValue/organism=Oryza sativa",
"category": {
"@id": "#MaterialAttribute/OBI:0100026",
"characteristicType": {
"@id": "OBI:0100026",
"annotationValue": "organism",
"termSource": "OBI",
"termAccession": "OBI:0100026"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/C_5438",
"annotationValue": "Oryza sativa",
"termSource": "C",
"termAccession": "http://purl.obolibrary.org/obo/C_5438"
}
},
{
"@id": "#EmptyMaterialAttributeValue",
"category": {
"@id": "#MaterialAttribute/MCO:0000059",
"characteristicType": {
"@id": "MCO:0000059",
"annotationValue": "OD600",
"termSource": "MCO",
"termAccession": "MCO:0000059"
}
}
}
]
},
{
"@id": "#Sample_\u2206suxA",
"name": "\u2206suxA",
"characteristics": [
{
"@id": "#MaterialAttributeValue/organism=Xanthomonas oryzae pv. oryzae PXO99A",
"category": {
"@id": "#MaterialAttribute/OBI:0100026",
"characteristicType": {
"@id": "OBI:0100026",
"annotationValue": "organism",
"termSource": "OBI",
"termAccession": "OBI:0100026"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/NCBITAXON_360094",
"annotationValue": "Xanthomonas oryzae pv. oryzae PXO99A",
"termSource": "NCBITAXON",
"termAccession": "http://purl.obolibrary.org/obo/NCBITAXON_360094"
}
},
{
"@id": "#MaterialAttributeValue/OD600=0,5",
"category": {
"@id": "#MaterialAttribute/MCO:0000059",
"characteristicType": {
"@id": "MCO:0000059",
"annotationValue": "OD600",
"termSource": "MCO",
"termAccession": "MCO:0000059"
}
},
"value": {
"@id": "#UserTerm_0,5",
"annotationValue": "0,5"
}
}
]
},
{
"@id": "#Sample_Oryza_sativa_IR24",
"name": "Oryza sativa IR24",
"characteristics": [
{
"@id": "#MaterialAttributeValue/organism=Oryza sativa",
"category": {
"@id": "#MaterialAttribute/OBI:0100026",
"characteristicType": {
"@id": "OBI:0100026",
"annotationValue": "organism",
"termSource": "OBI",
"termAccession": "OBI:0100026"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/C_5438",
"annotationValue": "Oryza sativa",
"termSource": "C",
"termAccession": "http://purl.obolibrary.org/obo/C_5438"
}
},
{
"@id": "#EmptyMaterialAttributeValue",
"category": {
"@id": "#MaterialAttribute/MCO:0000059",
"characteristicType": {
"@id": "MCO:0000059",
"annotationValue": "OD600",
"termSource": "MCO",
"termAccession": "MCO:0000059"
}
}
}
]
},
{
"@id": "#Sample_\u2206suxB",
"name": "\u2206suxB",
"characteristics": [
{
"@id": "#MaterialAttributeValue/organism=Xanthomonas oryzae pv. oryzae PXO99A",
"category": {
"@id": "#MaterialAttribute/OBI:0100026",
"characteristicType": {
"@id": "OBI:0100026",
"annotationValue": "organism",
"termSource": "OBI",
"termAccession": "OBI:0100026"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/NCBITAXON_360094",
"annotationValue": "Xanthomonas oryzae pv. oryzae PXO99A",
"termSource": "NCBITAXON",
"termAccession": "http://purl.obolibrary.org/obo/NCBITAXON_360094"
}
},
{
"@id": "#MaterialAttributeValue/OD600=0,5",
"category": {
"@id": "#MaterialAttribute/MCO:0000059",
"characteristicType": {
"@id": "MCO:0000059",
"annotationValue": "OD600",
"termSource": "MCO",
"termAccession": "MCO:0000059"
}
},
"value": {
"@id": "#UserTerm_0,5",
"annotationValue": "0,5"
}
}
]
},
{
"@id": "#Sample_Oryza_sativa_Kitaake\t\t",
"name": "Oryza sativa Kitaake\t\t",
"characteristics": [
{
"@id": "#MaterialAttributeValue/organism=Oryza sativa",
"category": {
"@id": "#MaterialAttribute/OBI:0100026",
"characteristicType": {
"@id": "OBI:0100026",
"annotationValue": "organism",
"termSource": "OBI",
"termAccession": "OBI:0100026"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/C_5438",
"annotationValue": "Oryza sativa",
"termSource": "C",
"termAccession": "http://purl.obolibrary.org/obo/C_5438"
}
},
{
"@id": "#EmptyMaterialAttributeValue",
"category": {
"@id": "#MaterialAttribute/MCO:0000059",
"characteristicType": {
"@id": "MCO:0000059",
"annotationValue": "OD600",
"termSource": "MCO",
"termAccession": "MCO:0000059"
}
}
}
]
},
{
"@id": "#Sample_Xoo_wt",
"name": "Xoo wt",
"characteristics": [
{
"@id": "#MaterialAttributeValue/organism=Xanthomonas oryzae pv. oryzae PXO99A",
"category": {
"@id": "#MaterialAttribute/OBI:0100026",
"characteristicType": {
"@id": "OBI:0100026",
"annotationValue": "organism",
"termSource": "OBI",
"termAccession": "OBI:0100026"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/NCBITAXON_360094",
"annotationValue": "Xanthomonas oryzae pv. oryzae PXO99A",
"termSource": "NCBITAXON",
"termAccession": "http://purl.obolibrary.org/obo/NCBITAXON_360094"
}
},
{
"@id": "#MaterialAttributeValue/OD600=0,5",
"category": {
"@id": "#MaterialAttribute/MCO:0000059",
"characteristicType": {
"@id": "MCO:0000059",
"annotationValue": "OD600",
"termSource": "MCO",
"termAccession": "MCO:0000059"
}
},
"value": {
"@id": "#UserTerm_0,5",
"annotationValue": "0,5"
}
}
]
},
{
"@id": "#Sample_Oryza_sativa_Kitaake\t\t",
"name": "Oryza sativa Kitaake\t\t",
"characteristics": [
{
"@id": "#MaterialAttributeValue/organism=Oryza sativa",
"category": {
"@id": "#MaterialAttribute/OBI:0100026",
"characteristicType": {
"@id": "OBI:0100026",
"annotationValue": "organism",
"termSource": "OBI",
"termAccession": "OBI:0100026"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/C_5438",
"annotationValue": "Oryza sativa",
"termSource": "C",
"termAccession": "http://purl.obolibrary.org/obo/C_5438"
}
},
{
"@id": "#EmptyMaterialAttributeValue",
"category": {
"@id": "#MaterialAttribute/MCO:0000059",
"characteristicType": {
"@id": "MCO:0000059",
"annotationValue": "OD600",
"termSource": "MCO",
"termAccession": "MCO:0000059"
}
}
}
]
},
{
"@id": "#Sample_\u2206sux",
"name": "\u2206sux",
"characteristics": [
{
"@id": "#MaterialAttributeValue/organism=Xanthomonas oryzae pv. oryzae PXO99A",
"category": {
"@id": "#MaterialAttribute/OBI:0100026",
"characteristicType": {
"@id": "OBI:0100026",
"annotationValue": "organism",
"termSource": "OBI",
"termAccession": "OBI:0100026"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/NCBITAXON_360094",
"annotationValue": "Xanthomonas oryzae pv. oryzae PXO99A",
"termSource": "NCBITAXON",
"termAccession": "http://purl.obolibrary.org/obo/NCBITAXON_360094"
}
},
{
"@id": "#MaterialAttributeValue/OD600=0,5",
"category": {
"@id": "#MaterialAttribute/MCO:0000059",
"characteristicType": {
"@id": "MCO:0000059",
"annotationValue": "OD600",
"termSource": "MCO",
"termAccession": "MCO:0000059"
}
},
"value": {
"@id": "#UserTerm_0,5",
"annotationValue": "0,5"
}
}
]
},
{
"@id": "#Sample_Oryza_sativa_Kitaake\t\t",
"name": "Oryza sativa Kitaake\t\t",
"characteristics": [
{
"@id": "#MaterialAttributeValue/organism=Oryza sativa",
"category": {
"@id": "#MaterialAttribute/OBI:0100026",
"characteristicType": {
"@id": "OBI:0100026",
"annotationValue": "organism",
"termSource": "OBI",
"termAccession": "OBI:0100026"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/C_5438",
"annotationValue": "Oryza sativa",
"termSource": "C",
"termAccession": "http://purl.obolibrary.org/obo/C_5438"
}
},
{
"@id": "#EmptyMaterialAttributeValue",
"category": {
"@id": "#MaterialAttribute/MCO:0000059",
"characteristicType": {
"@id": "MCO:0000059",
"annotationValue": "OD600",
"termSource": "MCO",
"termAccession": "MCO:0000059"
}
}
}
]
},
{
"@id": "#Sample_\u2206suxC",
"name": "\u2206suxC",
"characteristics": [
{
"@id": "#MaterialAttributeValue/organism=Xanthomonas oryzae pv. oryzae PXO99A",
"category": {
"@id": "#MaterialAttribute/OBI:0100026",
"characteristicType": {
"@id": "OBI:0100026",
"annotationValue": "organism",
"termSource": "OBI",
"termAccession": "OBI:0100026"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/NCBITAXON_360094",
"annotationValue": "Xanthomonas oryzae pv. oryzae PXO99A",
"termSource": "NCBITAXON",
"termAccession": "http://purl.obolibrary.org/obo/NCBITAXON_360094"
}
},
{
"@id": "#MaterialAttributeValue/OD600=0,5",
"category": {
"@id": "#MaterialAttribute/MCO:0000059",
"characteristicType": {
"@id": "MCO:0000059",
"annotationValue": "OD600",
"termSource": "MCO",
"termAccession": "MCO:0000059"
}
},
"value": {
"@id": "#UserTerm_0,5",
"annotationValue": "0,5"
}
}
]
},
{
"@id": "#Sample_Oryza_sativa_Kitaake\t\t",
"name": "Oryza sativa Kitaake\t\t",
"characteristics": [
{
"@id": "#MaterialAttributeValue/organism=Oryza sativa",
"category": {
"@id": "#MaterialAttribute/OBI:0100026",
"characteristicType": {
"@id": "OBI:0100026",
"annotationValue": "organism",
"termSource": "OBI",
"termAccession": "OBI:0100026"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/C_5438",
"annotationValue": "Oryza sativa",
"termSource": "C",
"termAccession": "http://purl.obolibrary.org/obo/C_5438"
}
},
{
"@id": "#EmptyMaterialAttributeValue",
"category": {
"@id": "#MaterialAttribute/MCO:0000059",
"characteristicType": {
"@id": "MCO:0000059",
"annotationValue": "OD600",
"termSource": "MCO",
"termAccession": "MCO:0000059"
}
}
}
]
},
{
"@id": "#Sample_\u2206suxA",
"name": "\u2206suxA",
"characteristics": [
{
"@id": "#MaterialAttributeValue/organism=Xanthomonas oryzae pv. oryzae PXO99A",
"category": {
"@id": "#MaterialAttribute/OBI:0100026",
"characteristicType": {
"@id": "OBI:0100026",
"annotationValue": "organism",
"termSource": "OBI",
"termAccession": "OBI:0100026"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/NCBITAXON_360094",
"annotationValue": "Xanthomonas oryzae pv. oryzae PXO99A",
"termSource": "NCBITAXON",
"termAccession": "http://purl.obolibrary.org/obo/NCBITAXON_360094"
}
},
{
"@id": "#MaterialAttributeValue/OD600=0,5",
"category": {
"@id": "#MaterialAttribute/MCO:0000059",
"characteristicType": {
"@id": "MCO:0000059",
"annotationValue": "OD600",
"termSource": "MCO",
"termAccession": "MCO:0000059"
}
},
"value": {
"@id": "#UserTerm_0,5",
"annotationValue": "0,5"
}
}
]
},
{
"@id": "#Sample_Oryza_sativa_Kitaake\t\t",
"name": "Oryza sativa Kitaake\t\t",
"characteristics": [
{
"@id": "#MaterialAttributeValue/organism=Oryza sativa",
"category": {
"@id": "#MaterialAttribute/OBI:0100026",
"characteristicType": {
"@id": "OBI:0100026",
"annotationValue": "organism",
"termSource": "OBI",
"termAccession": "OBI:0100026"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/C_5438",
"annotationValue": "Oryza sativa",
"termSource": "C",
"termAccession": "http://purl.obolibrary.org/obo/C_5438"
}
},
{
"@id": "#EmptyMaterialAttributeValue",
"category": {
"@id": "#MaterialAttribute/MCO:0000059",
"characteristicType": {
"@id": "MCO:0000059",
"annotationValue": "OD600",
"termSource": "MCO",
"termAccession": "MCO:0000059"
}
}
}
]
},
{
"@id": "#Sample_\u2206suxB",
"name": "\u2206suxB",
"characteristics": [
{
"@id": "#MaterialAttributeValue/organism=Xanthomonas oryzae pv. oryzae PXO99A",
"category": {
"@id": "#MaterialAttribute/OBI:0100026",
"characteristicType": {
"@id": "OBI:0100026",
"annotationValue": "organism",
"termSource": "OBI",
"termAccession": "OBI:0100026"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/NCBITAXON_360094",
"annotationValue": "Xanthomonas oryzae pv. oryzae PXO99A",
"termSource": "NCBITAXON",
"termAccession": "http://purl.obolibrary.org/obo/NCBITAXON_360094"
}
},
{
"@id": "#MaterialAttributeValue/OD600=0,5",
"category": {
"@id": "#MaterialAttribute/MCO:0000059",
"characteristicType": {
"@id": "MCO:0000059",
"annotationValue": "OD600",
"termSource": "MCO",
"termAccession": "MCO:0000059"
}
},
"value": {
"@id": "#UserTerm_0,5",
"annotationValue": "0,5"
}
}
]
},
{
"@id": "#Sample_Oryzae_sativa_Nipponbare",
"name": "Oryzae sativa Nipponbare",
"characteristics": [
{
"@id": "#MaterialAttributeValue/organism=Oryza sativa",
"category": {
"@id": "#MaterialAttribute/OBI:0100026",
"characteristicType": {
"@id": "OBI:0100026",
"annotationValue": "organism",
"termSource": "OBI",
"termAccession": "OBI:0100026"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/C_5438",
"annotationValue": "Oryza sativa",
"termSource": "C",
"termAccession": "http://purl.obolibrary.org/obo/C_5438"
}
},
{
"@id": "#EmptyMaterialAttributeValue",
"category": {
"@id": "#MaterialAttribute/MCO:0000059",
"characteristicType": {
"@id": "MCO:0000059",
"annotationValue": "OD600",
"termSource": "MCO",
"termAccession": "MCO:0000059"
}
}
}
]
},
{
"@id": "#Sample_Xoo_wt",
"name": "Xoo wt",
"characteristics": [
{
"@id": "#MaterialAttributeValue/organism=Xanthomonas oryzae pv. oryzae PXO99A",
"category": {
"@id": "#MaterialAttribute/OBI:0100026",
"characteristicType": {
"@id": "OBI:0100026",
"annotationValue": "organism",
"termSource": "OBI",
"termAccession": "OBI:0100026"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/NCBITAXON_360094",
"annotationValue": "Xanthomonas oryzae pv. oryzae PXO99A",
"termSource": "NCBITAXON",
"termAccession": "http://purl.obolibrary.org/obo/NCBITAXON_360094"
}
},
{
"@id": "#MaterialAttributeValue/OD600=0,5",
"category": {
"@id": "#MaterialAttribute/MCO:0000059",
"characteristicType": {
"@id": "MCO:0000059",
"annotationValue": "OD600",
"termSource": "MCO",
"termAccession": "MCO:0000059"
}
},
"value": {
"@id": "#UserTerm_0,5",
"annotationValue": "0,5"
}
}
]
},
{
"@id": "#Sample_Oryzae_sativa_Nipponbare",
"name": "Oryzae sativa Nipponbare",
"characteristics": [
{
"@id": "#MaterialAttributeValue/organism=Oryza sativa",
"category": {
"@id": "#MaterialAttribute/OBI:0100026",
"characteristicType": {
"@id": "OBI:0100026",
"annotationValue": "organism",
"termSource": "OBI",
"termAccession": "OBI:0100026"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/C_5438",
"annotationValue": "Oryza sativa",
"termSource": "C",
"termAccession": "http://purl.obolibrary.org/obo/C_5438"
}
},
{
"@id": "#EmptyMaterialAttributeValue",
"category": {
"@id": "#MaterialAttribute/MCO:0000059",
"characteristicType": {
"@id": "MCO:0000059",
"annotationValue": "OD600",
"termSource": "MCO",
"termAccession": "MCO:0000059"
}
}
}
]
},
{
"@id": "#Sample_\u2206sux",
"name": "\u2206sux",
"characteristics": [
{
"@id": "#MaterialAttributeValue/organism=Xanthomonas oryzae pv. oryzae PXO99A",
"category": {
"@id": "#MaterialAttribute/OBI:0100026",
"characteristicType": {
"@id": "OBI:0100026",
"annotationValue": "organism",
"termSource": "OBI",
"termAccession": "OBI:0100026"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/NCBITAXON_360094",
"annotationValue": "Xanthomonas oryzae pv. oryzae PXO99A",
"termSource": "NCBITAXON",
"termAccession": "http://purl.obolibrary.org/obo/NCBITAXON_360094"
}
},
{
"@id": "#MaterialAttributeValue/OD600=0,5",
"category": {
"@id": "#MaterialAttribute/MCO:0000059",
"characteristicType": {
"@id": "MCO:0000059",
"annotationValue": "OD600",
"termSource": "MCO",
"termAccession": "MCO:0000059"
}
},
"value": {
"@id": "#UserTerm_0,5",
"annotationValue": "0,5"
}
}
]
},
{
"@id": "#Sample_Oryzae_sativa_Nipponbare",
"name": "Oryzae sativa Nipponbare",
"characteristics": [
{
"@id": "#MaterialAttributeValue/organism=Oryza sativa",
"category": {
"@id": "#MaterialAttribute/OBI:0100026",
"characteristicType": {
"@id": "OBI:0100026",
"annotationValue": "organism",
"termSource": "OBI",
"termAccession": "OBI:0100026"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/C_5438",
"annotationValue": "Oryza sativa",
"termSource": "C",
"termAccession": "http://purl.obolibrary.org/obo/C_5438"
}
},
{
"@id": "#EmptyMaterialAttributeValue",
"category": {
"@id": "#MaterialAttribute/MCO:0000059",
"characteristicType": {
"@id": "MCO:0000059",
"annotationValue": "OD600",
"termSource": "MCO",
"termAccession": "MCO:0000059"
}
}
}
]
},
{
"@id": "#Sample_\u2206suxC",
"name": "\u2206suxC",
"characteristics": [
{
"@id": "#MaterialAttributeValue/organism=Xanthomonas oryzae pv. oryzae exposure",
"category": {
"@id": "#MaterialAttribute/OBI:0100026",
"characteristicType": {
"@id": "OBI:0100026",
"annotationValue": "organism",
"termSource": "OBI",
"termAccession": "OBI:0100026"
}
},
"value": {
"@id": "https://bioregistry.io/PECO:0007257",
"annotationValue": "Xanthomonas oryzae pv. oryzae exposure",
"termSource": "PECO",
"termAccession": "https://bioregistry.io/PECO:0007257"
}
},
{
"@id": "#MaterialAttributeValue/OD600=0,5",
"category": {
"@id": "#MaterialAttribute/MCO:0000059",
"characteristicType": {
"@id": "MCO:0000059",
"annotationValue": "OD600",
"termSource": "MCO",
"termAccession": "MCO:0000059"
}
},
"value": {
"@id": "#UserTerm_0,5",
"annotationValue": "0,5"
}
}
]
},
{
"@id": "#Sample_Oryzae_sativa_Nipponbare",
"name": "Oryzae sativa Nipponbare",
"characteristics": [
{
"@id": "#MaterialAttributeValue/organism=Oryza sativa",
"category": {
"@id": "#MaterialAttribute/OBI:0100026",
"characteristicType": {
"@id": "OBI:0100026",
"annotationValue": "organism",
"termSource": "OBI",
"termAccession": "OBI:0100026"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/C_5438",
"annotationValue": "Oryza sativa",
"termSource": "C",
"termAccession": "http://purl.obolibrary.org/obo/C_5438"
}
},
{
"@id": "#EmptyMaterialAttributeValue",
"category": {
"@id": "#MaterialAttribute/MCO:0000059",
"characteristicType": {
"@id": "MCO:0000059",
"annotationValue": "OD600",
"termSource": "MCO",
"termAccession": "MCO:0000059"
}
}
}
]
},
{
"@id": "#Sample_\u2206suxA",
"name": "\u2206suxA",
"characteristics": [
{
"@id": "#MaterialAttributeValue/organism=Xanthomonas oryzae pv. oryzae PXO99A",
"category": {
"@id": "#MaterialAttribute/OBI:0100026",
"characteristicType": {
"@id": "OBI:0100026",
"annotationValue": "organism",
"termSource": "OBI",
"termAccession": "OBI:0100026"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/NCBITAXON_360094",
"annotationValue": "Xanthomonas oryzae pv. oryzae PXO99A",
"termSource": "NCBITAXON",
"termAccession": "http://purl.obolibrary.org/obo/NCBITAXON_360094"
}
},
{
"@id": "#MaterialAttributeValue/OD600=0,5",
"category": {
"@id": "#MaterialAttribute/MCO:0000059",
"characteristicType": {
"@id": "MCO:0000059",
"annotationValue": "OD600",
"termSource": "MCO",
"termAccession": "MCO:0000059"
}
},
"value": {
"@id": "#UserTerm_0,5",
"annotationValue": "0,5"
}
}
]
},
{
"@id": "#Sample_Oryzae_sativa_Nipponbare",
"name": "Oryzae sativa Nipponbare",
"characteristics": [
{
"@id": "#MaterialAttributeValue/organism=Oryza sativa",
"category": {
"@id": "#MaterialAttribute/OBI:0100026",
"characteristicType": {
"@id": "OBI:0100026",
"annotationValue": "organism",
"termSource": "OBI",
"termAccession": "OBI:0100026"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/C_5438",
"annotationValue": "Oryza sativa",
"termSource": "C",
"termAccession": "http://purl.obolibrary.org/obo/C_5438"
}
},
{
"@id": "#EmptyMaterialAttributeValue",
"category": {
"@id": "#MaterialAttribute/MCO:0000059",
"characteristicType": {
"@id": "MCO:0000059",
"annotationValue": "OD600",
"termSource": "MCO",
"termAccession": "MCO:0000059"
}
}
}
]
},
{
"@id": "#Sample_\u2206suxB",
"name": "\u2206suxB",
"characteristics": [
{
"@id": "#MaterialAttributeValue/organism=Xanthomonas oryzae pv. oryzae PXO99A",
"category": {
"@id": "#MaterialAttribute/OBI:0100026",
"characteristicType": {
"@id": "OBI:0100026",
"annotationValue": "organism",
"termSource": "OBI",
"termAccession": "OBI:0100026"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/NCBITAXON_360094",
"annotationValue": "Xanthomonas oryzae pv. oryzae PXO99A",
"termSource": "NCBITAXON",
"termAccession": "http://purl.obolibrary.org/obo/NCBITAXON_360094"
}
},
{
"@id": "#MaterialAttributeValue/OD600=0,5",
"category": {
"@id": "#MaterialAttribute/MCO:0000059",
"characteristicType": {
"@id": "MCO:0000059",
"annotationValue": "OD600",
"termSource": "MCO",
"termAccession": "MCO:0000059"
}
},
"value": {
"@id": "#UserTerm_0,5",
"annotationValue": "0,5"
}
}
]
}
],
"outputs": [
{
"@id": "#Sample_Oryza_sativa_IR24_Xoo_wt",
"name": "Oryza sativa IR24_Xoo wt"
},
{
"@id": "#Sample_Oryza_sativa_IR24_Xoo_wt",
"name": "Oryza sativa IR24_Xoo wt"
},
{
"@id": "#Sample_Oryza_sativa_IR24_\u2206sux",
"name": "Oryza sativa IR24_\u2206sux"
},
{
"@id": "#Sample_Oryza_sativa_IR24_\u2206sux",
"name": "Oryza sativa IR24_\u2206sux"
},
{
"@id": "#Sample_Oryza_sativa_IR24_\u2206suxC",
"name": "Oryza sativa IR24_\u2206suxC"
},
{
"@id": "#Sample_Oryza_sativa_IR24_\u2206suxC",
"name": "Oryza sativa IR24_\u2206suxC"
},
{
"@id": "#Sample_Oryza_sativa_IR24_\u2206suxA",
"name": "Oryza sativa IR24_\u2206suxA"
},
{
"@id": "#Sample_Oryza_sativa_IR24_\u2206suxA",
"name": "Oryza sativa IR24_\u2206suxA"
},
{
"@id": "#Sample_Oryza_sativa_IR24_\u2206suxB",
"name": "Oryza sativa IR24_\u2206suxB"
},
{
"@id": "#Sample_Oryza_sativa_IR24_\u2206suxB",
"name": "Oryza sativa IR24_\u2206suxB"
},
{
"@id": "#Sample_Oryza_sativa_Kitaake_Xoo_wt",
"name": "Oryza sativa Kitaake_Xoo wt"
},
{
"@id": "#Sample_Oryza_sativa_Kitaake_Xoo_wt",
"name": "Oryza sativa Kitaake_Xoo wt"
},
{
"@id": "#Sample_Oryza_sativa_Kitaake_\u2206sux",
"name": "Oryza sativa Kitaake_\u2206sux"
},
{
"@id": "#Sample_Oryza_sativa_Kitaake_\u2206sux",
"name": "Oryza sativa Kitaake_\u2206sux"
},
{
"@id": "#Sample_Oryza_sativa_Kitaake_\u2206suxC",
"name": "Oryza sativa Kitaake_\u2206suxC"
},
{
"@id": "#Sample_Oryza_sativa_Kitaake_\u2206suxC",
"name": "Oryza sativa Kitaake_\u2206suxC"
},
{
"@id": "#Sample_Oryza_sativa_Kitaake_\u2206suxA",
"name": "Oryza sativa Kitaake_\u2206suxA"
},
{
"@id": "#Sample_Oryza_sativa_Kitaake_\u2206suxA",
"name": "Oryza sativa Kitaake_\u2206suxA"
},
{
"@id": "#Sample_Oryza_sativa_Kitaake_\u2206suxB",
"name": "Oryza sativa Kitaake_\u2206suxB"
},
{
"@id": "#Sample_Oryza_sativa_Kitaake_\u2206suxB",
"name": "Oryza sativa Kitaake_\u2206suxB"
},
{
"@id": "#Sample_Oryzae_sativa_Nipponbare_Xoo_wt",
"name": "Oryzae sativa Nipponbare_Xoo wt"
},
{
"@id": "#Sample_Oryzae_sativa_Nipponbare_Xoo_wt",
"name": "Oryzae sativa Nipponbare_Xoo wt"
},
{
"@id": "#Sample_Oryzae_sativa_Nipponbare_\u2206sux",
"name": "Oryzae sativa Nipponbare_\u2206sux"
},
{
"@id": "#Sample_Oryzae_sativa_Nipponbare_\u2206sux",
"name": "Oryzae sativa Nipponbare_\u2206sux"
},
{
"@id": "#Sample_Oryzae_sativa_Nipponbare_\u2206suxC",
"name": "Oryzae sativa Nipponbare_\u2206suxC"
},
{
"@id": "#Sample_Oryzae_sativa_Nipponbare_\u2206suxC",
"name": "Oryzae sativa Nipponbare_\u2206suxC"
},
{
"@id": "#Sample_Oryzae_sativa_Nipponbare_\u2206suxA",
"name": "Oryzae sativa Nipponbare_\u2206suxA"
},
{
"@id": "#Sample_Oryzae_sativa_Nipponbare_\u2206suxA",
"name": "Oryzae sativa Nipponbare_\u2206suxA"
},
{
"@id": "#Sample_Oryzae_sativa_Nipponbare_\u2206suxB",
"name": "Oryzae sativa Nipponbare_\u2206suxB"
},
{
"@id": "#Sample_Oryzae_sativa_Nipponbare_\u2206suxB",
"name": "Oryzae sativa Nipponbare_\u2206suxB"
}
]
},
{
"@id": "#Process_lesion_measurement",
"name": "lesion measurement",
"executesProtocol": {
"@id": "#Protocol_clippingassay.docx",
"name": "clippingassay.docx",
"parameters": [
{
"@id": "#ProtocolParameter/NCIT:C25207",
"parameterName": {
"@id": "NCIT:C25207",
"annotationValue": "Time",
"termSource": "NCIT",
"termAccession": "NCIT:C25207"
}
}
]
},
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NCIT:C25207",
"parameterName": {
"@id": "NCIT:C25207",
"annotationValue": "Time",
"termSource": "NCIT",
"termAccession": "NCIT:C25207"
}
},
"value": {
"@id": "#UserTerm_12_DAI",
"annotationValue": "12 DAI"
}
}
],
"inputs": [
{
"@id": "#Sample_Oryza_sativa_IR24_Xoo_wt",
"name": "Oryza sativa IR24_Xoo wt"
},
{
"@id": "#Sample_Oryza_sativa_IR24_\u2206sux",
"name": "Oryza sativa IR24_\u2206sux"
},
{
"@id": "#Sample_Oryza_sativa_IR24_\u2206suxC",
"name": "Oryza sativa IR24_\u2206suxC"
},
{
"@id": "#Sample_Oryza_sativa_IR24_\u2206suxA",
"name": "Oryza sativa IR24_\u2206suxA"
},
{
"@id": "#Sample_Oryza_sativa_IR24_\u2206suxB",
"name": "Oryza sativa IR24_\u2206suxB"
},
{
"@id": "#Sample_Oryza_sativa_IR24_\u2206suxB",
"name": "Oryza sativa IR24_\u2206suxB"
},
{
"@id": "#Sample_Oryza_sativa_Kitaake_Xoo_wt",
"name": "Oryza sativa Kitaake_Xoo wt"
},
{
"@id": "#Sample_Oryza_sativa_Kitaake_\u2206sux",
"name": "Oryza sativa Kitaake_\u2206sux"
},
{
"@id": "#Sample_Oryza_sativa_Kitaake_\u2206suxC",
"name": "Oryza sativa Kitaake_\u2206suxC"
},
{
"@id": "#Sample_Oryza_sativa_Kitaake_\u2206suxA",
"name": "Oryza sativa Kitaake_\u2206suxA"
},
{
"@id": "#Sample_Oryza_sativa_Kitaake_\u2206suxB",
"name": "Oryza sativa Kitaake_\u2206suxB"
},
{
"@id": "#Sample_Oryza_sativa_Kitaake_\u2206suxC",
"name": "Oryza sativa Kitaake_\u2206suxC"
},
{
"@id": "#Sample_Oryzae_sativa_Nipponbare_Xoo_wt",
"name": "Oryzae sativa Nipponbare_Xoo wt"
},
{
"@id": "#Sample_Oryzae_sativa_Nipponbare_\u2206sux",
"name": "Oryzae sativa Nipponbare_\u2206sux"
},
{
"@id": "#Sample_Oryzae_sativa_Nipponbare_\u2206suxC",
"name": "Oryzae sativa Nipponbare_\u2206suxC"
},
{
"@id": "#Sample_Oryzae_sativa_Nipponbare_\u2206suxA",
"name": "Oryzae sativa Nipponbare_\u2206suxA"
},
{
"@id": "#Sample_Oryzae_sativa_Nipponbare_\u2206suxB",
"name": "Oryzae sativa Nipponbare_\u2206suxB"
}
],
"outputs": [
{
"@id": "assays/Clipping/dataset/Inoculation_data_IR24.xlsx",
"name": "assays/Clipping/dataset/Inoculation data_IR24.xlsx",
"type": "Raw Data File"
},
{
"@id": "assays/Clipping/dataset/Inoculation_data_IR24.xlsx",
"name": "assays/Clipping/dataset/Inoculation data_IR24.xlsx",
"type": "Raw Data File"
},
{
"@id": "assays/Clipping/dataset/Inoculation_data_IR24.xlsx",
"name": "assays/Clipping/dataset/Inoculation data_IR24.xlsx",
"type": "Raw Data File"
},
{
"@id": "assays/Clipping/dataset/Inoculation_data_IR24.xlsx",
"name": "assays/Clipping/dataset/Inoculation data_IR24.xlsx",
"type": "Raw Data File"
},
{
"@id": "assays/Clipping/dataset/Inoculation_data_IR24.xlsx",
"name": "assays/Clipping/dataset/Inoculation data_IR24.xlsx",
"type": "Raw Data File"
},
{
"@id": "assays/Clipping/dataset/Inoculation_data_IR24.xlsx",
"name": "assays/Clipping/dataset/Inoculation data_IR24.xlsx",
"type": "Raw Data File"
},
{
"@id": "assays/Clipping/dataset/Inoculation_data_Kitaake.xlsx",
"name": "assays/Clipping/dataset/Inoculation data_Kitaake.xlsx",
"type": "Raw Data File"
},
{
"@id": "assays/Clipping/dataset/Inoculation_data_Kitaake.xlsx",
"name": "assays/Clipping/dataset/Inoculation data_Kitaake.xlsx",
"type": "Raw Data File"
},
{
"@id": "assays/Clipping/dataset/Inoculation_data_Kitaake.xlsx",
"name": "assays/Clipping/dataset/Inoculation data_Kitaake.xlsx",
"type": "Raw Data File"
},
{
"@id": "assays/Clipping/dataset/Inoculation_data_Kitaake.xlsx",
"name": "assays/Clipping/dataset/Inoculation data_Kitaake.xlsx",
"type": "Raw Data File"
},
{
"@id": "assays/Clipping/dataset/Inoculation_data_Kitaake.xlsx",
"name": "assays/Clipping/dataset/Inoculation data_Kitaake.xlsx",
"type": "Raw Data File"
},
{
"@id": "assays/Clipping/dataset/Inoculation_data_Kitaake.xlsx",
"name": "assays/Clipping/dataset/Inoculation data_Kitaake.xlsx",
"type": "Raw Data File"
},
{
"@id": "assays/Clipping/dataset/sucrose_gene_on_Nip_V2.xlsx",
"name": "assays/Clipping/dataset/sucrose gene on Nip_V2.xlsx",
"type": "Raw Data File"
},
{
"@id": "assays/Clipping/dataset/sucrose_gene_on_Nip_V2.xlsx",
"name": "assays/Clipping/dataset/sucrose gene on Nip_V2.xlsx",
"type": "Raw Data File"
},
{
"@id": "assays/Clipping/dataset/sucrose_gene_on_Nip_V2.xlsx",
"name": "assays/Clipping/dataset/sucrose gene on Nip_V2.xlsx",
"type": "Raw Data File"
},
{
"@id": "assays/Clipping/dataset/sucrose_gene_on_Nip_V2.xlsx",
"name": "assays/Clipping/dataset/sucrose gene on Nip_V2.xlsx",
"type": "Raw Data File"
},
{
"@id": "assays/Clipping/dataset/sucrose_gene_on_Nip_V2.xlsx",
"name": "assays/Clipping/dataset/sucrose gene on Nip_V2.xlsx",
"type": "Raw Data File"
}
]
}
]
}
]
},
{
"@id": "studies/Transcriptomics/",
"filename": "studies/Transcriptomics/isa.study.xlsx",
"identifier": "Transcriptomics",
"title": "Transcriptomics",
"description": "RNAseq of PXO99A grown in NB media either with supplementation of sucrose or glucose or without supplementation. Sampling over 8 hours.",
"people": [
{
"@id": "0000-0002-0961-5680",
"firstName": "Nora R.",
"lastName": "Z\u00f6llner",
"email": "nora.zoellner@hhu.de",
"affiliation": "Heinrich Heine University D\u00fcsseldorf, Institute for Molecular Physiology",
"comments": [
{
"name": "performer (ARC:00000168) Growth Curves",
"value": "Growth Curves"
},
{
"name": "ORCID",
"value": "0000-0002-0961-5680"
}
]
}
],
"studyDesignDescriptors": [
{
"@id": "https://bioregistry.io/EFO:0008896",
"annotationValue": "RNA-Seq",
"termSource": "EFO",
"termAccession": "https://bioregistry.io/EFO:0008896",
"comments": [
{
"name": "description",
"value": "\"RNA-seq is a method that involves purifying RNA and making cDNA, followed by high-throughput sequencing.\" []"
},
{
"name": "isObsolete",
"value": "false"
}
]
}
],
"protocols": [
{
"@id": "#EmptyProtocol",
"parameters": [
{
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
}
],
"components": [
{
"componentName": "None (NCIT:C41132)",
"componentType": {
"@id": "C:1301",
"annotationValue": "carbon",
"termSource": "C",
"termAccession": "C:1301"
}
},
{
"componentName": "0 mM ()",
"componentType": {
"@id": "C:1301",
"annotationValue": "carbon",
"termSource": "C",
"termAccession": "C:1301"
}
}
]
},
{
"@id": "#EmptyProtocol",
"parameters": [
{
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
}
],
"components": [
{
"componentName": "sucrose (C:7495)",
"componentType": {
"@id": "C:1301",
"annotationValue": "carbon",
"termSource": "C",
"termAccession": "C:1301"
}
},
{
"componentName": "30 mM ()",
"componentType": {
"@id": "C:1301",
"annotationValue": "carbon",
"termSource": "C",
"termAccession": "C:1301"
}
}
]
},
{
"@id": "#EmptyProtocol",
"parameters": [
{
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
}
],
"components": [
{
"componentName": "glucose (C:3287)",
"componentType": {
"@id": "C:1301",
"annotationValue": "carbon",
"termSource": "C",
"termAccession": "C:1301"
}
},
{
"componentName": "30 mM ()",
"componentType": {
"@id": "C:1301",
"annotationValue": "carbon",
"termSource": "C",
"termAccession": "C:1301"
}
}
]
},
{
"@id": "#EmptyProtocol",
"parameters": [
{
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
}
],
"components": [
{
"componentName": "glucose (C:3287)",
"componentType": {
"@id": "C:1301",
"annotationValue": "carbon",
"termSource": "C",
"termAccession": "C:1301"
}
},
{
"componentName": "3 mM ()",
"componentType": {
"@id": "C:1301",
"annotationValue": "carbon",
"termSource": "C",
"termAccession": "C:1301"
}
}
]
}
],
"materials": {
"samples": [
{
"@id": "#Sample_Xoo_wt",
"name": "Xoo wt",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Input [Sample Name]=Xanthomonas oryzae pv. oryzae PXO99A",
"category": {
"@id": "#MaterialAttribute/#UserTerm_Input_[Sample_Name]",
"characteristicType": {
"@id": "#UserTerm_Input_[Sample_Name]",
"annotationValue": "Input [Sample Name]"
}
},
"value": {
"@id": "#UserTerm_Xanthomonas_oryzae_pv._oryzae_PXO99A",
"annotationValue": "Xanthomonas oryzae pv. oryzae PXO99A"
}
}
]
},
{
"@id": "#Sample_NB0",
"name": "NB0",
"factorValues": [
{
"@id": "#FactorValue/Time=0hour",
"category": {
"@id": "#Factor/Factor [Time]",
"factorName": "Factor [Time]",
"factorType": {
"@id": "NCIT:C25207",
"annotationValue": "Time",
"termSource": "NCIT",
"termAccession": "NCIT:C25207"
}
},
"value": 0,
"unit": {
"@id": "https://bioregistry.io/UO:0000032",
"annotationValue": "hour",
"termSource": "UO",
"termAccession": "https://bioregistry.io/UO:0000032"
}
}
]
},
{
"@id": "#Sample_NB2",
"name": "NB2",
"factorValues": [
{
"@id": "#FactorValue/Time=2hour",
"category": {
"@id": "#Factor/Factor [Time]",
"factorName": "Factor [Time]",
"factorType": {
"@id": "NCIT:C25207",
"annotationValue": "Time",
"termSource": "NCIT",
"termAccession": "NCIT:C25207"
}
},
"value": 2,
"unit": {
"@id": "https://bioregistry.io/UO:0000032",
"annotationValue": "hour",
"termSource": "UO",
"termAccession": "https://bioregistry.io/UO:0000032"
}
}
]
},
{
"@id": "#Sample_NB4",
"name": "NB4",
"factorValues": [
{
"@id": "#FactorValue/Time=4hour",
"category": {
"@id": "#Factor/Factor [Time]",
"factorName": "Factor [Time]",
"factorType": {
"@id": "NCIT:C25207",
"annotationValue": "Time",
"termSource": "NCIT",
"termAccession": "NCIT:C25207"
}
},
"value": 4,
"unit": {
"@id": "https://bioregistry.io/UO:0000032",
"annotationValue": "hour",
"termSource": "UO",
"termAccession": "https://bioregistry.io/UO:0000032"
}
}
]
},
{
"@id": "#Sample_NB6",
"name": "NB6",
"factorValues": [
{
"@id": "#FactorValue/Time=6hour",
"category": {
"@id": "#Factor/Factor [Time]",
"factorName": "Factor [Time]",
"factorType": {
"@id": "NCIT:C25207",
"annotationValue": "Time",
"termSource": "NCIT",
"termAccession": "NCIT:C25207"
}
},
"value": 6,
"unit": {
"@id": "https://bioregistry.io/UO:0000032",
"annotationValue": "hour",
"termSource": "UO",
"termAccession": "https://bioregistry.io/UO:0000032"
}
}
]
},
{
"@id": "#Sample_NB8",
"name": "NB8",
"factorValues": [
{
"@id": "#FactorValue/Time=8hour",
"category": {
"@id": "#Factor/Factor [Time]",
"factorName": "Factor [Time]",
"factorType": {
"@id": "NCIT:C25207",
"annotationValue": "Time",
"termSource": "NCIT",
"termAccession": "NCIT:C25207"
}
},
"value": 8,
"unit": {
"@id": "https://bioregistry.io/UO:0000032",
"annotationValue": "hour",
"termSource": "UO",
"termAccession": "https://bioregistry.io/UO:0000032"
}
}
]
},
{
"@id": "#Sample_NB1Suc0",
"name": "NB1Suc0",
"factorValues": [
{
"@id": "#FactorValue/Time=0hour",
"category": {
"@id": "#Factor/Factor [Time]",
"factorName": "Factor [Time]",
"factorType": {
"@id": "NCIT:C25207",
"annotationValue": "Time",
"termSource": "NCIT",
"termAccession": "NCIT:C25207"
}
},
"value": 0,
"unit": {
"@id": "https://bioregistry.io/UO:0000032",
"annotationValue": "hour",
"termSource": "UO",
"termAccession": "https://bioregistry.io/UO:0000032"
}
}
]
},
{
"@id": "#Sample_NB1Suc2",
"name": "NB1Suc2",
"factorValues": [
{
"@id": "#FactorValue/Time=2hour",
"category": {
"@id": "#Factor/Factor [Time]",
"factorName": "Factor [Time]",
"factorType": {
"@id": "NCIT:C25207",
"annotationValue": "Time",
"termSource": "NCIT",
"termAccession": "NCIT:C25207"
}
},
"value": 2,
"unit": {
"@id": "https://bioregistry.io/UO:0000032",
"annotationValue": "hour",
"termSource": "UO",
"termAccession": "https://bioregistry.io/UO:0000032"
}
}
]
},
{
"@id": "#Sample_NB1Suc4",
"name": "NB1Suc4",
"factorValues": [
{
"@id": "#FactorValue/Time=4hour",
"category": {
"@id": "#Factor/Factor [Time]",
"factorName": "Factor [Time]",
"factorType": {
"@id": "NCIT:C25207",
"annotationValue": "Time",
"termSource": "NCIT",
"termAccession": "NCIT:C25207"
}
},
"value": 4,
"unit": {
"@id": "https://bioregistry.io/UO:0000032",
"annotationValue": "hour",
"termSource": "UO",
"termAccession": "https://bioregistry.io/UO:0000032"
}
}
]
},
{
"@id": "#Sample_NB1Suc6",
"name": "NB1Suc6",
"factorValues": [
{
"@id": "#FactorValue/Time=6hour",
"category": {
"@id": "#Factor/Factor [Time]",
"factorName": "Factor [Time]",
"factorType": {
"@id": "NCIT:C25207",
"annotationValue": "Time",
"termSource": "NCIT",
"termAccession": "NCIT:C25207"
}
},
"value": 6,
"unit": {
"@id": "https://bioregistry.io/UO:0000032",
"annotationValue": "hour",
"termSource": "UO",
"termAccession": "https://bioregistry.io/UO:0000032"
}
}
]
},
{
"@id": "#Sample_NB1Suc8",
"name": "NB1Suc8",
"factorValues": [
{
"@id": "#FactorValue/Time=8hour",
"category": {
"@id": "#Factor/Factor [Time]",
"factorName": "Factor [Time]",
"factorType": {
"@id": "NCIT:C25207",
"annotationValue": "Time",
"termSource": "NCIT",
"termAccession": "NCIT:C25207"
}
},
"value": 8,
"unit": {
"@id": "https://bioregistry.io/UO:0000032",
"annotationValue": "hour",
"termSource": "UO",
"termAccession": "https://bioregistry.io/UO:0000032"
}
}
]
},
{
"@id": "#Sample_NB2Glc0",
"name": "NB2Glc0",
"factorValues": [
{
"@id": "#FactorValue/Time=0hour",
"category": {
"@id": "#Factor/Factor [Time]",
"factorName": "Factor [Time]",
"factorType": {
"@id": "NCIT:C25207",
"annotationValue": "Time",
"termSource": "NCIT",
"termAccession": "NCIT:C25207"
}
},
"value": 0,
"unit": {
"@id": "https://bioregistry.io/UO:0000032",
"annotationValue": "hour",
"termSource": "UO",
"termAccession": "https://bioregistry.io/UO:0000032"
}
}
]
},
{
"@id": "#Sample_NB2Glc2",
"name": "NB2Glc2",
"factorValues": [
{
"@id": "#FactorValue/Time=2hour",
"category": {
"@id": "#Factor/Factor [Time]",
"factorName": "Factor [Time]",
"factorType": {
"@id": "NCIT:C25207",
"annotationValue": "Time",
"termSource": "NCIT",
"termAccession": "NCIT:C25207"
}
},
"value": 2,
"unit": {
"@id": "https://bioregistry.io/UO:0000032",
"annotationValue": "hour",
"termSource": "UO",
"termAccession": "https://bioregistry.io/UO:0000032"
}
}
]
},
{
"@id": "#Sample_NB2Glc4",
"name": "NB2Glc4",
"factorValues": [
{
"@id": "#FactorValue/Time=4hour",
"category": {
"@id": "#Factor/Factor [Time]",
"factorName": "Factor [Time]",
"factorType": {
"@id": "NCIT:C25207",
"annotationValue": "Time",
"termSource": "NCIT",
"termAccession": "NCIT:C25207"
}
},
"value": 4,
"unit": {
"@id": "https://bioregistry.io/UO:0000032",
"annotationValue": "hour",
"termSource": "UO",
"termAccession": "https://bioregistry.io/UO:0000032"
}
}
]
},
{
"@id": "#Sample_NB2Glc6",
"name": "NB2Glc6",
"factorValues": [
{
"@id": "#FactorValue/Time=6hour",
"category": {
"@id": "#Factor/Factor [Time]",
"factorName": "Factor [Time]",
"factorType": {
"@id": "NCIT:C25207",
"annotationValue": "Time",
"termSource": "NCIT",
"termAccession": "NCIT:C25207"
}
},
"value": 6,
"unit": {
"@id": "https://bioregistry.io/UO:0000032",
"annotationValue": "hour",
"termSource": "UO",
"termAccession": "https://bioregistry.io/UO:0000032"
}
}
]
},
{
"@id": "#Sample_NB2Glc8",
"name": "NB2Glc8",
"factorValues": [
{
"@id": "#FactorValue/Time=8hour",
"category": {
"@id": "#Factor/Factor [Time]",
"factorName": "Factor [Time]",
"factorType": {
"@id": "NCIT:C25207",
"annotationValue": "Time",
"termSource": "NCIT",
"termAccession": "NCIT:C25207"
}
},
"value": 8,
"unit": {
"@id": "https://bioregistry.io/UO:0000032",
"annotationValue": "hour",
"termSource": "UO",
"termAccession": "https://bioregistry.io/UO:0000032"
}
}
]
},
{
"@id": "#Sample_NB02Glc0",
"name": "NB02Glc0",
"factorValues": [
{
"@id": "#FactorValue/Time=0hour",
"category": {
"@id": "#Factor/Factor [Time]",
"factorName": "Factor [Time]",
"factorType": {
"@id": "NCIT:C25207",
"annotationValue": "Time",
"termSource": "NCIT",
"termAccession": "NCIT:C25207"
}
},
"value": 0,
"unit": {
"@id": "https://bioregistry.io/UO:0000032",
"annotationValue": "hour",
"termSource": "UO",
"termAccession": "https://bioregistry.io/UO:0000032"
}
}
]
},
{
"@id": "#Sample_NB02Glc2",
"name": "NB02Glc2",
"factorValues": [
{
"@id": "#FactorValue/Time=2hour",
"category": {
"@id": "#Factor/Factor [Time]",
"factorName": "Factor [Time]",
"factorType": {
"@id": "NCIT:C25207",
"annotationValue": "Time",
"termSource": "NCIT",
"termAccession": "NCIT:C25207"
}
},
"value": 2,
"unit": {
"@id": "https://bioregistry.io/UO:0000032",
"annotationValue": "hour",
"termSource": "UO",
"termAccession": "https://bioregistry.io/UO:0000032"
}
}
]
},
{
"@id": "#Sample_NB02Glc4",
"name": "NB02Glc4",
"factorValues": [
{
"@id": "#FactorValue/Time=4hour",
"category": {
"@id": "#Factor/Factor [Time]",
"factorName": "Factor [Time]",
"factorType": {
"@id": "NCIT:C25207",
"annotationValue": "Time",
"termSource": "NCIT",
"termAccession": "NCIT:C25207"
}
},
"value": 4,
"unit": {
"@id": "https://bioregistry.io/UO:0000032",
"annotationValue": "hour",
"termSource": "UO",
"termAccession": "https://bioregistry.io/UO:0000032"
}
}
]
},
{
"@id": "#Sample_NB02Glc6",
"name": "NB02Glc6",
"factorValues": [
{
"@id": "#FactorValue/Time=6hour",
"category": {
"@id": "#Factor/Factor [Time]",
"factorName": "Factor [Time]",
"factorType": {
"@id": "NCIT:C25207",
"annotationValue": "Time",
"termSource": "NCIT",
"termAccession": "NCIT:C25207"
}
},
"value": 6,
"unit": {
"@id": "https://bioregistry.io/UO:0000032",
"annotationValue": "hour",
"termSource": "UO",
"termAccession": "https://bioregistry.io/UO:0000032"
}
}
]
},
{
"@id": "#Sample_NB02Glc8",
"name": "NB02Glc8",
"factorValues": [
{
"@id": "#FactorValue/Time=8hour",
"category": {
"@id": "#Factor/Factor [Time]",
"factorName": "Factor [Time]",
"factorType": {
"@id": "NCIT:C25207",
"annotationValue": "Time",
"termSource": "NCIT",
"termAccession": "NCIT:C25207"
}
},
"value": 8,
"unit": {
"@id": "https://bioregistry.io/UO:0000032",
"annotationValue": "hour",
"termSource": "UO",
"termAccession": "https://bioregistry.io/UO:0000032"
}
}
]
}
]
},
"processSequence": [
{
"@id": "#Process_StudyOutline_0",
"name": "StudyOutline_0",
"executesProtocol": {
"@id": "#Protocol_Transcriptomics_StudyOutline_0",
"parameters": [
{
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
}
],
"components": [
{
"componentName": "None (NCIT:C41132)",
"componentType": {
"@id": "C:1301",
"annotationValue": "carbon",
"termSource": "C",
"termAccession": "C:1301"
}
},
{
"componentName": "0 mM ()",
"componentType": {
"@id": "C:1301",
"annotationValue": "carbon",
"termSource": "C",
"termAccession": "C:1301"
}
}
]
},
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_NB",
"annotationValue": "NB"
}
}
],
"inputs": [
{
"@id": "#Sample_Xoo_wt",
"name": "Xoo wt",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Input [Sample Name]=Xanthomonas oryzae pv. oryzae PXO99A",
"category": {
"@id": "#MaterialAttribute/#UserTerm_Input_[Sample_Name]",
"characteristicType": {
"@id": "#UserTerm_Input_[Sample_Name]",
"annotationValue": "Input [Sample Name]"
}
},
"value": {
"@id": "#UserTerm_Xanthomonas_oryzae_pv._oryzae_PXO99A",
"annotationValue": "Xanthomonas oryzae pv. oryzae PXO99A"
}
}
]
},
{
"@id": "#Sample_Xoo_wt",
"name": "Xoo wt",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Input [Sample Name]=Xanthomonas oryzae pv. oryzae PXO99A",
"category": {
"@id": "#MaterialAttribute/#UserTerm_Input_[Sample_Name]",
"characteristicType": {
"@id": "#UserTerm_Input_[Sample_Name]",
"annotationValue": "Input [Sample Name]"
}
},
"value": {
"@id": "#UserTerm_Xanthomonas_oryzae_pv._oryzae_PXO99A",
"annotationValue": "Xanthomonas oryzae pv. oryzae PXO99A"
}
}
]
},
{
"@id": "#Sample_Xoo_wt",
"name": "Xoo wt",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Input [Sample Name]=Xanthomonas oryzae pv. oryzae PXO99A",
"category": {
"@id": "#MaterialAttribute/#UserTerm_Input_[Sample_Name]",
"characteristicType": {
"@id": "#UserTerm_Input_[Sample_Name]",
"annotationValue": "Input [Sample Name]"
}
},
"value": {
"@id": "#UserTerm_Xanthomonas_oryzae_pv._oryzae_PXO99A",
"annotationValue": "Xanthomonas oryzae pv. oryzae PXO99A"
}
}
]
},
{
"@id": "#Sample_Xoo_wt",
"name": "Xoo wt",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Input [Sample Name]=Xanthomonas oryzae pv. oryzae PXO99A",
"category": {
"@id": "#MaterialAttribute/#UserTerm_Input_[Sample_Name]",
"characteristicType": {
"@id": "#UserTerm_Input_[Sample_Name]",
"annotationValue": "Input [Sample Name]"
}
},
"value": {
"@id": "#UserTerm_Xanthomonas_oryzae_pv._oryzae_PXO99A",
"annotationValue": "Xanthomonas oryzae pv. oryzae PXO99A"
}
}
]
},
{
"@id": "#Sample_Xoo_wt",
"name": "Xoo wt",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Input [Sample Name]=Xanthomonas oryzae pv. oryzae PXO99A",
"category": {
"@id": "#MaterialAttribute/#UserTerm_Input_[Sample_Name]",
"characteristicType": {
"@id": "#UserTerm_Input_[Sample_Name]",
"annotationValue": "Input [Sample Name]"
}
},
"value": {
"@id": "#UserTerm_Xanthomonas_oryzae_pv._oryzae_PXO99A",
"annotationValue": "Xanthomonas oryzae pv. oryzae PXO99A"
}
}
]
}
],
"outputs": [
{
"@id": "#Sample_NB0",
"name": "NB0",
"factorValues": [
{
"@id": "#FactorValue/Time=0hour",
"category": {
"@id": "#Factor/Factor [Time]",
"factorName": "Factor [Time]",
"factorType": {
"@id": "NCIT:C25207",
"annotationValue": "Time",
"termSource": "NCIT",
"termAccession": "NCIT:C25207"
}
},
"value": 0,
"unit": {
"@id": "https://bioregistry.io/UO:0000032",
"annotationValue": "hour",
"termSource": "UO",
"termAccession": "https://bioregistry.io/UO:0000032"
}
}
]
},
{
"@id": "#Sample_NB2",
"name": "NB2",
"factorValues": [
{
"@id": "#FactorValue/Time=2hour",
"category": {
"@id": "#Factor/Factor [Time]",
"factorName": "Factor [Time]",
"factorType": {
"@id": "NCIT:C25207",
"annotationValue": "Time",
"termSource": "NCIT",
"termAccession": "NCIT:C25207"
}
},
"value": 2,
"unit": {
"@id": "https://bioregistry.io/UO:0000032",
"annotationValue": "hour",
"termSource": "UO",
"termAccession": "https://bioregistry.io/UO:0000032"
}
}
]
},
{
"@id": "#Sample_NB4",
"name": "NB4",
"factorValues": [
{
"@id": "#FactorValue/Time=4hour",
"category": {
"@id": "#Factor/Factor [Time]",
"factorName": "Factor [Time]",
"factorType": {
"@id": "NCIT:C25207",
"annotationValue": "Time",
"termSource": "NCIT",
"termAccession": "NCIT:C25207"
}
},
"value": 4,
"unit": {
"@id": "https://bioregistry.io/UO:0000032",
"annotationValue": "hour",
"termSource": "UO",
"termAccession": "https://bioregistry.io/UO:0000032"
}
}
]
},
{
"@id": "#Sample_NB6",
"name": "NB6",
"factorValues": [
{
"@id": "#FactorValue/Time=6hour",
"category": {
"@id": "#Factor/Factor [Time]",
"factorName": "Factor [Time]",
"factorType": {
"@id": "NCIT:C25207",
"annotationValue": "Time",
"termSource": "NCIT",
"termAccession": "NCIT:C25207"
}
},
"value": 6,
"unit": {
"@id": "https://bioregistry.io/UO:0000032",
"annotationValue": "hour",
"termSource": "UO",
"termAccession": "https://bioregistry.io/UO:0000032"
}
}
]
},
{
"@id": "#Sample_NB8",
"name": "NB8",
"factorValues": [
{
"@id": "#FactorValue/Time=8hour",
"category": {
"@id": "#Factor/Factor [Time]",
"factorName": "Factor [Time]",
"factorType": {
"@id": "NCIT:C25207",
"annotationValue": "Time",
"termSource": "NCIT",
"termAccession": "NCIT:C25207"
}
},
"value": 8,
"unit": {
"@id": "https://bioregistry.io/UO:0000032",
"annotationValue": "hour",
"termSource": "UO",
"termAccession": "https://bioregistry.io/UO:0000032"
}
}
]
}
]
},
{
"@id": "#Process_StudyOutline_1",
"name": "StudyOutline_1",
"executesProtocol": {
"@id": "#Protocol_Transcriptomics_StudyOutline_1",
"parameters": [
{
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
}
],
"components": [
{
"componentName": "sucrose (C:7495)",
"componentType": {
"@id": "C:1301",
"annotationValue": "carbon",
"termSource": "C",
"termAccession": "C:1301"
}
},
{
"componentName": "30 mM ()",
"componentType": {
"@id": "C:1301",
"annotationValue": "carbon",
"termSource": "C",
"termAccession": "C:1301"
}
}
]
},
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_NB",
"annotationValue": "NB"
}
}
],
"inputs": [
{
"@id": "#Sample_Xoo_wt",
"name": "Xoo wt",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Input [Sample Name]=Xanthomonas oryzae pv. oryzae PXO99A",
"category": {
"@id": "#MaterialAttribute/#UserTerm_Input_[Sample_Name]",
"characteristicType": {
"@id": "#UserTerm_Input_[Sample_Name]",
"annotationValue": "Input [Sample Name]"
}
},
"value": {
"@id": "#UserTerm_Xanthomonas_oryzae_pv._oryzae_PXO99A",
"annotationValue": "Xanthomonas oryzae pv. oryzae PXO99A"
}
}
]
},
{
"@id": "#Sample_Xoo_wt",
"name": "Xoo wt",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Input [Sample Name]=Xanthomonas oryzae pv. oryzae PXO99A",
"category": {
"@id": "#MaterialAttribute/#UserTerm_Input_[Sample_Name]",
"characteristicType": {
"@id": "#UserTerm_Input_[Sample_Name]",
"annotationValue": "Input [Sample Name]"
}
},
"value": {
"@id": "#UserTerm_Xanthomonas_oryzae_pv._oryzae_PXO99A",
"annotationValue": "Xanthomonas oryzae pv. oryzae PXO99A"
}
}
]
},
{
"@id": "#Sample_Xoo_wt",
"name": "Xoo wt",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Input [Sample Name]=Xanthomonas oryzae pv. oryzae PXO99A",
"category": {
"@id": "#MaterialAttribute/#UserTerm_Input_[Sample_Name]",
"characteristicType": {
"@id": "#UserTerm_Input_[Sample_Name]",
"annotationValue": "Input [Sample Name]"
}
},
"value": {
"@id": "#UserTerm_Xanthomonas_oryzae_pv._oryzae_PXO99A",
"annotationValue": "Xanthomonas oryzae pv. oryzae PXO99A"
}
}
]
},
{
"@id": "#Sample_Xoo_wt",
"name": "Xoo wt",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Input [Sample Name]=Xanthomonas oryzae pv. oryzae PXO99A",
"category": {
"@id": "#MaterialAttribute/#UserTerm_Input_[Sample_Name]",
"characteristicType": {
"@id": "#UserTerm_Input_[Sample_Name]",
"annotationValue": "Input [Sample Name]"
}
},
"value": {
"@id": "#UserTerm_Xanthomonas_oryzae_pv._oryzae_PXO99A",
"annotationValue": "Xanthomonas oryzae pv. oryzae PXO99A"
}
}
]
},
{
"@id": "#Sample_Xoo_wt",
"name": "Xoo wt",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Input [Sample Name]=Xanthomonas oryzae pv. oryzae PXO99A",
"category": {
"@id": "#MaterialAttribute/#UserTerm_Input_[Sample_Name]",
"characteristicType": {
"@id": "#UserTerm_Input_[Sample_Name]",
"annotationValue": "Input [Sample Name]"
}
},
"value": {
"@id": "#UserTerm_Xanthomonas_oryzae_pv._oryzae_PXO99A",
"annotationValue": "Xanthomonas oryzae pv. oryzae PXO99A"
}
}
]
}
],
"outputs": [
{
"@id": "#Sample_NB1Suc0",
"name": "NB1Suc0",
"factorValues": [
{
"@id": "#FactorValue/Time=0hour",
"category": {
"@id": "#Factor/Factor [Time]",
"factorName": "Factor [Time]",
"factorType": {
"@id": "NCIT:C25207",
"annotationValue": "Time",
"termSource": "NCIT",
"termAccession": "NCIT:C25207"
}
},
"value": 0,
"unit": {
"@id": "https://bioregistry.io/UO:0000032",
"annotationValue": "hour",
"termSource": "UO",
"termAccession": "https://bioregistry.io/UO:0000032"
}
}
]
},
{
"@id": "#Sample_NB1Suc2",
"name": "NB1Suc2",
"factorValues": [
{
"@id": "#FactorValue/Time=2hour",
"category": {
"@id": "#Factor/Factor [Time]",
"factorName": "Factor [Time]",
"factorType": {
"@id": "NCIT:C25207",
"annotationValue": "Time",
"termSource": "NCIT",
"termAccession": "NCIT:C25207"
}
},
"value": 2,
"unit": {
"@id": "https://bioregistry.io/UO:0000032",
"annotationValue": "hour",
"termSource": "UO",
"termAccession": "https://bioregistry.io/UO:0000032"
}
}
]
},
{
"@id": "#Sample_NB1Suc4",
"name": "NB1Suc4",
"factorValues": [
{
"@id": "#FactorValue/Time=4hour",
"category": {
"@id": "#Factor/Factor [Time]",
"factorName": "Factor [Time]",
"factorType": {
"@id": "NCIT:C25207",
"annotationValue": "Time",
"termSource": "NCIT",
"termAccession": "NCIT:C25207"
}
},
"value": 4,
"unit": {
"@id": "https://bioregistry.io/UO:0000032",
"annotationValue": "hour",
"termSource": "UO",
"termAccession": "https://bioregistry.io/UO:0000032"
}
}
]
},
{
"@id": "#Sample_NB1Suc6",
"name": "NB1Suc6",
"factorValues": [
{
"@id": "#FactorValue/Time=6hour",
"category": {
"@id": "#Factor/Factor [Time]",
"factorName": "Factor [Time]",
"factorType": {
"@id": "NCIT:C25207",
"annotationValue": "Time",
"termSource": "NCIT",
"termAccession": "NCIT:C25207"
}
},
"value": 6,
"unit": {
"@id": "https://bioregistry.io/UO:0000032",
"annotationValue": "hour",
"termSource": "UO",
"termAccession": "https://bioregistry.io/UO:0000032"
}
}
]
},
{
"@id": "#Sample_NB1Suc8",
"name": "NB1Suc8",
"factorValues": [
{
"@id": "#FactorValue/Time=8hour",
"category": {
"@id": "#Factor/Factor [Time]",
"factorName": "Factor [Time]",
"factorType": {
"@id": "NCIT:C25207",
"annotationValue": "Time",
"termSource": "NCIT",
"termAccession": "NCIT:C25207"
}
},
"value": 8,
"unit": {
"@id": "https://bioregistry.io/UO:0000032",
"annotationValue": "hour",
"termSource": "UO",
"termAccession": "https://bioregistry.io/UO:0000032"
}
}
]
}
]
},
{
"@id": "#Process_StudyOutline_2",
"name": "StudyOutline_2",
"executesProtocol": {
"@id": "#Protocol_Transcriptomics_StudyOutline_2",
"parameters": [
{
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
}
],
"components": [
{
"componentName": "glucose (C:3287)",
"componentType": {
"@id": "C:1301",
"annotationValue": "carbon",
"termSource": "C",
"termAccession": "C:1301"
}
},
{
"componentName": "30 mM ()",
"componentType": {
"@id": "C:1301",
"annotationValue": "carbon",
"termSource": "C",
"termAccession": "C:1301"
}
}
]
},
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_NB",
"annotationValue": "NB"
}
}
],
"inputs": [
{
"@id": "#Sample_Xoo_wt",
"name": "Xoo wt",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Input [Sample Name]=Xanthomonas oryzae pv. oryzae PXO99A",
"category": {
"@id": "#MaterialAttribute/#UserTerm_Input_[Sample_Name]",
"characteristicType": {
"@id": "#UserTerm_Input_[Sample_Name]",
"annotationValue": "Input [Sample Name]"
}
},
"value": {
"@id": "#UserTerm_Xanthomonas_oryzae_pv._oryzae_PXO99A",
"annotationValue": "Xanthomonas oryzae pv. oryzae PXO99A"
}
}
]
},
{
"@id": "#Sample_Xoo_wt",
"name": "Xoo wt",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Input [Sample Name]=Xanthomonas oryzae pv. oryzae PXO99A",
"category": {
"@id": "#MaterialAttribute/#UserTerm_Input_[Sample_Name]",
"characteristicType": {
"@id": "#UserTerm_Input_[Sample_Name]",
"annotationValue": "Input [Sample Name]"
}
},
"value": {
"@id": "#UserTerm_Xanthomonas_oryzae_pv._oryzae_PXO99A",
"annotationValue": "Xanthomonas oryzae pv. oryzae PXO99A"
}
}
]
},
{
"@id": "#Sample_Xoo_wt",
"name": "Xoo wt",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Input [Sample Name]=Xanthomonas oryzae pv. oryzae PXO99A",
"category": {
"@id": "#MaterialAttribute/#UserTerm_Input_[Sample_Name]",
"characteristicType": {
"@id": "#UserTerm_Input_[Sample_Name]",
"annotationValue": "Input [Sample Name]"
}
},
"value": {
"@id": "#UserTerm_Xanthomonas_oryzae_pv._oryzae_PXO99A",
"annotationValue": "Xanthomonas oryzae pv. oryzae PXO99A"
}
}
]
},
{
"@id": "#Sample_Xoo_wt",
"name": "Xoo wt",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Input [Sample Name]=Xanthomonas oryzae pv. oryzae PXO99A",
"category": {
"@id": "#MaterialAttribute/#UserTerm_Input_[Sample_Name]",
"characteristicType": {
"@id": "#UserTerm_Input_[Sample_Name]",
"annotationValue": "Input [Sample Name]"
}
},
"value": {
"@id": "#UserTerm_Xanthomonas_oryzae_pv._oryzae_PXO99A",
"annotationValue": "Xanthomonas oryzae pv. oryzae PXO99A"
}
}
]
},
{
"@id": "#Sample_Xoo_wt",
"name": "Xoo wt",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Input [Sample Name]=Xanthomonas oryzae pv. oryzae PXO99A",
"category": {
"@id": "#MaterialAttribute/#UserTerm_Input_[Sample_Name]",
"characteristicType": {
"@id": "#UserTerm_Input_[Sample_Name]",
"annotationValue": "Input [Sample Name]"
}
},
"value": {
"@id": "#UserTerm_Xanthomonas_oryzae_pv._oryzae_PXO99A",
"annotationValue": "Xanthomonas oryzae pv. oryzae PXO99A"
}
}
]
}
],
"outputs": [
{
"@id": "#Sample_NB2Glc0",
"name": "NB2Glc0",
"factorValues": [
{
"@id": "#FactorValue/Time=0hour",
"category": {
"@id": "#Factor/Factor [Time]",
"factorName": "Factor [Time]",
"factorType": {
"@id": "NCIT:C25207",
"annotationValue": "Time",
"termSource": "NCIT",
"termAccession": "NCIT:C25207"
}
},
"value": 0,
"unit": {
"@id": "https://bioregistry.io/UO:0000032",
"annotationValue": "hour",
"termSource": "UO",
"termAccession": "https://bioregistry.io/UO:0000032"
}
}
]
},
{
"@id": "#Sample_NB2Glc2",
"name": "NB2Glc2",
"factorValues": [
{
"@id": "#FactorValue/Time=2hour",
"category": {
"@id": "#Factor/Factor [Time]",
"factorName": "Factor [Time]",
"factorType": {
"@id": "NCIT:C25207",
"annotationValue": "Time",
"termSource": "NCIT",
"termAccession": "NCIT:C25207"
}
},
"value": 2,
"unit": {
"@id": "https://bioregistry.io/UO:0000032",
"annotationValue": "hour",
"termSource": "UO",
"termAccession": "https://bioregistry.io/UO:0000032"
}
}
]
},
{
"@id": "#Sample_NB2Glc4",
"name": "NB2Glc4",
"factorValues": [
{
"@id": "#FactorValue/Time=4hour",
"category": {
"@id": "#Factor/Factor [Time]",
"factorName": "Factor [Time]",
"factorType": {
"@id": "NCIT:C25207",
"annotationValue": "Time",
"termSource": "NCIT",
"termAccession": "NCIT:C25207"
}
},
"value": 4,
"unit": {
"@id": "https://bioregistry.io/UO:0000032",
"annotationValue": "hour",
"termSource": "UO",
"termAccession": "https://bioregistry.io/UO:0000032"
}
}
]
},
{
"@id": "#Sample_NB2Glc6",
"name": "NB2Glc6",
"factorValues": [
{
"@id": "#FactorValue/Time=6hour",
"category": {
"@id": "#Factor/Factor [Time]",
"factorName": "Factor [Time]",
"factorType": {
"@id": "NCIT:C25207",
"annotationValue": "Time",
"termSource": "NCIT",
"termAccession": "NCIT:C25207"
}
},
"value": 6,
"unit": {
"@id": "https://bioregistry.io/UO:0000032",
"annotationValue": "hour",
"termSource": "UO",
"termAccession": "https://bioregistry.io/UO:0000032"
}
}
]
},
{
"@id": "#Sample_NB2Glc8",
"name": "NB2Glc8",
"factorValues": [
{
"@id": "#FactorValue/Time=8hour",
"category": {
"@id": "#Factor/Factor [Time]",
"factorName": "Factor [Time]",
"factorType": {
"@id": "NCIT:C25207",
"annotationValue": "Time",
"termSource": "NCIT",
"termAccession": "NCIT:C25207"
}
},
"value": 8,
"unit": {
"@id": "https://bioregistry.io/UO:0000032",
"annotationValue": "hour",
"termSource": "UO",
"termAccession": "https://bioregistry.io/UO:0000032"
}
}
]
}
]
},
{
"@id": "#Process_StudyOutline_3",
"name": "StudyOutline_3",
"executesProtocol": {
"@id": "#Protocol_Transcriptomics_StudyOutline_3",
"parameters": [
{
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
}
],
"components": [
{
"componentName": "glucose (C:3287)",
"componentType": {
"@id": "C:1301",
"annotationValue": "carbon",
"termSource": "C",
"termAccession": "C:1301"
}
},
{
"componentName": "3 mM ()",
"componentType": {
"@id": "C:1301",
"annotationValue": "carbon",
"termSource": "C",
"termAccession": "C:1301"
}
}
]
},
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_NB",
"annotationValue": "NB"
}
}
],
"inputs": [
{
"@id": "#Sample_Xoo_wt",
"name": "Xoo wt",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Input [Sample Name]=Xanthomonas oryzae pv. oryzae PXO99A",
"category": {
"@id": "#MaterialAttribute/#UserTerm_Input_[Sample_Name]",
"characteristicType": {
"@id": "#UserTerm_Input_[Sample_Name]",
"annotationValue": "Input [Sample Name]"
}
},
"value": {
"@id": "#UserTerm_Xanthomonas_oryzae_pv._oryzae_PXO99A",
"annotationValue": "Xanthomonas oryzae pv. oryzae PXO99A"
}
}
]
},
{
"@id": "#Sample_Xoo_wt",
"name": "Xoo wt",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Input [Sample Name]=Xanthomonas oryzae pv. oryzae PXO99A",
"category": {
"@id": "#MaterialAttribute/#UserTerm_Input_[Sample_Name]",
"characteristicType": {
"@id": "#UserTerm_Input_[Sample_Name]",
"annotationValue": "Input [Sample Name]"
}
},
"value": {
"@id": "#UserTerm_Xanthomonas_oryzae_pv._oryzae_PXO99A",
"annotationValue": "Xanthomonas oryzae pv. oryzae PXO99A"
}
}
]
},
{
"@id": "#Sample_Xoo_wt",
"name": "Xoo wt",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Input [Sample Name]=Xanthomonas oryzae pv. oryzae PXO99A",
"category": {
"@id": "#MaterialAttribute/#UserTerm_Input_[Sample_Name]",
"characteristicType": {
"@id": "#UserTerm_Input_[Sample_Name]",
"annotationValue": "Input [Sample Name]"
}
},
"value": {
"@id": "#UserTerm_Xanthomonas_oryzae_pv._oryzae_PXO99A",
"annotationValue": "Xanthomonas oryzae pv. oryzae PXO99A"
}
}
]
},
{
"@id": "#Sample_Xoo_wt",
"name": "Xoo wt",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Input [Sample Name]=Xanthomonas oryzae pv. oryzae PXO99A",
"category": {
"@id": "#MaterialAttribute/#UserTerm_Input_[Sample_Name]",
"characteristicType": {
"@id": "#UserTerm_Input_[Sample_Name]",
"annotationValue": "Input [Sample Name]"
}
},
"value": {
"@id": "#UserTerm_Xanthomonas_oryzae_pv._oryzae_PXO99A",
"annotationValue": "Xanthomonas oryzae pv. oryzae PXO99A"
}
}
]
},
{
"@id": "#Sample_Xoo_wt",
"name": "Xoo wt",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Input [Sample Name]=Xanthomonas oryzae pv. oryzae PXO99A",
"category": {
"@id": "#MaterialAttribute/#UserTerm_Input_[Sample_Name]",
"characteristicType": {
"@id": "#UserTerm_Input_[Sample_Name]",
"annotationValue": "Input [Sample Name]"
}
},
"value": {
"@id": "#UserTerm_Xanthomonas_oryzae_pv._oryzae_PXO99A",
"annotationValue": "Xanthomonas oryzae pv. oryzae PXO99A"
}
}
]
}
],
"outputs": [
{
"@id": "#Sample_NB02Glc0",
"name": "NB02Glc0",
"factorValues": [
{
"@id": "#FactorValue/Time=0hour",
"category": {
"@id": "#Factor/Factor [Time]",
"factorName": "Factor [Time]",
"factorType": {
"@id": "NCIT:C25207",
"annotationValue": "Time",
"termSource": "NCIT",
"termAccession": "NCIT:C25207"
}
},
"value": 0,
"unit": {
"@id": "https://bioregistry.io/UO:0000032",
"annotationValue": "hour",
"termSource": "UO",
"termAccession": "https://bioregistry.io/UO:0000032"
}
}
]
},
{
"@id": "#Sample_NB02Glc2",
"name": "NB02Glc2",
"factorValues": [
{
"@id": "#FactorValue/Time=2hour",
"category": {
"@id": "#Factor/Factor [Time]",
"factorName": "Factor [Time]",
"factorType": {
"@id": "NCIT:C25207",
"annotationValue": "Time",
"termSource": "NCIT",
"termAccession": "NCIT:C25207"
}
},
"value": 2,
"unit": {
"@id": "https://bioregistry.io/UO:0000032",
"annotationValue": "hour",
"termSource": "UO",
"termAccession": "https://bioregistry.io/UO:0000032"
}
}
]
},
{
"@id": "#Sample_NB02Glc4",
"name": "NB02Glc4",
"factorValues": [
{
"@id": "#FactorValue/Time=4hour",
"category": {
"@id": "#Factor/Factor [Time]",
"factorName": "Factor [Time]",
"factorType": {
"@id": "NCIT:C25207",
"annotationValue": "Time",
"termSource": "NCIT",
"termAccession": "NCIT:C25207"
}
},
"value": 4,
"unit": {
"@id": "https://bioregistry.io/UO:0000032",
"annotationValue": "hour",
"termSource": "UO",
"termAccession": "https://bioregistry.io/UO:0000032"
}
}
]
},
{
"@id": "#Sample_NB02Glc6",
"name": "NB02Glc6",
"factorValues": [
{
"@id": "#FactorValue/Time=6hour",
"category": {
"@id": "#Factor/Factor [Time]",
"factorName": "Factor [Time]",
"factorType": {
"@id": "NCIT:C25207",
"annotationValue": "Time",
"termSource": "NCIT",
"termAccession": "NCIT:C25207"
}
},
"value": 6,
"unit": {
"@id": "https://bioregistry.io/UO:0000032",
"annotationValue": "hour",
"termSource": "UO",
"termAccession": "https://bioregistry.io/UO:0000032"
}
}
]
},
{
"@id": "#Sample_NB02Glc8",
"name": "NB02Glc8",
"factorValues": [
{
"@id": "#FactorValue/Time=8hour",
"category": {
"@id": "#Factor/Factor [Time]",
"factorName": "Factor [Time]",
"factorType": {
"@id": "NCIT:C25207",
"annotationValue": "Time",
"termSource": "NCIT",
"termAccession": "NCIT:C25207"
}
},
"value": 8,
"unit": {
"@id": "https://bioregistry.io/UO:0000032",
"annotationValue": "hour",
"termSource": "UO",
"termAccession": "https://bioregistry.io/UO:0000032"
}
}
]
}
]
}
],
"assays": [
{
"filename": "assays/RNAseq_Xoo_15012024/isa.assay.xlsx",
"@id": "assays/RNAseq_Xoo_15012024/",
"measurementType": {
"@id": "#UserTerm_RNAseq",
"annotationValue": "RNAseq"
},
"dataFiles": [
{
"@id": "assays/RNAseq_Xoo_15012024/dataset/raw_data/NB0_2.fq.gz",
"name": "assays/RNAseq_Xoo_15012024/dataset/raw_data/NB0_2.fq.gz",
"type": "Raw Data File"
},
{
"@id": "assays/RNAseq_Xoo_15012024/dataset/raw_data/NB2_1.fq.gz",
"name": "assays/RNAseq_Xoo_15012024/dataset/raw_data/NB2_1.fq.gz",
"type": "Raw Data File"
},
{
"@id": "assays/RNAseq_Xoo_15012024/dataset/raw_data/NB2_2.fq.gz",
"name": "assays/RNAseq_Xoo_15012024/dataset/raw_data/NB2_2.fq.gz",
"type": "Raw Data File"
},
{
"@id": "assays/RNAseq_Xoo_15012024/dataset/raw_data/NB8_1.fq.gz",
"name": "assays/RNAseq_Xoo_15012024/dataset/raw_data/NB8_1.fq.gz",
"type": "Raw Data File"
},
{
"@id": "assays/RNAseq_Xoo_15012024/dataset/raw_data/NB8_2.fq.gz",
"name": "assays/RNAseq_Xoo_15012024/dataset/raw_data/NB8_2.fq.gz",
"type": "Raw Data File"
},
{
"@id": "assays/RNAseq_Xoo_15012024/dataset/raw_data/NB6_1.fq.gz",
"name": "assays/RNAseq_Xoo_15012024/dataset/raw_data/NB6_1.fq.gz",
"type": "Raw Data File"
},
{
"@id": "assays/RNAseq_Xoo_15012024/dataset/raw_data/NB6_2.fq.gz",
"name": "assays/RNAseq_Xoo_15012024/dataset/raw_data/NB6_2.fq.gz",
"type": "Raw Data File"
},
{
"@id": "assays/RNAseq_Xoo_15012024/dataset/raw_data/NB4_2.fq.gz",
"name": "assays/RNAseq_Xoo_15012024/dataset/raw_data/NB4_2.fq.gz",
"type": "Raw Data File"
},
{
"@id": "assays/RNAseq_Xoo_15012024/dataset/raw_data/NB4_1.fq.gz",
"name": "assays/RNAseq_Xoo_15012024/dataset/raw_data/NB4_1.fq.gz",
"type": "Raw Data File"
},
{
"@id": "assays/RNAseq_Xoo_15012024/dataset/raw_data/NB2Glc6_1.fq.gz",
"name": "assays/RNAseq_Xoo_15012024/dataset/raw_data/NB2Glc6_1.fq.gz",
"type": "Raw Data File"
},
{
"@id": "assays/RNAseq_Xoo_15012024/dataset/raw_data/NB2Glc6_2.fq.gz",
"name": "assays/RNAseq_Xoo_15012024/dataset/raw_data/NB2Glc6_2.fq.gz",
"type": "Raw Data File"
},
{
"@id": "assays/RNAseq_Xoo_15012024/dataset/raw_data/NB2Glc4_1.fq.gz",
"name": "assays/RNAseq_Xoo_15012024/dataset/raw_data/NB2Glc4_1.fq.gz",
"type": "Raw Data File"
},
{
"@id": "assays/RNAseq_Xoo_15012024/dataset/raw_data/NB2Glc4_2.fq.gz",
"name": "assays/RNAseq_Xoo_15012024/dataset/raw_data/NB2Glc4_2.fq.gz",
"type": "Raw Data File"
},
{
"@id": "assays/RNAseq_Xoo_15012024/dataset/raw_data/NB2Glc2_1.fq.gz",
"name": "assays/RNAseq_Xoo_15012024/dataset/raw_data/NB2Glc2_1.fq.gz",
"type": "Raw Data File"
},
{
"@id": "assays/RNAseq_Xoo_15012024/dataset/raw_data/NB2Glc2_2.fq.gz",
"name": "assays/RNAseq_Xoo_15012024/dataset/raw_data/NB2Glc2_2.fq.gz",
"type": "Raw Data File"
},
{
"@id": "assays/RNAseq_Xoo_15012024/dataset/raw_data/NB1Suc8_1.fq.gz",
"name": "assays/RNAseq_Xoo_15012024/dataset/raw_data/NB1Suc8_1.fq.gz",
"type": "Raw Data File"
},
{
"@id": "assays/RNAseq_Xoo_15012024/dataset/raw_data/NB1Suc8_2.fq.gz",
"name": "assays/RNAseq_Xoo_15012024/dataset/raw_data/NB1Suc8_2.fq.gz",
"type": "Raw Data File"
},
{
"@id": "assays/RNAseq_Xoo_15012024/dataset/raw_data/NB1Suc6_2.fq.gz",
"name": "assays/RNAseq_Xoo_15012024/dataset/raw_data/NB1Suc6_2.fq.gz",
"type": "Raw Data File"
},
{
"@id": "assays/RNAseq_Xoo_15012024/dataset/raw_data/NB1Suc6_1.fq.gz",
"name": "assays/RNAseq_Xoo_15012024/dataset/raw_data/NB1Suc6_1.fq.gz",
"type": "Raw Data File"
},
{
"@id": "assays/RNAseq_Xoo_15012024/dataset/raw_data/NB1Suc4_1.fq.gz",
"name": "assays/RNAseq_Xoo_15012024/dataset/raw_data/NB1Suc4_1.fq.gz",
"type": "Raw Data File"
},
{
"@id": "assays/RNAseq_Xoo_15012024/dataset/raw_data/NB1Suc4_2.fq.gz",
"name": "assays/RNAseq_Xoo_15012024/dataset/raw_data/NB1Suc4_2.fq.gz",
"type": "Raw Data File"
},
{
"@id": "assays/RNAseq_Xoo_15012024/dataset/raw_data/NB1Suc2_1.fq.gz",
"name": "assays/RNAseq_Xoo_15012024/dataset/raw_data/NB1Suc2_1.fq.gz",
"type": "Raw Data File"
},
{
"@id": "assays/RNAseq_Xoo_15012024/dataset/raw_data/NB1Suc2_2.fq.gz",
"name": "assays/RNAseq_Xoo_15012024/dataset/raw_data/NB1Suc2_2.fq.gz",
"type": "Raw Data File"
},
{
"@id": "assays/RNAseq_Xoo_15012024/dataset/raw_data/NB02Glc6_1.fq.gz",
"name": "assays/RNAseq_Xoo_15012024/dataset/raw_data/NB02Glc6_1.fq.gz",
"type": "Raw Data File"
},
{
"@id": "assays/RNAseq_Xoo_15012024/dataset/raw_data/NB02Glc6_2.fq.gz",
"name": "assays/RNAseq_Xoo_15012024/dataset/raw_data/NB02Glc6_2.fq.gz",
"type": "Raw Data File"
},
{
"@id": "assays/RNAseq_Xoo_15012024/dataset/raw_data/NB02Glc4_1.fq.gz",
"name": "assays/RNAseq_Xoo_15012024/dataset/raw_data/NB02Glc4_1.fq.gz",
"type": "Raw Data File"
},
{
"@id": "assays/RNAseq_Xoo_15012024/dataset/raw_data/NB02Glc4_2.fq.gz",
"name": "assays/RNAseq_Xoo_15012024/dataset/raw_data/NB02Glc4_2.fq.gz",
"type": "Raw Data File"
},
{
"@id": "assays/RNAseq_Xoo_15012024/dataset/raw_data/NB02Glc2_1.fq.gz",
"name": "assays/RNAseq_Xoo_15012024/dataset/raw_data/NB02Glc2_1.fq.gz",
"type": "Raw Data File"
},
{
"@id": "assays/RNAseq_Xoo_15012024/dataset/raw_data/NB02Glc2_2.fq.gz",
"name": "assays/RNAseq_Xoo_15012024/dataset/raw_data/NB02Glc2_2.fq.gz",
"type": "Raw Data File"
},
{
"@id": "assays/RNAseq_Xoo_15012024/dataset/raw_data/NB0_1.fq.gz",
"name": "assays/RNAseq_Xoo_15012024/dataset/raw_data/NB0_1.fq.gz",
"type": "Raw Data File"
},
{
"@id": "assays/RNAseq_Xoo_15012024/dataset/",
"name": "assays/RNAseq_Xoo_15012024/dataset/",
"type": "Raw Data File"
},
{
"@id": "assays/RNAseq_Xoo_15012024/dataset/read_counts/1.count/gene_count.xls",
"name": "assays/RNAseq_Xoo_15012024/dataset/read_counts/1.count/gene_count.xls",
"type": "Raw Data File"
}
],
"materials": {
"samples": [
{
"@id": "#Sample_Xoo_wt",
"name": "Xoo wt"
},
{
"@id": "#Sample_NB0",
"name": "NB0",
"factorValues": [
{
"@id": "#FactorValue/Time=0 hours",
"category": {
"@id": "#Factor/Factor [Time]",
"factorName": "Factor [Time]",
"factorType": {
"@id": "#UserTerm_Time",
"annotationValue": "Time"
}
},
"value": {
"@id": "#UserTerm_0_hours",
"annotationValue": "0 hours"
}
},
{
"@id": "#FactorValue/Media=NB",
"category": {
"@id": "#Factor/Factor [Media]",
"factorName": "Factor [Media]",
"factorType": {
"@id": "#UserTerm_Media",
"annotationValue": "Media"
}
},
"value": {
"@id": "#UserTerm_NB",
"annotationValue": "NB"
}
}
]
},
{
"@id": "#Sample_NB2",
"name": "NB2",
"factorValues": [
{
"@id": "#FactorValue/Time=2 hours",
"category": {
"@id": "#Factor/Factor [Time]",
"factorName": "Factor [Time]",
"factorType": {
"@id": "#UserTerm_Time",
"annotationValue": "Time"
}
},
"value": {
"@id": "#UserTerm_2_hours",
"annotationValue": "2 hours"
}
},
{
"@id": "#FactorValue/Media=NB",
"category": {
"@id": "#Factor/Factor [Media]",
"factorName": "Factor [Media]",
"factorType": {
"@id": "#UserTerm_Media",
"annotationValue": "Media"
}
},
"value": {
"@id": "#UserTerm_NB",
"annotationValue": "NB"
}
}
]
},
{
"@id": "#Sample_NB6",
"name": "NB6",
"factorValues": [
{
"@id": "#FactorValue/Time=6 hours",
"category": {
"@id": "#Factor/Factor [Time]",
"factorName": "Factor [Time]",
"factorType": {
"@id": "#UserTerm_Time",
"annotationValue": "Time"
}
},
"value": {
"@id": "#UserTerm_6_hours",
"annotationValue": "6 hours"
}
},
{
"@id": "#FactorValue/Media=NB",
"category": {
"@id": "#Factor/Factor [Media]",
"factorName": "Factor [Media]",
"factorType": {
"@id": "#UserTerm_Media",
"annotationValue": "Media"
}
},
"value": {
"@id": "#UserTerm_NB",
"annotationValue": "NB"
}
}
]
},
{
"@id": "#Sample_NB8",
"name": "NB8",
"factorValues": [
{
"@id": "#FactorValue/Time=8 hours",
"category": {
"@id": "#Factor/Factor [Time]",
"factorName": "Factor [Time]",
"factorType": {
"@id": "#UserTerm_Time",
"annotationValue": "Time"
}
},
"value": {
"@id": "#UserTerm_8_hours",
"annotationValue": "8 hours"
}
},
{
"@id": "#FactorValue/Media=NB",
"category": {
"@id": "#Factor/Factor [Media]",
"factorName": "Factor [Media]",
"factorType": {
"@id": "#UserTerm_Media",
"annotationValue": "Media"
}
},
"value": {
"@id": "#UserTerm_NB",
"annotationValue": "NB"
}
}
]
},
{
"@id": "#Sample_NB2Suc0",
"name": "NB2Suc0",
"factorValues": [
{
"@id": "#FactorValue/Time=0 hours",
"category": {
"@id": "#Factor/Factor [Time]",
"factorName": "Factor [Time]",
"factorType": {
"@id": "#UserTerm_Time",
"annotationValue": "Time"
}
},
"value": {
"@id": "#UserTerm_0_hours",
"annotationValue": "0 hours"
}
},
{
"@id": "#FactorValue/Media=NB with 30 mM sucrose",
"category": {
"@id": "#Factor/Factor [Media]",
"factorName": "Factor [Media]",
"factorType": {
"@id": "#UserTerm_Media",
"annotationValue": "Media"
}
},
"value": {
"@id": "#UserTerm_NB_with_30_mM_sucrose",
"annotationValue": "NB with 30 mM sucrose"
}
}
]
},
{
"@id": "#Sample_NB2Suc4",
"name": "NB2Suc4",
"factorValues": [
{
"@id": "#FactorValue/Time=4 hours",
"category": {
"@id": "#Factor/Factor [Time]",
"factorName": "Factor [Time]",
"factorType": {
"@id": "#UserTerm_Time",
"annotationValue": "Time"
}
},
"value": {
"@id": "#UserTerm_4_hours",
"annotationValue": "4 hours"
}
},
{
"@id": "#FactorValue/Media=NB with 30 mM sucrose",
"category": {
"@id": "#Factor/Factor [Media]",
"factorName": "Factor [Media]",
"factorType": {
"@id": "#UserTerm_Media",
"annotationValue": "Media"
}
},
"value": {
"@id": "#UserTerm_NB_with_30_mM_sucrose",
"annotationValue": "NB with 30 mM sucrose"
}
}
]
},
{
"@id": "#Sample_NB2Suc8",
"name": "NB2Suc8",
"factorValues": [
{
"@id": "#FactorValue/Time=8 hours",
"category": {
"@id": "#Factor/Factor [Time]",
"factorName": "Factor [Time]",
"factorType": {
"@id": "#UserTerm_Time",
"annotationValue": "Time"
}
},
"value": {
"@id": "#UserTerm_8_hours",
"annotationValue": "8 hours"
}
},
{
"@id": "#FactorValue/Media=NB with 30 mM sucrose",
"category": {
"@id": "#Factor/Factor [Media]",
"factorName": "Factor [Media]",
"factorType": {
"@id": "#UserTerm_Media",
"annotationValue": "Media"
}
},
"value": {
"@id": "#UserTerm_NB_with_30_mM_sucrose",
"annotationValue": "NB with 30 mM sucrose"
}
}
]
},
{
"@id": "#Sample_NB2Glc0",
"name": "NB2Glc0",
"factorValues": [
{
"@id": "#FactorValue/Time=0 hours",
"category": {
"@id": "#Factor/Factor [Time]",
"factorName": "Factor [Time]",
"factorType": {
"@id": "#UserTerm_Time",
"annotationValue": "Time"
}
},
"value": {
"@id": "#UserTerm_0_hours",
"annotationValue": "0 hours"
}
},
{
"@id": "#FactorValue/Media=NB with 30 mM glucose",
"category": {
"@id": "#Factor/Factor [Media]",
"factorName": "Factor [Media]",
"factorType": {
"@id": "#UserTerm_Media",
"annotationValue": "Media"
}
},
"value": {
"@id": "#UserTerm_NB_with_30_mM_glucose",
"annotationValue": "NB with 30 mM glucose"
}
}
]
},
{
"@id": "#Sample_NB2Glc2",
"name": "NB2Glc2",
"factorValues": [
{
"@id": "#FactorValue/Time=2 hours",
"category": {
"@id": "#Factor/Factor [Time]",
"factorName": "Factor [Time]",
"factorType": {
"@id": "#UserTerm_Time",
"annotationValue": "Time"
}
},
"value": {
"@id": "#UserTerm_2_hours",
"annotationValue": "2 hours"
}
},
{
"@id": "#FactorValue/Media=NB with 30 mM glucose\t\t",
"category": {
"@id": "#Factor/Factor [Media]",
"factorName": "Factor [Media]",
"factorType": {
"@id": "#UserTerm_Media",
"annotationValue": "Media"
}
},
"value": {
"@id": "#UserTerm_NB_with_30_mM_glucose\t\t",
"annotationValue": "NB with 30 mM glucose\t\t"
}
}
]
},
{
"@id": "#Sample_NB2Glc4",
"name": "NB2Glc4",
"factorValues": [
{
"@id": "#FactorValue/Time=4 hours",
"category": {
"@id": "#Factor/Factor [Time]",
"factorName": "Factor [Time]",
"factorType": {
"@id": "#UserTerm_Time",
"annotationValue": "Time"
}
},
"value": {
"@id": "#UserTerm_4_hours",
"annotationValue": "4 hours"
}
},
{
"@id": "#FactorValue/Media=NB with 30 mM glucose\t\t",
"category": {
"@id": "#Factor/Factor [Media]",
"factorName": "Factor [Media]",
"factorType": {
"@id": "#UserTerm_Media",
"annotationValue": "Media"
}
},
"value": {
"@id": "#UserTerm_NB_with_30_mM_glucose\t\t",
"annotationValue": "NB with 30 mM glucose\t\t"
}
}
]
},
{
"@id": "#Sample_NB2Glc6",
"name": "NB2Glc6",
"factorValues": [
{
"@id": "#FactorValue/Time=6 hours",
"category": {
"@id": "#Factor/Factor [Time]",
"factorName": "Factor [Time]",
"factorType": {
"@id": "#UserTerm_Time",
"annotationValue": "Time"
}
},
"value": {
"@id": "#UserTerm_6_hours",
"annotationValue": "6 hours"
}
},
{
"@id": "#FactorValue/Media=NB with 30 mM glucose\t\t",
"category": {
"@id": "#Factor/Factor [Media]",
"factorName": "Factor [Media]",
"factorType": {
"@id": "#UserTerm_Media",
"annotationValue": "Media"
}
},
"value": {
"@id": "#UserTerm_NB_with_30_mM_glucose\t\t",
"annotationValue": "NB with 30 mM glucose\t\t"
}
}
]
},
{
"@id": "#Sample_NB2Glc8",
"name": "NB2Glc8",
"factorValues": [
{
"@id": "#FactorValue/Time=8 hours",
"category": {
"@id": "#Factor/Factor [Time]",
"factorName": "Factor [Time]",
"factorType": {
"@id": "#UserTerm_Time",
"annotationValue": "Time"
}
},
"value": {
"@id": "#UserTerm_8_hours",
"annotationValue": "8 hours"
}
},
{
"@id": "#FactorValue/Media=NB with 30 mM glucose\t\t",
"category": {
"@id": "#Factor/Factor [Media]",
"factorName": "Factor [Media]",
"factorType": {
"@id": "#UserTerm_Media",
"annotationValue": "Media"
}
},
"value": {
"@id": "#UserTerm_NB_with_30_mM_glucose\t\t",
"annotationValue": "NB with 30 mM glucose\t\t"
}
}
]
},
{
"@id": "#Sample_NB02Glc0",
"name": "NB02Glc0",
"factorValues": [
{
"@id": "#FactorValue/Time=0 hours",
"category": {
"@id": "#Factor/Factor [Time]",
"factorName": "Factor [Time]",
"factorType": {
"@id": "#UserTerm_Time",
"annotationValue": "Time"
}
},
"value": {
"@id": "#UserTerm_0_hours",
"annotationValue": "0 hours"
}
},
{
"@id": "#FactorValue/Media=NB with 3 mM glucose\t\t",
"category": {
"@id": "#Factor/Factor [Media]",
"factorName": "Factor [Media]",
"factorType": {
"@id": "#UserTerm_Media",
"annotationValue": "Media"
}
},
"value": {
"@id": "#UserTerm_NB_with_3_mM_glucose\t\t",
"annotationValue": "NB with 3 mM glucose\t\t"
}
}
]
},
{
"@id": "#Sample_NB02Glc2",
"name": "NB02Glc2",
"factorValues": [
{
"@id": "#FactorValue/Time=2 hours",
"category": {
"@id": "#Factor/Factor [Time]",
"factorName": "Factor [Time]",
"factorType": {
"@id": "#UserTerm_Time",
"annotationValue": "Time"
}
},
"value": {
"@id": "#UserTerm_2_hours",
"annotationValue": "2 hours"
}
},
{
"@id": "#FactorValue/Media=NB with 3 mM glucose\t\t",
"category": {
"@id": "#Factor/Factor [Media]",
"factorName": "Factor [Media]",
"factorType": {
"@id": "#UserTerm_Media",
"annotationValue": "Media"
}
},
"value": {
"@id": "#UserTerm_NB_with_3_mM_glucose\t\t",
"annotationValue": "NB with 3 mM glucose\t\t"
}
}
]
},
{
"@id": "#Sample_NB02Glc4",
"name": "NB02Glc4",
"factorValues": [
{
"@id": "#FactorValue/Time=4 hours",
"category": {
"@id": "#Factor/Factor [Time]",
"factorName": "Factor [Time]",
"factorType": {
"@id": "#UserTerm_Time",
"annotationValue": "Time"
}
},
"value": {
"@id": "#UserTerm_4_hours",
"annotationValue": "4 hours"
}
},
{
"@id": "#FactorValue/Media=NB with 3 mM glucose\t\t",
"category": {
"@id": "#Factor/Factor [Media]",
"factorName": "Factor [Media]",
"factorType": {
"@id": "#UserTerm_Media",
"annotationValue": "Media"
}
},
"value": {
"@id": "#UserTerm_NB_with_3_mM_glucose\t\t",
"annotationValue": "NB with 3 mM glucose\t\t"
}
}
]
},
{
"@id": "#Sample_NB02Glc6",
"name": "NB02Glc6",
"factorValues": [
{
"@id": "#FactorValue/Time=6 hours",
"category": {
"@id": "#Factor/Factor [Time]",
"factorName": "Factor [Time]",
"factorType": {
"@id": "#UserTerm_Time",
"annotationValue": "Time"
}
},
"value": {
"@id": "#UserTerm_6_hours",
"annotationValue": "6 hours"
}
},
{
"@id": "#FactorValue/Media=NB with 3 mM glucose\t\t",
"category": {
"@id": "#Factor/Factor [Media]",
"factorName": "Factor [Media]",
"factorType": {
"@id": "#UserTerm_Media",
"annotationValue": "Media"
}
},
"value": {
"@id": "#UserTerm_NB_with_3_mM_glucose\t\t",
"annotationValue": "NB with 3 mM glucose\t\t"
}
}
]
},
{
"@id": "#Sample_NB02Glc8",
"name": "NB02Glc8",
"factorValues": [
{
"@id": "#FactorValue/Time=8 hours",
"category": {
"@id": "#Factor/Factor [Time]",
"factorName": "Factor [Time]",
"factorType": {
"@id": "#UserTerm_Time",
"annotationValue": "Time"
}
},
"value": {
"@id": "#UserTerm_8_hours",
"annotationValue": "8 hours"
}
},
{
"@id": "#FactorValue/Media=NB with 3 mM glucose\t\t",
"category": {
"@id": "#Factor/Factor [Media]",
"factorName": "Factor [Media]",
"factorType": {
"@id": "#UserTerm_Media",
"annotationValue": "Media"
}
},
"value": {
"@id": "#UserTerm_NB_with_3_mM_glucose\t\t",
"annotationValue": "NB with 3 mM glucose\t\t"
}
}
]
},
{
"@id": "#Sample_NB4",
"name": "NB4",
"factorValues": [
{
"@id": "#FactorValue/Time=4 hours",
"category": {
"@id": "#Factor/Factor [Time]",
"factorName": "Factor [Time]",
"factorType": {
"@id": "#UserTerm_Time",
"annotationValue": "Time"
}
},
"value": {
"@id": "#UserTerm_4_hours",
"annotationValue": "4 hours"
}
},
{
"@id": "#FactorValue/Media=NB",
"category": {
"@id": "#Factor/Factor [Media]",
"factorName": "Factor [Media]",
"factorType": {
"@id": "#UserTerm_Media",
"annotationValue": "Media"
}
},
"value": {
"@id": "#UserTerm_NB",
"annotationValue": "NB"
}
}
]
},
{
"@id": "#Sample_NB2Suc2",
"name": "NB2Suc2",
"factorValues": [
{
"@id": "#FactorValue/Time=2 hours",
"category": {
"@id": "#Factor/Factor [Time]",
"factorName": "Factor [Time]",
"factorType": {
"@id": "#UserTerm_Time",
"annotationValue": "Time"
}
},
"value": {
"@id": "#UserTerm_2_hours",
"annotationValue": "2 hours"
}
},
{
"@id": "#FactorValue/Media=NB with 30 mM sucrose",
"category": {
"@id": "#Factor/Factor [Media]",
"factorName": "Factor [Media]",
"factorType": {
"@id": "#UserTerm_Media",
"annotationValue": "Media"
}
},
"value": {
"@id": "#UserTerm_NB_with_30_mM_sucrose",
"annotationValue": "NB with 30 mM sucrose"
}
}
]
},
{
"@id": "#Sample_NB2Suc6",
"name": "NB2Suc6",
"factorValues": [
{
"@id": "#FactorValue/Time=6 hours",
"category": {
"@id": "#Factor/Factor [Time]",
"factorName": "Factor [Time]",
"factorType": {
"@id": "#UserTerm_Time",
"annotationValue": "Time"
}
},
"value": {
"@id": "#UserTerm_6_hours",
"annotationValue": "6 hours"
}
},
{
"@id": "#FactorValue/Media=NB with 30 mM sucrose",
"category": {
"@id": "#Factor/Factor [Media]",
"factorName": "Factor [Media]",
"factorType": {
"@id": "#UserTerm_Media",
"annotationValue": "Media"
}
},
"value": {
"@id": "#UserTerm_NB_with_30_mM_sucrose",
"annotationValue": "NB with 30 mM sucrose"
}
}
]
},
{
"@id": "#Sample_NB0",
"name": "NB0"
},
{
"@id": "#Sample_NB2",
"name": "NB2"
},
{
"@id": "#Sample_NB4",
"name": "NB4"
},
{
"@id": "#Sample_NB6",
"name": "NB6"
},
{
"@id": "#Sample_NB8",
"name": "NB8"
},
{
"@id": "#Sample_NB02Glc2",
"name": "NB02Glc2"
},
{
"@id": "#Sample_NB02Glc4",
"name": "NB02Glc4"
},
{
"@id": "#Sample_NB02Glc6",
"name": "NB02Glc6"
},
{
"@id": "#Sample_NB2Glc2",
"name": "NB2Glc2"
},
{
"@id": "#Sample_NB2Glc4",
"name": "NB2Glc4"
},
{
"@id": "#Sample_NB2Glc6",
"name": "NB2Glc6"
},
{
"@id": "#Sample_NB2Suc2",
"name": "NB2Suc2"
},
{
"@id": "#Sample_NB2Suc4",
"name": "NB2Suc4"
},
{
"@id": "#Sample_NB2Suc6",
"name": "NB2Suc6"
},
{
"@id": "#Sample_NB2Suc8",
"name": "NB2Suc8"
},
{
"@id": "#Sample_RNA_NB0",
"name": "RNA NB0"
},
{
"@id": "#Sample_RNA_NB2",
"name": "RNA NB2"
},
{
"@id": "#Sample_RNA_NB4",
"name": "RNA NB4"
},
{
"@id": "#Sample_RNA_NB6",
"name": "RNA NB6"
},
{
"@id": "#Sample_RNA_NB8",
"name": "RNA NB8"
},
{
"@id": "#Sample_RNA_NB02Glc2",
"name": "RNA NB02Glc2"
},
{
"@id": "#Sample_RNA_NB02Glc4",
"name": "RNA NB02Glc4"
},
{
"@id": "#Sample_RNA_NB02Glc6",
"name": "RNA NB02Glc6"
},
{
"@id": "#Sample_RNA_NB2Glc2",
"name": "RNA NB2Glc2"
},
{
"@id": "#Sample_RNA_NB2Glc4",
"name": "RNA NB2Glc4"
},
{
"@id": "#Sample_RNA_NB2Glc6",
"name": "RNA NB2Glc6"
},
{
"@id": "#Sample_RNA_NB2Suc2",
"name": "RNA NB2Suc2"
},
{
"@id": "#Sample_RNA_NB2Suc4",
"name": "RNA NB2Suc4"
},
{
"@id": "#Sample_RNA_NB2Suc6",
"name": "RNA NB2Suc6"
},
{
"@id": "#Sample_RNA_NB2Suc8",
"name": "RNA NB2Suc8"
}
]
},
"processSequence": [
{
"@id": "#Process_RNAseq_sample_cultivation_0",
"name": "RNAseq sample cultivation_0",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_Temperature",
"parameterName": {
"@id": "#UserTerm_Temperature",
"annotationValue": "Temperature"
}
},
"value": {
"@id": "#UserTerm_28\u00b0C_",
"annotationValue": "28\u00b0C "
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_Shaking",
"parameterName": {
"@id": "#UserTerm_Shaking",
"annotationValue": "Shaking"
}
},
"value": {
"@id": "#UserTerm_180_rpm",
"annotationValue": "180 rpm"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_OD600",
"parameterName": {
"@id": "#UserTerm_OD600",
"annotationValue": "OD600"
}
},
"value": {
"@id": "#UserTerm_OD600_Measurements_20231212.xlsx",
"annotationValue": "OD600 Measurements 20231212.xlsx"
}
}
],
"inputs": [
{
"@id": "#Sample_Xoo_wt",
"name": "Xoo wt"
},
{
"@id": "#Sample_Xoo_wt",
"name": "Xoo wt"
},
{
"@id": "#Sample_Xoo_wt",
"name": "Xoo wt"
},
{
"@id": "#Sample_Xoo_wt",
"name": "Xoo wt"
},
{
"@id": "#Sample_Xoo_wt",
"name": "Xoo wt"
},
{
"@id": "#Sample_Xoo_wt",
"name": "Xoo wt"
},
{
"@id": "#Sample_Xoo_wt",
"name": "Xoo wt"
},
{
"@id": "#Sample_Xoo_wt",
"name": "Xoo wt"
},
{
"@id": "#Sample_Xoo_wt",
"name": "Xoo wt"
},
{
"@id": "#Sample_Xoo_wt",
"name": "Xoo wt"
},
{
"@id": "#Sample_Xoo_wt",
"name": "Xoo wt"
},
{
"@id": "#Sample_Xoo_wt",
"name": "Xoo wt"
},
{
"@id": "#Sample_Xoo_wt",
"name": "Xoo wt"
},
{
"@id": "#Sample_Xoo_wt",
"name": "Xoo wt"
},
{
"@id": "#Sample_Xoo_wt",
"name": "Xoo wt"
},
{
"@id": "#Sample_Xoo_wt",
"name": "Xoo wt"
},
{
"@id": "#Sample_Xoo_wt",
"name": "Xoo wt"
}
],
"outputs": [
{
"@id": "#Sample_NB0",
"name": "NB0",
"factorValues": [
{
"@id": "#FactorValue/Time=0 hours",
"category": {
"@id": "#Factor/Factor [Time]",
"factorName": "Factor [Time]",
"factorType": {
"@id": "#UserTerm_Time",
"annotationValue": "Time"
}
},
"value": {
"@id": "#UserTerm_0_hours",
"annotationValue": "0 hours"
}
},
{
"@id": "#FactorValue/Media=NB",
"category": {
"@id": "#Factor/Factor [Media]",
"factorName": "Factor [Media]",
"factorType": {
"@id": "#UserTerm_Media",
"annotationValue": "Media"
}
},
"value": {
"@id": "#UserTerm_NB",
"annotationValue": "NB"
}
}
]
},
{
"@id": "#Sample_NB2",
"name": "NB2",
"factorValues": [
{
"@id": "#FactorValue/Time=2 hours",
"category": {
"@id": "#Factor/Factor [Time]",
"factorName": "Factor [Time]",
"factorType": {
"@id": "#UserTerm_Time",
"annotationValue": "Time"
}
},
"value": {
"@id": "#UserTerm_2_hours",
"annotationValue": "2 hours"
}
},
{
"@id": "#FactorValue/Media=NB",
"category": {
"@id": "#Factor/Factor [Media]",
"factorName": "Factor [Media]",
"factorType": {
"@id": "#UserTerm_Media",
"annotationValue": "Media"
}
},
"value": {
"@id": "#UserTerm_NB",
"annotationValue": "NB"
}
}
]
},
{
"@id": "#Sample_NB6",
"name": "NB6",
"factorValues": [
{
"@id": "#FactorValue/Time=6 hours",
"category": {
"@id": "#Factor/Factor [Time]",
"factorName": "Factor [Time]",
"factorType": {
"@id": "#UserTerm_Time",
"annotationValue": "Time"
}
},
"value": {
"@id": "#UserTerm_6_hours",
"annotationValue": "6 hours"
}
},
{
"@id": "#FactorValue/Media=NB",
"category": {
"@id": "#Factor/Factor [Media]",
"factorName": "Factor [Media]",
"factorType": {
"@id": "#UserTerm_Media",
"annotationValue": "Media"
}
},
"value": {
"@id": "#UserTerm_NB",
"annotationValue": "NB"
}
}
]
},
{
"@id": "#Sample_NB8",
"name": "NB8",
"factorValues": [
{
"@id": "#FactorValue/Time=8 hours",
"category": {
"@id": "#Factor/Factor [Time]",
"factorName": "Factor [Time]",
"factorType": {
"@id": "#UserTerm_Time",
"annotationValue": "Time"
}
},
"value": {
"@id": "#UserTerm_8_hours",
"annotationValue": "8 hours"
}
},
{
"@id": "#FactorValue/Media=NB",
"category": {
"@id": "#Factor/Factor [Media]",
"factorName": "Factor [Media]",
"factorType": {
"@id": "#UserTerm_Media",
"annotationValue": "Media"
}
},
"value": {
"@id": "#UserTerm_NB",
"annotationValue": "NB"
}
}
]
},
{
"@id": "#Sample_NB2Suc0",
"name": "NB2Suc0",
"factorValues": [
{
"@id": "#FactorValue/Time=0 hours",
"category": {
"@id": "#Factor/Factor [Time]",
"factorName": "Factor [Time]",
"factorType": {
"@id": "#UserTerm_Time",
"annotationValue": "Time"
}
},
"value": {
"@id": "#UserTerm_0_hours",
"annotationValue": "0 hours"
}
},
{
"@id": "#FactorValue/Media=NB with 30 mM sucrose",
"category": {
"@id": "#Factor/Factor [Media]",
"factorName": "Factor [Media]",
"factorType": {
"@id": "#UserTerm_Media",
"annotationValue": "Media"
}
},
"value": {
"@id": "#UserTerm_NB_with_30_mM_sucrose",
"annotationValue": "NB with 30 mM sucrose"
}
}
]
},
{
"@id": "#Sample_NB2Suc4",
"name": "NB2Suc4",
"factorValues": [
{
"@id": "#FactorValue/Time=4 hours",
"category": {
"@id": "#Factor/Factor [Time]",
"factorName": "Factor [Time]",
"factorType": {
"@id": "#UserTerm_Time",
"annotationValue": "Time"
}
},
"value": {
"@id": "#UserTerm_4_hours",
"annotationValue": "4 hours"
}
},
{
"@id": "#FactorValue/Media=NB with 30 mM sucrose",
"category": {
"@id": "#Factor/Factor [Media]",
"factorName": "Factor [Media]",
"factorType": {
"@id": "#UserTerm_Media",
"annotationValue": "Media"
}
},
"value": {
"@id": "#UserTerm_NB_with_30_mM_sucrose",
"annotationValue": "NB with 30 mM sucrose"
}
}
]
},
{
"@id": "#Sample_NB2Suc8",
"name": "NB2Suc8",
"factorValues": [
{
"@id": "#FactorValue/Time=8 hours",
"category": {
"@id": "#Factor/Factor [Time]",
"factorName": "Factor [Time]",
"factorType": {
"@id": "#UserTerm_Time",
"annotationValue": "Time"
}
},
"value": {
"@id": "#UserTerm_8_hours",
"annotationValue": "8 hours"
}
},
{
"@id": "#FactorValue/Media=NB with 30 mM sucrose",
"category": {
"@id": "#Factor/Factor [Media]",
"factorName": "Factor [Media]",
"factorType": {
"@id": "#UserTerm_Media",
"annotationValue": "Media"
}
},
"value": {
"@id": "#UserTerm_NB_with_30_mM_sucrose",
"annotationValue": "NB with 30 mM sucrose"
}
}
]
},
{
"@id": "#Sample_NB2Glc0",
"name": "NB2Glc0",
"factorValues": [
{
"@id": "#FactorValue/Time=0 hours",
"category": {
"@id": "#Factor/Factor [Time]",
"factorName": "Factor [Time]",
"factorType": {
"@id": "#UserTerm_Time",
"annotationValue": "Time"
}
},
"value": {
"@id": "#UserTerm_0_hours",
"annotationValue": "0 hours"
}
},
{
"@id": "#FactorValue/Media=NB with 30 mM glucose",
"category": {
"@id": "#Factor/Factor [Media]",
"factorName": "Factor [Media]",
"factorType": {
"@id": "#UserTerm_Media",
"annotationValue": "Media"
}
},
"value": {
"@id": "#UserTerm_NB_with_30_mM_glucose",
"annotationValue": "NB with 30 mM glucose"
}
}
]
},
{
"@id": "#Sample_NB2Glc2",
"name": "NB2Glc2",
"factorValues": [
{
"@id": "#FactorValue/Time=2 hours",
"category": {
"@id": "#Factor/Factor [Time]",
"factorName": "Factor [Time]",
"factorType": {
"@id": "#UserTerm_Time",
"annotationValue": "Time"
}
},
"value": {
"@id": "#UserTerm_2_hours",
"annotationValue": "2 hours"
}
},
{
"@id": "#FactorValue/Media=NB with 30 mM glucose\t\t",
"category": {
"@id": "#Factor/Factor [Media]",
"factorName": "Factor [Media]",
"factorType": {
"@id": "#UserTerm_Media",
"annotationValue": "Media"
}
},
"value": {
"@id": "#UserTerm_NB_with_30_mM_glucose\t\t",
"annotationValue": "NB with 30 mM glucose\t\t"
}
}
]
},
{
"@id": "#Sample_NB2Glc4",
"name": "NB2Glc4",
"factorValues": [
{
"@id": "#FactorValue/Time=4 hours",
"category": {
"@id": "#Factor/Factor [Time]",
"factorName": "Factor [Time]",
"factorType": {
"@id": "#UserTerm_Time",
"annotationValue": "Time"
}
},
"value": {
"@id": "#UserTerm_4_hours",
"annotationValue": "4 hours"
}
},
{
"@id": "#FactorValue/Media=NB with 30 mM glucose\t\t",
"category": {
"@id": "#Factor/Factor [Media]",
"factorName": "Factor [Media]",
"factorType": {
"@id": "#UserTerm_Media",
"annotationValue": "Media"
}
},
"value": {
"@id": "#UserTerm_NB_with_30_mM_glucose\t\t",
"annotationValue": "NB with 30 mM glucose\t\t"
}
}
]
},
{
"@id": "#Sample_NB2Glc6",
"name": "NB2Glc6",
"factorValues": [
{
"@id": "#FactorValue/Time=6 hours",
"category": {
"@id": "#Factor/Factor [Time]",
"factorName": "Factor [Time]",
"factorType": {
"@id": "#UserTerm_Time",
"annotationValue": "Time"
}
},
"value": {
"@id": "#UserTerm_6_hours",
"annotationValue": "6 hours"
}
},
{
"@id": "#FactorValue/Media=NB with 30 mM glucose\t\t",
"category": {
"@id": "#Factor/Factor [Media]",
"factorName": "Factor [Media]",
"factorType": {
"@id": "#UserTerm_Media",
"annotationValue": "Media"
}
},
"value": {
"@id": "#UserTerm_NB_with_30_mM_glucose\t\t",
"annotationValue": "NB with 30 mM glucose\t\t"
}
}
]
},
{
"@id": "#Sample_NB2Glc8",
"name": "NB2Glc8",
"factorValues": [
{
"@id": "#FactorValue/Time=8 hours",
"category": {
"@id": "#Factor/Factor [Time]",
"factorName": "Factor [Time]",
"factorType": {
"@id": "#UserTerm_Time",
"annotationValue": "Time"
}
},
"value": {
"@id": "#UserTerm_8_hours",
"annotationValue": "8 hours"
}
},
{
"@id": "#FactorValue/Media=NB with 30 mM glucose\t\t",
"category": {
"@id": "#Factor/Factor [Media]",
"factorName": "Factor [Media]",
"factorType": {
"@id": "#UserTerm_Media",
"annotationValue": "Media"
}
},
"value": {
"@id": "#UserTerm_NB_with_30_mM_glucose\t\t",
"annotationValue": "NB with 30 mM glucose\t\t"
}
}
]
},
{
"@id": "#Sample_NB02Glc0",
"name": "NB02Glc0",
"factorValues": [
{
"@id": "#FactorValue/Time=0 hours",
"category": {
"@id": "#Factor/Factor [Time]",
"factorName": "Factor [Time]",
"factorType": {
"@id": "#UserTerm_Time",
"annotationValue": "Time"
}
},
"value": {
"@id": "#UserTerm_0_hours",
"annotationValue": "0 hours"
}
},
{
"@id": "#FactorValue/Media=NB with 3 mM glucose\t\t",
"category": {
"@id": "#Factor/Factor [Media]",
"factorName": "Factor [Media]",
"factorType": {
"@id": "#UserTerm_Media",
"annotationValue": "Media"
}
},
"value": {
"@id": "#UserTerm_NB_with_3_mM_glucose\t\t",
"annotationValue": "NB with 3 mM glucose\t\t"
}
}
]
},
{
"@id": "#Sample_NB02Glc2",
"name": "NB02Glc2",
"factorValues": [
{
"@id": "#FactorValue/Time=2 hours",
"category": {
"@id": "#Factor/Factor [Time]",
"factorName": "Factor [Time]",
"factorType": {
"@id": "#UserTerm_Time",
"annotationValue": "Time"
}
},
"value": {
"@id": "#UserTerm_2_hours",
"annotationValue": "2 hours"
}
},
{
"@id": "#FactorValue/Media=NB with 3 mM glucose\t\t",
"category": {
"@id": "#Factor/Factor [Media]",
"factorName": "Factor [Media]",
"factorType": {
"@id": "#UserTerm_Media",
"annotationValue": "Media"
}
},
"value": {
"@id": "#UserTerm_NB_with_3_mM_glucose\t\t",
"annotationValue": "NB with 3 mM glucose\t\t"
}
}
]
},
{
"@id": "#Sample_NB02Glc4",
"name": "NB02Glc4",
"factorValues": [
{
"@id": "#FactorValue/Time=4 hours",
"category": {
"@id": "#Factor/Factor [Time]",
"factorName": "Factor [Time]",
"factorType": {
"@id": "#UserTerm_Time",
"annotationValue": "Time"
}
},
"value": {
"@id": "#UserTerm_4_hours",
"annotationValue": "4 hours"
}
},
{
"@id": "#FactorValue/Media=NB with 3 mM glucose\t\t",
"category": {
"@id": "#Factor/Factor [Media]",
"factorName": "Factor [Media]",
"factorType": {
"@id": "#UserTerm_Media",
"annotationValue": "Media"
}
},
"value": {
"@id": "#UserTerm_NB_with_3_mM_glucose\t\t",
"annotationValue": "NB with 3 mM glucose\t\t"
}
}
]
},
{
"@id": "#Sample_NB02Glc6",
"name": "NB02Glc6",
"factorValues": [
{
"@id": "#FactorValue/Time=6 hours",
"category": {
"@id": "#Factor/Factor [Time]",
"factorName": "Factor [Time]",
"factorType": {
"@id": "#UserTerm_Time",
"annotationValue": "Time"
}
},
"value": {
"@id": "#UserTerm_6_hours",
"annotationValue": "6 hours"
}
},
{
"@id": "#FactorValue/Media=NB with 3 mM glucose\t\t",
"category": {
"@id": "#Factor/Factor [Media]",
"factorName": "Factor [Media]",
"factorType": {
"@id": "#UserTerm_Media",
"annotationValue": "Media"
}
},
"value": {
"@id": "#UserTerm_NB_with_3_mM_glucose\t\t",
"annotationValue": "NB with 3 mM glucose\t\t"
}
}
]
},
{
"@id": "#Sample_NB02Glc8",
"name": "NB02Glc8",
"factorValues": [
{
"@id": "#FactorValue/Time=8 hours",
"category": {
"@id": "#Factor/Factor [Time]",
"factorName": "Factor [Time]",
"factorType": {
"@id": "#UserTerm_Time",
"annotationValue": "Time"
}
},
"value": {
"@id": "#UserTerm_8_hours",
"annotationValue": "8 hours"
}
},
{
"@id": "#FactorValue/Media=NB with 3 mM glucose\t\t",
"category": {
"@id": "#Factor/Factor [Media]",
"factorName": "Factor [Media]",
"factorType": {
"@id": "#UserTerm_Media",
"annotationValue": "Media"
}
},
"value": {
"@id": "#UserTerm_NB_with_3_mM_glucose\t\t",
"annotationValue": "NB with 3 mM glucose\t\t"
}
}
]
}
]
},
{
"@id": "#Process_RNAseq_sample_cultivation_1",
"name": "RNAseq sample cultivation_1",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_Temperature",
"parameterName": {
"@id": "#UserTerm_Temperature",
"annotationValue": "Temperature"
}
},
"value": {
"@id": "#UserTerm_28\u00b0C",
"annotationValue": "28\u00b0C"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_Shaking",
"parameterName": {
"@id": "#UserTerm_Shaking",
"annotationValue": "Shaking"
}
},
"value": {
"@id": "#UserTerm_180_rpm",
"annotationValue": "180 rpm"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_OD600",
"parameterName": {
"@id": "#UserTerm_OD600",
"annotationValue": "OD600"
}
},
"value": {
"@id": "#UserTerm_OD600_Measurements_20231212.xlsx",
"annotationValue": "OD600 Measurements 20231212.xlsx"
}
}
],
"inputs": [
{
"@id": "#Sample_Xoo_wt",
"name": "Xoo wt"
},
{
"@id": "#Sample_Xoo_wt",
"name": "Xoo wt"
},
{
"@id": "#Sample_Xoo_wt",
"name": "Xoo wt"
}
],
"outputs": [
{
"@id": "#Sample_NB4",
"name": "NB4",
"factorValues": [
{
"@id": "#FactorValue/Time=4 hours",
"category": {
"@id": "#Factor/Factor [Time]",
"factorName": "Factor [Time]",
"factorType": {
"@id": "#UserTerm_Time",
"annotationValue": "Time"
}
},
"value": {
"@id": "#UserTerm_4_hours",
"annotationValue": "4 hours"
}
},
{
"@id": "#FactorValue/Media=NB",
"category": {
"@id": "#Factor/Factor [Media]",
"factorName": "Factor [Media]",
"factorType": {
"@id": "#UserTerm_Media",
"annotationValue": "Media"
}
},
"value": {
"@id": "#UserTerm_NB",
"annotationValue": "NB"
}
}
]
},
{
"@id": "#Sample_NB2Suc2",
"name": "NB2Suc2",
"factorValues": [
{
"@id": "#FactorValue/Time=2 hours",
"category": {
"@id": "#Factor/Factor [Time]",
"factorName": "Factor [Time]",
"factorType": {
"@id": "#UserTerm_Time",
"annotationValue": "Time"
}
},
"value": {
"@id": "#UserTerm_2_hours",
"annotationValue": "2 hours"
}
},
{
"@id": "#FactorValue/Media=NB with 30 mM sucrose",
"category": {
"@id": "#Factor/Factor [Media]",
"factorName": "Factor [Media]",
"factorType": {
"@id": "#UserTerm_Media",
"annotationValue": "Media"
}
},
"value": {
"@id": "#UserTerm_NB_with_30_mM_sucrose",
"annotationValue": "NB with 30 mM sucrose"
}
}
]
},
{
"@id": "#Sample_NB2Suc6",
"name": "NB2Suc6",
"factorValues": [
{
"@id": "#FactorValue/Time=6 hours",
"category": {
"@id": "#Factor/Factor [Time]",
"factorName": "Factor [Time]",
"factorType": {
"@id": "#UserTerm_Time",
"annotationValue": "Time"
}
},
"value": {
"@id": "#UserTerm_6_hours",
"annotationValue": "6 hours"
}
},
{
"@id": "#FactorValue/Media=NB with 30 mM sucrose",
"category": {
"@id": "#Factor/Factor [Media]",
"factorName": "Factor [Media]",
"factorType": {
"@id": "#UserTerm_Media",
"annotationValue": "Media"
}
},
"value": {
"@id": "#UserTerm_NB_with_30_mM_sucrose",
"annotationValue": "NB with 30 mM sucrose"
}
}
]
}
]
},
{
"@id": "#Process_RNAseq_RNA_extraction",
"name": "RNAseq RNA extraction",
"executesProtocol": {
"@id": "#Protocol_2024-02-01-RNAseq-of-PXO99A-in-NB-with-different-C-sources-I.pdf",
"name": "2024-02-01-RNAseq-of-PXO99A-in-NB-with-different-C-sources-I.pdf"
},
"inputs": [
{
"@id": "#Sample_NB0",
"name": "NB0"
},
{
"@id": "#Sample_NB2",
"name": "NB2"
},
{
"@id": "#Sample_NB4",
"name": "NB4"
},
{
"@id": "#Sample_NB6",
"name": "NB6"
},
{
"@id": "#Sample_NB8",
"name": "NB8"
},
{
"@id": "#Sample_NB02Glc2",
"name": "NB02Glc2"
},
{
"@id": "#Sample_NB02Glc4",
"name": "NB02Glc4"
},
{
"@id": "#Sample_NB02Glc6",
"name": "NB02Glc6"
},
{
"@id": "#Sample_NB2Glc2",
"name": "NB2Glc2"
},
{
"@id": "#Sample_NB2Glc4",
"name": "NB2Glc4"
},
{
"@id": "#Sample_NB2Glc6",
"name": "NB2Glc6"
},
{
"@id": "#Sample_NB2Suc2",
"name": "NB2Suc2"
},
{
"@id": "#Sample_NB2Suc4",
"name": "NB2Suc4"
},
{
"@id": "#Sample_NB2Suc6",
"name": "NB2Suc6"
},
{
"@id": "#Sample_NB2Suc8",
"name": "NB2Suc8"
}
],
"outputs": [
{
"@id": "#Sample_RNA_NB0",
"name": "RNA NB0"
},
{
"@id": "#Sample_RNA_NB2",
"name": "RNA NB2"
},
{
"@id": "#Sample_RNA_NB4",
"name": "RNA NB4"
},
{
"@id": "#Sample_RNA_NB6",
"name": "RNA NB6"
},
{
"@id": "#Sample_RNA_NB8",
"name": "RNA NB8"
},
{
"@id": "#Sample_RNA_NB02Glc2",
"name": "RNA NB02Glc2"
},
{
"@id": "#Sample_RNA_NB02Glc4",
"name": "RNA NB02Glc4"
},
{
"@id": "#Sample_RNA_NB02Glc6",
"name": "RNA NB02Glc6"
},
{
"@id": "#Sample_RNA_NB2Glc2",
"name": "RNA NB2Glc2"
},
{
"@id": "#Sample_RNA_NB2Glc4",
"name": "RNA NB2Glc4"
},
{
"@id": "#Sample_RNA_NB2Glc6",
"name": "RNA NB2Glc6"
},
{
"@id": "#Sample_RNA_NB2Suc2",
"name": "RNA NB2Suc2"
},
{
"@id": "#Sample_RNA_NB2Suc4",
"name": "RNA NB2Suc4"
},
{
"@id": "#Sample_RNA_NB2Suc6",
"name": "RNA NB2Suc6"
},
{
"@id": "#Sample_RNA_NB2Suc8",
"name": "RNA NB2Suc8"
}
]
},
{
"@id": "#Process_RNAseq_analysis",
"name": "RNAseq analysis",
"executesProtocol": {
"@id": "#Protocol_Methods_prokaryote-seq.pdf",
"name": "Methods_prokaryote-seq.pdf",
"protocolType": {
"@id": "https://bioregistry.io/EFO:0008896",
"annotationValue": "RNA-Seq",
"termSource": "EFO",
"termAccession": "https://bioregistry.io/EFO:0008896"
},
"parameters": [
{
"@id": "#ProtocolParameter/DPBO:0000062",
"parameterName": {
"@id": "DPBO:0000062",
"annotationValue": "RNA quality check",
"termSource": "DPBO",
"termAccession": "DPBO:0000062"
}
},
{
"@id": "#ProtocolParameter/OBI:0001177",
"parameterName": {
"@id": "OBI:0001177",
"annotationValue": "RNA sequencing assay",
"termSource": "OBI",
"termAccession": "OBI:0001177"
}
}
]
},
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000062",
"parameterName": {
"@id": "DPBO:0000062",
"annotationValue": "RNA quality check",
"termSource": "DPBO",
"termAccession": "DPBO:0000062"
}
},
"value": {
"@id": "https://bioregistry.io/NCIT:C183239",
"annotationValue": "Qubit Assay",
"termSource": "NCIT",
"termAccession": "https://bioregistry.io/NCIT:C183239"
}
},
{
"category": {
"@id": "#ProtocolParameter/OBI:0001177",
"parameterName": {
"@id": "OBI:0001177",
"annotationValue": "RNA sequencing assay",
"termSource": "OBI",
"termAccession": "OBI:0001177"
}
},
"value": {
"@id": "#UserTerm_Illumina",
"annotationValue": "Illumina"
}
}
],
"inputs": [
{
"@id": "#Source_RNA_NB0",
"name": "RNA NB0"
},
{
"@id": "#Source_RNA_NB2",
"name": "RNA NB2"
},
{
"@id": "#Source_RNA_NB2",
"name": "RNA NB2"
},
{
"@id": "#Source_RNA_NB8",
"name": "RNA NB8"
},
{
"@id": "#Source_RNA_NB8",
"name": "RNA NB8"
},
{
"@id": "#Source_RNA_NB6",
"name": "RNA NB6"
},
{
"@id": "#Source_RNA_NB6",
"name": "RNA NB6"
},
{
"@id": "#Source_RNA_NB4",
"name": "RNA NB4"
},
{
"@id": "#Source_RNA_NB4",
"name": "RNA NB4"
},
{
"@id": "#Source_RNA_NB2Glc6",
"name": "RNA NB2Glc6"
},
{
"@id": "#Source_RNA_NB2Glc6",
"name": "RNA NB2Glc6"
},
{
"@id": "#Source_RNA_NB2Glc4",
"name": "RNA NB2Glc4"
},
{
"@id": "#Source_RNA_NB2Glc6",
"name": "RNA NB2Glc6"
},
{
"@id": "#Source_RNA_NB2Glc2",
"name": "RNA NB2Glc2"
},
{
"@id": "#Source_RNA_NB2Glc2",
"name": "RNA NB2Glc2"
},
{
"@id": "#Source_RNA_NB1Suc8",
"name": "RNA NB1Suc8"
},
{
"@id": "#Source_RNA_NB1Suc8",
"name": "RNA NB1Suc8"
},
{
"@id": "#Source_RNA_NB1Suc6",
"name": "RNA NB1Suc6"
},
{
"@id": "#Source_RNA_NB1Suc6",
"name": "RNA NB1Suc6"
},
{
"@id": "#Source_RNA_NB1Suc4",
"name": "RNA NB1Suc4"
},
{
"@id": "#Source_RNA_NB1Suc4",
"name": "RNA NB1Suc4"
},
{
"@id": "#Source_RNA_NB1Suc2",
"name": "RNA NB1Suc2"
},
{
"@id": "#Source_RNA_NB1Suc2",
"name": "RNA NB1Suc2"
},
{
"@id": "#Source_RNA_NB02Glc6",
"name": "RNA NB02Glc6"
},
{
"@id": "#Source_RNA_NB02Glc6",
"name": "RNA NB02Glc6"
},
{
"@id": "#Source_RNA_NB02Glc4",
"name": "RNA NB02Glc4"
},
{
"@id": "#Source_RNA_NB02Glc4",
"name": "RNA NB02Glc4"
},
{
"@id": "#Source_RNA_NB02Glc2",
"name": "RNA NB02Glc2"
},
{
"@id": "#Source_RNA_NB02Glc2",
"name": "RNA NB02Glc2"
},
{
"@id": "#Source_RNA_NB0",
"name": "RNA NB0"
}
],
"outputs": [
{
"@id": "assays/RNAseq_Xoo_15012024/dataset/raw_data/NB0_2.fq.gz",
"name": "assays/RNAseq_Xoo_15012024/dataset/raw_data/NB0_2.fq.gz",
"type": "Raw Data File"
},
{
"@id": "assays/RNAseq_Xoo_15012024/dataset/raw_data/NB2_1.fq.gz",
"name": "assays/RNAseq_Xoo_15012024/dataset/raw_data/NB2_1.fq.gz",
"type": "Raw Data File"
},
{
"@id": "assays/RNAseq_Xoo_15012024/dataset/raw_data/NB2_2.fq.gz",
"name": "assays/RNAseq_Xoo_15012024/dataset/raw_data/NB2_2.fq.gz",
"type": "Raw Data File"
},
{
"@id": "assays/RNAseq_Xoo_15012024/dataset/raw_data/NB8_1.fq.gz",
"name": "assays/RNAseq_Xoo_15012024/dataset/raw_data/NB8_1.fq.gz",
"type": "Raw Data File"
},
{
"@id": "assays/RNAseq_Xoo_15012024/dataset/raw_data/NB8_2.fq.gz",
"name": "assays/RNAseq_Xoo_15012024/dataset/raw_data/NB8_2.fq.gz",
"type": "Raw Data File"
},
{
"@id": "assays/RNAseq_Xoo_15012024/dataset/raw_data/NB6_1.fq.gz",
"name": "assays/RNAseq_Xoo_15012024/dataset/raw_data/NB6_1.fq.gz",
"type": "Raw Data File"
},
{
"@id": "assays/RNAseq_Xoo_15012024/dataset/raw_data/NB6_2.fq.gz",
"name": "assays/RNAseq_Xoo_15012024/dataset/raw_data/NB6_2.fq.gz",
"type": "Raw Data File"
},
{
"@id": "assays/RNAseq_Xoo_15012024/dataset/raw_data/NB4_2.fq.gz",
"name": "assays/RNAseq_Xoo_15012024/dataset/raw_data/NB4_2.fq.gz",
"type": "Raw Data File"
},
{
"@id": "assays/RNAseq_Xoo_15012024/dataset/raw_data/NB4_1.fq.gz",
"name": "assays/RNAseq_Xoo_15012024/dataset/raw_data/NB4_1.fq.gz",
"type": "Raw Data File"
},
{
"@id": "assays/RNAseq_Xoo_15012024/dataset/raw_data/NB2Glc6_1.fq.gz",
"name": "assays/RNAseq_Xoo_15012024/dataset/raw_data/NB2Glc6_1.fq.gz",
"type": "Raw Data File"
},
{
"@id": "assays/RNAseq_Xoo_15012024/dataset/raw_data/NB2Glc6_2.fq.gz",
"name": "assays/RNAseq_Xoo_15012024/dataset/raw_data/NB2Glc6_2.fq.gz",
"type": "Raw Data File"
},
{
"@id": "assays/RNAseq_Xoo_15012024/dataset/raw_data/NB2Glc4_1.fq.gz",
"name": "assays/RNAseq_Xoo_15012024/dataset/raw_data/NB2Glc4_1.fq.gz",
"type": "Raw Data File"
},
{
"@id": "assays/RNAseq_Xoo_15012024/dataset/raw_data/NB2Glc4_2.fq.gz",
"name": "assays/RNAseq_Xoo_15012024/dataset/raw_data/NB2Glc4_2.fq.gz",
"type": "Raw Data File"
},
{
"@id": "assays/RNAseq_Xoo_15012024/dataset/raw_data/NB2Glc2_1.fq.gz",
"name": "assays/RNAseq_Xoo_15012024/dataset/raw_data/NB2Glc2_1.fq.gz",
"type": "Raw Data File"
},
{
"@id": "assays/RNAseq_Xoo_15012024/dataset/raw_data/NB2Glc2_2.fq.gz",
"name": "assays/RNAseq_Xoo_15012024/dataset/raw_data/NB2Glc2_2.fq.gz",
"type": "Raw Data File"
},
{
"@id": "assays/RNAseq_Xoo_15012024/dataset/raw_data/NB1Suc8_1.fq.gz",
"name": "assays/RNAseq_Xoo_15012024/dataset/raw_data/NB1Suc8_1.fq.gz",
"type": "Raw Data File"
},
{
"@id": "assays/RNAseq_Xoo_15012024/dataset/raw_data/NB1Suc8_2.fq.gz",
"name": "assays/RNAseq_Xoo_15012024/dataset/raw_data/NB1Suc8_2.fq.gz",
"type": "Raw Data File"
},
{
"@id": "assays/RNAseq_Xoo_15012024/dataset/raw_data/NB1Suc6_2.fq.gz",
"name": "assays/RNAseq_Xoo_15012024/dataset/raw_data/NB1Suc6_2.fq.gz",
"type": "Raw Data File"
},
{
"@id": "assays/RNAseq_Xoo_15012024/dataset/raw_data/NB1Suc6_1.fq.gz",
"name": "assays/RNAseq_Xoo_15012024/dataset/raw_data/NB1Suc6_1.fq.gz",
"type": "Raw Data File"
},
{
"@id": "assays/RNAseq_Xoo_15012024/dataset/raw_data/NB1Suc4_1.fq.gz",
"name": "assays/RNAseq_Xoo_15012024/dataset/raw_data/NB1Suc4_1.fq.gz",
"type": "Raw Data File"
},
{
"@id": "assays/RNAseq_Xoo_15012024/dataset/raw_data/NB1Suc4_2.fq.gz",
"name": "assays/RNAseq_Xoo_15012024/dataset/raw_data/NB1Suc4_2.fq.gz",
"type": "Raw Data File"
},
{
"@id": "assays/RNAseq_Xoo_15012024/dataset/raw_data/NB1Suc2_1.fq.gz",
"name": "assays/RNAseq_Xoo_15012024/dataset/raw_data/NB1Suc2_1.fq.gz",
"type": "Raw Data File"
},
{
"@id": "assays/RNAseq_Xoo_15012024/dataset/raw_data/NB1Suc2_2.fq.gz",
"name": "assays/RNAseq_Xoo_15012024/dataset/raw_data/NB1Suc2_2.fq.gz",
"type": "Raw Data File"
},
{
"@id": "assays/RNAseq_Xoo_15012024/dataset/raw_data/NB02Glc6_1.fq.gz",
"name": "assays/RNAseq_Xoo_15012024/dataset/raw_data/NB02Glc6_1.fq.gz",
"type": "Raw Data File"
},
{
"@id": "assays/RNAseq_Xoo_15012024/dataset/raw_data/NB02Glc6_2.fq.gz",
"name": "assays/RNAseq_Xoo_15012024/dataset/raw_data/NB02Glc6_2.fq.gz",
"type": "Raw Data File"
},
{
"@id": "assays/RNAseq_Xoo_15012024/dataset/raw_data/NB02Glc4_1.fq.gz",
"name": "assays/RNAseq_Xoo_15012024/dataset/raw_data/NB02Glc4_1.fq.gz",
"type": "Raw Data File"
},
{
"@id": "assays/RNAseq_Xoo_15012024/dataset/raw_data/NB02Glc4_2.fq.gz",
"name": "assays/RNAseq_Xoo_15012024/dataset/raw_data/NB02Glc4_2.fq.gz",
"type": "Raw Data File"
},
{
"@id": "assays/RNAseq_Xoo_15012024/dataset/raw_data/NB02Glc2_1.fq.gz",
"name": "assays/RNAseq_Xoo_15012024/dataset/raw_data/NB02Glc2_1.fq.gz",
"type": "Raw Data File"
},
{
"@id": "assays/RNAseq_Xoo_15012024/dataset/raw_data/NB02Glc2_2.fq.gz",
"name": "assays/RNAseq_Xoo_15012024/dataset/raw_data/NB02Glc2_2.fq.gz",
"type": "Raw Data File"
},
{
"@id": "assays/RNAseq_Xoo_15012024/dataset/raw_data/NB0_1.fq.gz",
"name": "assays/RNAseq_Xoo_15012024/dataset/raw_data/NB0_1.fq.gz",
"type": "Raw Data File"
}
]
},
{
"@id": "#Process_RNAseq_gene_expression",
"name": "RNAseq gene expression",
"executesProtocol": {
"@id": "#Protocol_Methods_prokaryote-seq.pdf",
"name": "Methods_prokaryote-seq.pdf",
"parameters": [
{
"@id": "#ProtocolParameter/DPBO:0000062",
"parameterName": {
"@id": "DPBO:0000062",
"annotationValue": "RNA quality check",
"termSource": "DPBO",
"termAccession": "DPBO:0000062"
}
},
{
"@id": "#ProtocolParameter/#UserTerm_RNA_read_alignment",
"parameterName": {
"@id": "#UserTerm_RNA_read_alignment",
"annotationValue": "RNA read alignment"
}
},
{
"@id": "#ProtocolParameter/#UserTerm_Gene_count",
"parameterName": {
"@id": "#UserTerm_Gene_count",
"annotationValue": "Gene count"
}
}
]
},
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000062",
"parameterName": {
"@id": "DPBO:0000062",
"annotationValue": "RNA quality check",
"termSource": "DPBO",
"termAccession": "DPBO:0000062"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/EDAM_1930",
"annotationValue": "FASTQ",
"termSource": "EDAM",
"termAccession": "http://purl.obolibrary.org/obo/EDAM_1930"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_RNA_read_alignment",
"parameterName": {
"@id": "#UserTerm_RNA_read_alignment",
"annotationValue": "RNA read alignment"
}
},
"value": {
"@id": "#UserTerm_Bowtie2",
"annotationValue": "Bowtie2"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_Gene_count",
"parameterName": {
"@id": "#UserTerm_Gene_count",
"annotationValue": "Gene count"
}
},
"value": {
"@id": "#UserTerm_FeatureCounts",
"annotationValue": "FeatureCounts"
}
}
],
"inputs": [
{
"@id": "assays/RNAseq_Xoo_15012024/dataset/raw_data/NB2_1.fq.gz",
"name": "assays/RNAseq_Xoo_15012024/dataset/raw_data/NB2_1.fq.gz",
"type": "Raw Data File"
},
{
"@id": "assays/RNAseq_Xoo_15012024/dataset/raw_data/NB2_2.fq.gz",
"name": "assays/RNAseq_Xoo_15012024/dataset/raw_data/NB2_2.fq.gz",
"type": "Raw Data File"
},
{
"@id": "assays/RNAseq_Xoo_15012024/dataset/raw_data/NB8_1.fq.gz",
"name": "assays/RNAseq_Xoo_15012024/dataset/raw_data/NB8_1.fq.gz",
"type": "Raw Data File"
},
{
"@id": "assays/RNAseq_Xoo_15012024/dataset/raw_data/NB8_2.fq.gz",
"name": "assays/RNAseq_Xoo_15012024/dataset/raw_data/NB8_2.fq.gz",
"type": "Raw Data File"
},
{
"@id": "assays/RNAseq_Xoo_15012024/dataset/raw_data/NB6_1.fq.gz",
"name": "assays/RNAseq_Xoo_15012024/dataset/raw_data/NB6_1.fq.gz",
"type": "Raw Data File"
},
{
"@id": "assays/RNAseq_Xoo_15012024/dataset/raw_data/NB6_2.fq.gz",
"name": "assays/RNAseq_Xoo_15012024/dataset/raw_data/NB6_2.fq.gz",
"type": "Raw Data File"
},
{
"@id": "assays/RNAseq_Xoo_15012024/dataset/raw_data/NB0_2.fq.gz",
"name": "assays/RNAseq_Xoo_15012024/dataset/raw_data/NB0_2.fq.gz",
"type": "Raw Data File"
},
{
"@id": "assays/RNAseq_Xoo_15012024/dataset/raw_data/NB4_1.fq.gz",
"name": "assays/RNAseq_Xoo_15012024/dataset/raw_data/NB4_1.fq.gz",
"type": "Raw Data File"
},
{
"@id": "assays/RNAseq_Xoo_15012024/dataset/raw_data/NB4_2.fq.gz",
"name": "assays/RNAseq_Xoo_15012024/dataset/raw_data/NB4_2.fq.gz",
"type": "Raw Data File"
},
{
"@id": "assays/RNAseq_Xoo_15012024/dataset/raw_data/NB2Glc6_1.fq.gz",
"name": "assays/RNAseq_Xoo_15012024/dataset/raw_data/NB2Glc6_1.fq.gz",
"type": "Raw Data File"
},
{
"@id": "assays/RNAseq_Xoo_15012024/dataset/raw_data/NB2Glc6_2.fq.gz",
"name": "assays/RNAseq_Xoo_15012024/dataset/raw_data/NB2Glc6_2.fq.gz",
"type": "Raw Data File"
},
{
"@id": "assays/RNAseq_Xoo_15012024/dataset/raw_data/NB2Glc4_1.fq.gz",
"name": "assays/RNAseq_Xoo_15012024/dataset/raw_data/NB2Glc4_1.fq.gz",
"type": "Raw Data File"
},
{
"@id": "assays/RNAseq_Xoo_15012024/dataset/raw_data/NB2Glc4_2.fq.gz",
"name": "assays/RNAseq_Xoo_15012024/dataset/raw_data/NB2Glc4_2.fq.gz",
"type": "Raw Data File"
},
{
"@id": "assays/RNAseq_Xoo_15012024/dataset/raw_data/NB2Glc2_1.fq.gz",
"name": "assays/RNAseq_Xoo_15012024/dataset/raw_data/NB2Glc2_1.fq.gz",
"type": "Raw Data File"
},
{
"@id": "assays/RNAseq_Xoo_15012024/dataset/raw_data/NB2Glc2_2.fq.gz",
"name": "assays/RNAseq_Xoo_15012024/dataset/raw_data/NB2Glc2_2.fq.gz",
"type": "Raw Data File"
},
{
"@id": "assays/RNAseq_Xoo_15012024/dataset/raw_data/NB1Suc8_1.fq.gz",
"name": "assays/RNAseq_Xoo_15012024/dataset/raw_data/NB1Suc8_1.fq.gz",
"type": "Raw Data File"
},
{
"@id": "assays/RNAseq_Xoo_15012024/dataset/raw_data/NB1Suc8_2.fq.gz",
"name": "assays/RNAseq_Xoo_15012024/dataset/raw_data/NB1Suc8_2.fq.gz",
"type": "Raw Data File"
},
{
"@id": "assays/RNAseq_Xoo_15012024/dataset/raw_data/NB1Suc6_2.fq.gz",
"name": "assays/RNAseq_Xoo_15012024/dataset/raw_data/NB1Suc6_2.fq.gz",
"type": "Raw Data File"
},
{
"@id": "assays/RNAseq_Xoo_15012024/dataset/raw_data/NB1Suc6_1.fq.gz",
"name": "assays/RNAseq_Xoo_15012024/dataset/raw_data/NB1Suc6_1.fq.gz",
"type": "Raw Data File"
},
{
"@id": "assays/RNAseq_Xoo_15012024/dataset/raw_data/NB1Suc4_1.fq.gz",
"name": "assays/RNAseq_Xoo_15012024/dataset/raw_data/NB1Suc4_1.fq.gz",
"type": "Raw Data File"
},
{
"@id": "assays/RNAseq_Xoo_15012024/dataset/raw_data/NB1Suc4_2.fq.gz",
"name": "assays/RNAseq_Xoo_15012024/dataset/raw_data/NB1Suc4_2.fq.gz",
"type": "Raw Data File"
},
{
"@id": "assays/RNAseq_Xoo_15012024/dataset/raw_data/NB1Suc2_1.fq.gz",
"name": "assays/RNAseq_Xoo_15012024/dataset/raw_data/NB1Suc2_1.fq.gz",
"type": "Raw Data File"
},
{
"@id": "assays/RNAseq_Xoo_15012024/dataset/raw_data/NB1Suc2_2.fq.gz",
"name": "assays/RNAseq_Xoo_15012024/dataset/raw_data/NB1Suc2_2.fq.gz",
"type": "Raw Data File"
},
{
"@id": "assays/RNAseq_Xoo_15012024/dataset/raw_data/NB02Glc6_1.fq.gz",
"name": "assays/RNAseq_Xoo_15012024/dataset/raw_data/NB02Glc6_1.fq.gz",
"type": "Raw Data File"
},
{
"@id": "assays/RNAseq_Xoo_15012024/dataset/raw_data/NB02Glc6_2.fq.gz",
"name": "assays/RNAseq_Xoo_15012024/dataset/raw_data/NB02Glc6_2.fq.gz",
"type": "Raw Data File"
},
{
"@id": "assays/RNAseq_Xoo_15012024/dataset/raw_data/NB02Glc4_1.fq.gz",
"name": "assays/RNAseq_Xoo_15012024/dataset/raw_data/NB02Glc4_1.fq.gz",
"type": "Raw Data File"
},
{
"@id": "assays/RNAseq_Xoo_15012024/dataset/raw_data/NB02Glc4_2.fq.gz",
"name": "assays/RNAseq_Xoo_15012024/dataset/raw_data/NB02Glc4_2.fq.gz",
"type": "Raw Data File"
},
{
"@id": "assays/RNAseq_Xoo_15012024/dataset/raw_data/NB02Glc2_1.fq.gz",
"name": "assays/RNAseq_Xoo_15012024/dataset/raw_data/NB02Glc2_1.fq.gz",
"type": "Raw Data File"
},
{
"@id": "assays/RNAseq_Xoo_15012024/dataset/raw_data/NB02Glc2_2.fq.gz",
"name": "assays/RNAseq_Xoo_15012024/dataset/raw_data/NB02Glc2_2.fq.gz",
"type": "Raw Data File"
},
{
"@id": "assays/RNAseq_Xoo_15012024/dataset/",
"name": "assays/RNAseq_Xoo_15012024/dataset/",
"type": "Raw Data File"
}
],
"outputs": [
{
"@id": "assays/RNAseq_Xoo_15012024/dataset/read_counts/1.count/gene_count.xls",
"name": "assays/RNAseq_Xoo_15012024/dataset/read_counts/1.count/gene_count.xls",
"type": "Raw Data File"
},
{
"@id": "assays/RNAseq_Xoo_15012024/dataset/read_counts/1.count/gene_count.xls",
"name": "assays/RNAseq_Xoo_15012024/dataset/read_counts/1.count/gene_count.xls",
"type": "Raw Data File"
},
{
"@id": "assays/RNAseq_Xoo_15012024/dataset/read_counts/1.count/gene_count.xls",
"name": "assays/RNAseq_Xoo_15012024/dataset/read_counts/1.count/gene_count.xls",
"type": "Raw Data File"
},
{
"@id": "assays/RNAseq_Xoo_15012024/dataset/read_counts/1.count/gene_count.xls",
"name": "assays/RNAseq_Xoo_15012024/dataset/read_counts/1.count/gene_count.xls",
"type": "Raw Data File"
},
{
"@id": "assays/RNAseq_Xoo_15012024/dataset/read_counts/1.count/gene_count.xls",
"name": "assays/RNAseq_Xoo_15012024/dataset/read_counts/1.count/gene_count.xls",
"type": "Raw Data File"
},
{
"@id": "assays/RNAseq_Xoo_15012024/dataset/read_counts/1.count/gene_count.xls",
"name": "assays/RNAseq_Xoo_15012024/dataset/read_counts/1.count/gene_count.xls",
"type": "Raw Data File"
},
{
"@id": "assays/RNAseq_Xoo_15012024/dataset/read_counts/1.count/gene_count.xls",
"name": "assays/RNAseq_Xoo_15012024/dataset/read_counts/1.count/gene_count.xls",
"type": "Raw Data File"
},
{
"@id": "assays/RNAseq_Xoo_15012024/dataset/read_counts/1.count/gene_count.xls",
"name": "assays/RNAseq_Xoo_15012024/dataset/read_counts/1.count/gene_count.xls",
"type": "Raw Data File"
},
{
"@id": "assays/RNAseq_Xoo_15012024/dataset/read_counts/1.count/gene_count.xls",
"name": "assays/RNAseq_Xoo_15012024/dataset/read_counts/1.count/gene_count.xls",
"type": "Raw Data File"
},
{
"@id": "assays/RNAseq_Xoo_15012024/dataset/read_counts/1.count/gene_count.xls",
"name": "assays/RNAseq_Xoo_15012024/dataset/read_counts/1.count/gene_count.xls",
"type": "Raw Data File"
},
{
"@id": "assays/RNAseq_Xoo_15012024/dataset/read_counts/1.count/gene_count.xls",
"name": "assays/RNAseq_Xoo_15012024/dataset/read_counts/1.count/gene_count.xls",
"type": "Raw Data File"
},
{
"@id": "assays/RNAseq_Xoo_15012024/dataset/read_counts/1.count/gene_count.xls",
"name": "assays/RNAseq_Xoo_15012024/dataset/read_counts/1.count/gene_count.xls",
"type": "Raw Data File"
},
{
"@id": "assays/RNAseq_Xoo_15012024/dataset/read_counts/1.count/gene_count.xls",
"name": "assays/RNAseq_Xoo_15012024/dataset/read_counts/1.count/gene_count.xls",
"type": "Raw Data File"
},
{
"@id": "assays/RNAseq_Xoo_15012024/dataset/read_counts/1.count/gene_count.xls",
"name": "assays/RNAseq_Xoo_15012024/dataset/read_counts/1.count/gene_count.xls",
"type": "Raw Data File"
},
{
"@id": "assays/RNAseq_Xoo_15012024/dataset/read_counts/1.count/gene_count.xls",
"name": "assays/RNAseq_Xoo_15012024/dataset/read_counts/1.count/gene_count.xls",
"type": "Raw Data File"
},
{
"@id": "assays/RNAseq_Xoo_15012024/dataset/read_counts/1.count/gene_count.xls",
"name": "assays/RNAseq_Xoo_15012024/dataset/read_counts/1.count/gene_count.xls",
"type": "Raw Data File"
},
{
"@id": "assays/RNAseq_Xoo_15012024/dataset/read_counts/1.count/gene_count.xls",
"name": "assays/RNAseq_Xoo_15012024/dataset/read_counts/1.count/gene_count.xls",
"type": "Raw Data File"
},
{
"@id": "assays/RNAseq_Xoo_15012024/dataset/read_counts/1.count/gene_count.xls",
"name": "assays/RNAseq_Xoo_15012024/dataset/read_counts/1.count/gene_count.xls",
"type": "Raw Data File"
},
{
"@id": "assays/RNAseq_Xoo_15012024/dataset/read_counts/1.count/gene_count.xls",
"name": "assays/RNAseq_Xoo_15012024/dataset/read_counts/1.count/gene_count.xls",
"type": "Raw Data File"
},
{
"@id": "assays/RNAseq_Xoo_15012024/dataset/read_counts/1.count/gene_count.xls",
"name": "assays/RNAseq_Xoo_15012024/dataset/read_counts/1.count/gene_count.xls",
"type": "Raw Data File"
},
{
"@id": "assays/RNAseq_Xoo_15012024/dataset/read_counts/1.count/gene_count.xls",
"name": "assays/RNAseq_Xoo_15012024/dataset/read_counts/1.count/gene_count.xls",
"type": "Raw Data File"
},
{
"@id": "assays/RNAseq_Xoo_15012024/dataset/read_counts/1.count/gene_count.xls",
"name": "assays/RNAseq_Xoo_15012024/dataset/read_counts/1.count/gene_count.xls",
"type": "Raw Data File"
},
{
"@id": "assays/RNAseq_Xoo_15012024/dataset/read_counts/1.count/gene_count.xls",
"name": "assays/RNAseq_Xoo_15012024/dataset/read_counts/1.count/gene_count.xls",
"type": "Raw Data File"
},
{
"@id": "assays/RNAseq_Xoo_15012024/dataset/read_counts/1.count/gene_count.xls",
"name": "assays/RNAseq_Xoo_15012024/dataset/read_counts/1.count/gene_count.xls",
"type": "Raw Data File"
},
{
"@id": "assays/RNAseq_Xoo_15012024/dataset/read_counts/1.count/gene_count.xls",
"name": "assays/RNAseq_Xoo_15012024/dataset/read_counts/1.count/gene_count.xls",
"type": "Raw Data File"
},
{
"@id": "assays/RNAseq_Xoo_15012024/dataset/read_counts/1.count/gene_count.xls",
"name": "assays/RNAseq_Xoo_15012024/dataset/read_counts/1.count/gene_count.xls",
"type": "Raw Data File"
},
{
"@id": "assays/RNAseq_Xoo_15012024/dataset/read_counts/1.count/gene_count.xls",
"name": "assays/RNAseq_Xoo_15012024/dataset/read_counts/1.count/gene_count.xls",
"type": "Raw Data File"
},
{
"@id": "assays/RNAseq_Xoo_15012024/dataset/read_counts/1.count/gene_count.xls",
"name": "assays/RNAseq_Xoo_15012024/dataset/read_counts/1.count/gene_count.xls",
"type": "Raw Data File"
},
{
"@id": "assays/RNAseq_Xoo_15012024/dataset/read_counts/1.count/gene_count.xls",
"name": "assays/RNAseq_Xoo_15012024/dataset/read_counts/1.count/gene_count.xls",
"type": "Raw Data File"
},
{
"@id": "assays/RNAseq_Xoo_15012024/dataset/read_counts/1.count/gene_count.xls",
"name": "assays/RNAseq_Xoo_15012024/dataset/read_counts/1.count/gene_count.xls",
"type": "Raw Data File"
}
]
}
]
},
{
"filename": "assays/Clipping/isa.assay.xlsx",
"@id": "assays/Clipping/",
"measurementType": {
"@id": "https://bioregistry.io/NCIT:C3824",
"annotationValue": "Lesion",
"termSource": "NCIT",
"termAccession": "https://bioregistry.io/NCIT:C3824"
},
"technologyPlatform": "Ruler (NCIT:C138178)",
"dataFiles": [
{
"@id": "assays/Clipping/dataset/Inoculation_data_IR24.xlsx",
"name": "assays/Clipping/dataset/Inoculation data_IR24.xlsx",
"type": "Raw Data File"
},
{
"@id": "assays/Clipping/dataset/Inoculation_data_Kitaake.xlsx",
"name": "assays/Clipping/dataset/Inoculation data_Kitaake.xlsx",
"type": "Raw Data File"
},
{
"@id": "assays/Clipping/dataset/sucrose_gene_on_Nip_V2.xlsx",
"name": "assays/Clipping/dataset/sucrose gene on Nip_V2.xlsx",
"type": "Raw Data File"
}
],
"materials": {
"samples": [
{
"@id": "#Sample_Oryza_sativa_IR24",
"name": "Oryza sativa IR24",
"characteristics": [
{
"@id": "#MaterialAttributeValue/organism=Oryza sativa",
"category": {
"@id": "#MaterialAttribute/OBI:0100026",
"characteristicType": {
"@id": "OBI:0100026",
"annotationValue": "organism",
"termSource": "OBI",
"termAccession": "OBI:0100026"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/C_5438",
"annotationValue": "Oryza sativa",
"termSource": "C",
"termAccession": "http://purl.obolibrary.org/obo/C_5438"
}
},
{
"@id": "#EmptyMaterialAttributeValue",
"category": {
"@id": "#MaterialAttribute/MCO:0000059",
"characteristicType": {
"@id": "MCO:0000059",
"annotationValue": "OD600",
"termSource": "MCO",
"termAccession": "MCO:0000059"
}
}
}
]
},
{
"@id": "#Sample_Xoo_wt",
"name": "Xoo wt",
"characteristics": [
{
"@id": "#MaterialAttributeValue/organism=Xanthomonas oryzae pv. oryzae PXO99A",
"category": {
"@id": "#MaterialAttribute/OBI:0100026",
"characteristicType": {
"@id": "OBI:0100026",
"annotationValue": "organism",
"termSource": "OBI",
"termAccession": "OBI:0100026"
}
},
"value": {
"@id": "#UserTerm_Xanthomonas_oryzae_pv._oryzae_PXO99A",
"annotationValue": "Xanthomonas oryzae pv. oryzae PXO99A"
}
},
{
"@id": "#MaterialAttributeValue/OD600=0,5",
"category": {
"@id": "#MaterialAttribute/MCO:0000059",
"characteristicType": {
"@id": "MCO:0000059",
"annotationValue": "OD600",
"termSource": "MCO",
"termAccession": "MCO:0000059"
}
},
"value": {
"@id": "#UserTerm_0,5",
"annotationValue": "0,5"
}
}
]
},
{
"@id": "#Sample_\u2206sux",
"name": "\u2206sux",
"characteristics": [
{
"@id": "#MaterialAttributeValue/organism=Xanthomonas oryzae pv. oryzae PXO99A",
"category": {
"@id": "#MaterialAttribute/OBI:0100026",
"characteristicType": {
"@id": "OBI:0100026",
"annotationValue": "organism",
"termSource": "OBI",
"termAccession": "OBI:0100026"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/NCBITAXON_360094",
"annotationValue": "Xanthomonas oryzae pv. oryzae PXO99A",
"termSource": "NCBITAXON",
"termAccession": "http://purl.obolibrary.org/obo/NCBITAXON_360094"
}
},
{
"@id": "#MaterialAttributeValue/OD600=0,5",
"category": {
"@id": "#MaterialAttribute/MCO:0000059",
"characteristicType": {
"@id": "MCO:0000059",
"annotationValue": "OD600",
"termSource": "MCO",
"termAccession": "MCO:0000059"
}
},
"value": {
"@id": "#UserTerm_0,5",
"annotationValue": "0,5"
}
}
]
},
{
"@id": "#Sample_\u2206suxC",
"name": "\u2206suxC",
"characteristics": [
{
"@id": "#MaterialAttributeValue/organism=Xanthomonas oryzae pv. oryzae PXO99A",
"category": {
"@id": "#MaterialAttribute/OBI:0100026",
"characteristicType": {
"@id": "OBI:0100026",
"annotationValue": "organism",
"termSource": "OBI",
"termAccession": "OBI:0100026"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/NCBITAXON_360094",
"annotationValue": "Xanthomonas oryzae pv. oryzae PXO99A",
"termSource": "NCBITAXON",
"termAccession": "http://purl.obolibrary.org/obo/NCBITAXON_360094"
}
},
{
"@id": "#MaterialAttributeValue/OD600=0,5",
"category": {
"@id": "#MaterialAttribute/MCO:0000059",
"characteristicType": {
"@id": "MCO:0000059",
"annotationValue": "OD600",
"termSource": "MCO",
"termAccession": "MCO:0000059"
}
},
"value": {
"@id": "#UserTerm_0,5",
"annotationValue": "0,5"
}
}
]
},
{
"@id": "#Sample_\u2206suxA",
"name": "\u2206suxA",
"characteristics": [
{
"@id": "#MaterialAttributeValue/organism=Xanthomonas oryzae pv. oryzae PXO99A",
"category": {
"@id": "#MaterialAttribute/OBI:0100026",
"characteristicType": {
"@id": "OBI:0100026",
"annotationValue": "organism",
"termSource": "OBI",
"termAccession": "OBI:0100026"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/NCBITAXON_360094",
"annotationValue": "Xanthomonas oryzae pv. oryzae PXO99A",
"termSource": "NCBITAXON",
"termAccession": "http://purl.obolibrary.org/obo/NCBITAXON_360094"
}
},
{
"@id": "#MaterialAttributeValue/OD600=0,5",
"category": {
"@id": "#MaterialAttribute/MCO:0000059",
"characteristicType": {
"@id": "MCO:0000059",
"annotationValue": "OD600",
"termSource": "MCO",
"termAccession": "MCO:0000059"
}
},
"value": {
"@id": "#UserTerm_0,5",
"annotationValue": "0,5"
}
}
]
},
{
"@id": "#Sample_\u2206suxB",
"name": "\u2206suxB",
"characteristics": [
{
"@id": "#MaterialAttributeValue/organism=Xanthomonas oryzae pv. oryzae PXO99A",
"category": {
"@id": "#MaterialAttribute/OBI:0100026",
"characteristicType": {
"@id": "OBI:0100026",
"annotationValue": "organism",
"termSource": "OBI",
"termAccession": "OBI:0100026"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/NCBITAXON_360094",
"annotationValue": "Xanthomonas oryzae pv. oryzae PXO99A",
"termSource": "NCBITAXON",
"termAccession": "http://purl.obolibrary.org/obo/NCBITAXON_360094"
}
},
{
"@id": "#MaterialAttributeValue/OD600=0,5",
"category": {
"@id": "#MaterialAttribute/MCO:0000059",
"characteristicType": {
"@id": "MCO:0000059",
"annotationValue": "OD600",
"termSource": "MCO",
"termAccession": "MCO:0000059"
}
},
"value": {
"@id": "#UserTerm_0,5",
"annotationValue": "0,5"
}
}
]
},
{
"@id": "#Sample_Oryza_sativa_Kitaake\t\t",
"name": "Oryza sativa Kitaake\t\t",
"characteristics": [
{
"@id": "#MaterialAttributeValue/organism=Oryza sativa",
"category": {
"@id": "#MaterialAttribute/OBI:0100026",
"characteristicType": {
"@id": "OBI:0100026",
"annotationValue": "organism",
"termSource": "OBI",
"termAccession": "OBI:0100026"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/C_5438",
"annotationValue": "Oryza sativa",
"termSource": "C",
"termAccession": "http://purl.obolibrary.org/obo/C_5438"
}
},
{
"@id": "#EmptyMaterialAttributeValue",
"category": {
"@id": "#MaterialAttribute/MCO:0000059",
"characteristicType": {
"@id": "MCO:0000059",
"annotationValue": "OD600",
"termSource": "MCO",
"termAccession": "MCO:0000059"
}
}
}
]
},
{
"@id": "#Sample_Xoo_wt",
"name": "Xoo wt",
"characteristics": [
{
"@id": "#MaterialAttributeValue/organism=Xanthomonas oryzae pv. oryzae PXO99A",
"category": {
"@id": "#MaterialAttribute/OBI:0100026",
"characteristicType": {
"@id": "OBI:0100026",
"annotationValue": "organism",
"termSource": "OBI",
"termAccession": "OBI:0100026"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/NCBITAXON_360094",
"annotationValue": "Xanthomonas oryzae pv. oryzae PXO99A",
"termSource": "NCBITAXON",
"termAccession": "http://purl.obolibrary.org/obo/NCBITAXON_360094"
}
},
{
"@id": "#MaterialAttributeValue/OD600=0,5",
"category": {
"@id": "#MaterialAttribute/MCO:0000059",
"characteristicType": {
"@id": "MCO:0000059",
"annotationValue": "OD600",
"termSource": "MCO",
"termAccession": "MCO:0000059"
}
},
"value": {
"@id": "#UserTerm_0,5",
"annotationValue": "0,5"
}
}
]
},
{
"@id": "#Sample_Oryzae_sativa_Nipponbare",
"name": "Oryzae sativa Nipponbare",
"characteristics": [
{
"@id": "#MaterialAttributeValue/organism=Oryza sativa",
"category": {
"@id": "#MaterialAttribute/OBI:0100026",
"characteristicType": {
"@id": "OBI:0100026",
"annotationValue": "organism",
"termSource": "OBI",
"termAccession": "OBI:0100026"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/C_5438",
"annotationValue": "Oryza sativa",
"termSource": "C",
"termAccession": "http://purl.obolibrary.org/obo/C_5438"
}
},
{
"@id": "#EmptyMaterialAttributeValue",
"category": {
"@id": "#MaterialAttribute/MCO:0000059",
"characteristicType": {
"@id": "MCO:0000059",
"annotationValue": "OD600",
"termSource": "MCO",
"termAccession": "MCO:0000059"
}
}
}
]
},
{
"@id": "#Sample_\u2206suxC",
"name": "\u2206suxC",
"characteristics": [
{
"@id": "#MaterialAttributeValue/organism=Xanthomonas oryzae pv. oryzae exposure",
"category": {
"@id": "#MaterialAttribute/OBI:0100026",
"characteristicType": {
"@id": "OBI:0100026",
"annotationValue": "organism",
"termSource": "OBI",
"termAccession": "OBI:0100026"
}
},
"value": {
"@id": "https://bioregistry.io/PECO:0007257",
"annotationValue": "Xanthomonas oryzae pv. oryzae exposure",
"termSource": "PECO",
"termAccession": "https://bioregistry.io/PECO:0007257"
}
},
{
"@id": "#MaterialAttributeValue/OD600=0,5",
"category": {
"@id": "#MaterialAttribute/MCO:0000059",
"characteristicType": {
"@id": "MCO:0000059",
"annotationValue": "OD600",
"termSource": "MCO",
"termAccession": "MCO:0000059"
}
},
"value": {
"@id": "#UserTerm_0,5",
"annotationValue": "0,5"
}
}
]
},
{
"@id": "#Sample_Oryza_sativa_IR24_Xoo_wt",
"name": "Oryza sativa IR24_Xoo wt"
},
{
"@id": "#Sample_Oryza_sativa_IR24_\u2206sux",
"name": "Oryza sativa IR24_\u2206sux"
},
{
"@id": "#Sample_Oryza_sativa_IR24_\u2206suxC",
"name": "Oryza sativa IR24_\u2206suxC"
},
{
"@id": "#Sample_Oryza_sativa_IR24_\u2206suxA",
"name": "Oryza sativa IR24_\u2206suxA"
},
{
"@id": "#Sample_Oryza_sativa_IR24_\u2206suxB",
"name": "Oryza sativa IR24_\u2206suxB"
},
{
"@id": "#Sample_Oryza_sativa_Kitaake_Xoo_wt",
"name": "Oryza sativa Kitaake_Xoo wt"
},
{
"@id": "#Sample_Oryza_sativa_Kitaake_\u2206sux",
"name": "Oryza sativa Kitaake_\u2206sux"
},
{
"@id": "#Sample_Oryza_sativa_Kitaake_\u2206suxC",
"name": "Oryza sativa Kitaake_\u2206suxC"
},
{
"@id": "#Sample_Oryza_sativa_Kitaake_\u2206suxA",
"name": "Oryza sativa Kitaake_\u2206suxA"
},
{
"@id": "#Sample_Oryza_sativa_Kitaake_\u2206suxB",
"name": "Oryza sativa Kitaake_\u2206suxB"
},
{
"@id": "#Sample_Oryzae_sativa_Nipponbare_Xoo_wt",
"name": "Oryzae sativa Nipponbare_Xoo wt"
},
{
"@id": "#Sample_Oryzae_sativa_Nipponbare_\u2206sux",
"name": "Oryzae sativa Nipponbare_\u2206sux"
},
{
"@id": "#Sample_Oryzae_sativa_Nipponbare_\u2206suxC",
"name": "Oryzae sativa Nipponbare_\u2206suxC"
},
{
"@id": "#Sample_Oryzae_sativa_Nipponbare_\u2206suxA",
"name": "Oryzae sativa Nipponbare_\u2206suxA"
},
{
"@id": "#Sample_Oryzae_sativa_Nipponbare_\u2206suxB",
"name": "Oryzae sativa Nipponbare_\u2206suxB"
}
]
},
"characteristicCategories": [
{
"@id": "#MaterialAttribute/OBI:0100026",
"characteristicType": {
"@id": "OBI:0100026",
"annotationValue": "organism",
"termSource": "OBI",
"termAccession": "OBI:0100026"
}
},
{
"@id": "#MaterialAttribute/MCO:0000059",
"characteristicType": {
"@id": "MCO:0000059",
"annotationValue": "OD600",
"termSource": "MCO",
"termAccession": "MCO:0000059"
}
}
],
"processSequence": [
{
"@id": "#Process_Inoculation",
"name": "Inoculation",
"inputs": [
{
"@id": "#Sample_Oryza_sativa_IR24",
"name": "Oryza sativa IR24",
"characteristics": [
{
"@id": "#MaterialAttributeValue/organism=Oryza sativa",
"category": {
"@id": "#MaterialAttribute/OBI:0100026",
"characteristicType": {
"@id": "OBI:0100026",
"annotationValue": "organism",
"termSource": "OBI",
"termAccession": "OBI:0100026"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/C_5438",
"annotationValue": "Oryza sativa",
"termSource": "C",
"termAccession": "http://purl.obolibrary.org/obo/C_5438"
}
},
{
"@id": "#EmptyMaterialAttributeValue",
"category": {
"@id": "#MaterialAttribute/MCO:0000059",
"characteristicType": {
"@id": "MCO:0000059",
"annotationValue": "OD600",
"termSource": "MCO",
"termAccession": "MCO:0000059"
}
}
}
]
},
{
"@id": "#Sample_Xoo_wt",
"name": "Xoo wt",
"characteristics": [
{
"@id": "#MaterialAttributeValue/organism=Xanthomonas oryzae pv. oryzae PXO99A",
"category": {
"@id": "#MaterialAttribute/OBI:0100026",
"characteristicType": {
"@id": "OBI:0100026",
"annotationValue": "organism",
"termSource": "OBI",
"termAccession": "OBI:0100026"
}
},
"value": {
"@id": "#UserTerm_Xanthomonas_oryzae_pv._oryzae_PXO99A",
"annotationValue": "Xanthomonas oryzae pv. oryzae PXO99A"
}
},
{
"@id": "#MaterialAttributeValue/OD600=0,5",
"category": {
"@id": "#MaterialAttribute/MCO:0000059",
"characteristicType": {
"@id": "MCO:0000059",
"annotationValue": "OD600",
"termSource": "MCO",
"termAccession": "MCO:0000059"
}
},
"value": {
"@id": "#UserTerm_0,5",
"annotationValue": "0,5"
}
}
]
},
{
"@id": "#Sample_Oryza_sativa_IR24",
"name": "Oryza sativa IR24",
"characteristics": [
{
"@id": "#MaterialAttributeValue/organism=Oryza sativa",
"category": {
"@id": "#MaterialAttribute/OBI:0100026",
"characteristicType": {
"@id": "OBI:0100026",
"annotationValue": "organism",
"termSource": "OBI",
"termAccession": "OBI:0100026"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/C_5438",
"annotationValue": "Oryza sativa",
"termSource": "C",
"termAccession": "http://purl.obolibrary.org/obo/C_5438"
}
},
{
"@id": "#EmptyMaterialAttributeValue",
"category": {
"@id": "#MaterialAttribute/MCO:0000059",
"characteristicType": {
"@id": "MCO:0000059",
"annotationValue": "OD600",
"termSource": "MCO",
"termAccession": "MCO:0000059"
}
}
}
]
},
{
"@id": "#Sample_\u2206sux",
"name": "\u2206sux",
"characteristics": [
{
"@id": "#MaterialAttributeValue/organism=Xanthomonas oryzae pv. oryzae PXO99A",
"category": {
"@id": "#MaterialAttribute/OBI:0100026",
"characteristicType": {
"@id": "OBI:0100026",
"annotationValue": "organism",
"termSource": "OBI",
"termAccession": "OBI:0100026"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/NCBITAXON_360094",
"annotationValue": "Xanthomonas oryzae pv. oryzae PXO99A",
"termSource": "NCBITAXON",
"termAccession": "http://purl.obolibrary.org/obo/NCBITAXON_360094"
}
},
{
"@id": "#MaterialAttributeValue/OD600=0,5",
"category": {
"@id": "#MaterialAttribute/MCO:0000059",
"characteristicType": {
"@id": "MCO:0000059",
"annotationValue": "OD600",
"termSource": "MCO",
"termAccession": "MCO:0000059"
}
},
"value": {
"@id": "#UserTerm_0,5",
"annotationValue": "0,5"
}
}
]
},
{
"@id": "#Sample_Oryza_sativa_IR24",
"name": "Oryza sativa IR24",
"characteristics": [
{
"@id": "#MaterialAttributeValue/organism=Oryza sativa",
"category": {
"@id": "#MaterialAttribute/OBI:0100026",
"characteristicType": {
"@id": "OBI:0100026",
"annotationValue": "organism",
"termSource": "OBI",
"termAccession": "OBI:0100026"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/C_5438",
"annotationValue": "Oryza sativa",
"termSource": "C",
"termAccession": "http://purl.obolibrary.org/obo/C_5438"
}
},
{
"@id": "#EmptyMaterialAttributeValue",
"category": {
"@id": "#MaterialAttribute/MCO:0000059",
"characteristicType": {
"@id": "MCO:0000059",
"annotationValue": "OD600",
"termSource": "MCO",
"termAccession": "MCO:0000059"
}
}
}
]
},
{
"@id": "#Sample_\u2206suxC",
"name": "\u2206suxC",
"characteristics": [
{
"@id": "#MaterialAttributeValue/organism=Xanthomonas oryzae pv. oryzae PXO99A",
"category": {
"@id": "#MaterialAttribute/OBI:0100026",
"characteristicType": {
"@id": "OBI:0100026",
"annotationValue": "organism",
"termSource": "OBI",
"termAccession": "OBI:0100026"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/NCBITAXON_360094",
"annotationValue": "Xanthomonas oryzae pv. oryzae PXO99A",
"termSource": "NCBITAXON",
"termAccession": "http://purl.obolibrary.org/obo/NCBITAXON_360094"
}
},
{
"@id": "#MaterialAttributeValue/OD600=0,5",
"category": {
"@id": "#MaterialAttribute/MCO:0000059",
"characteristicType": {
"@id": "MCO:0000059",
"annotationValue": "OD600",
"termSource": "MCO",
"termAccession": "MCO:0000059"
}
},
"value": {
"@id": "#UserTerm_0,5",
"annotationValue": "0,5"
}
}
]
},
{
"@id": "#Sample_Oryza_sativa_IR24",
"name": "Oryza sativa IR24",
"characteristics": [
{
"@id": "#MaterialAttributeValue/organism=Oryza sativa",
"category": {
"@id": "#MaterialAttribute/OBI:0100026",
"characteristicType": {
"@id": "OBI:0100026",
"annotationValue": "organism",
"termSource": "OBI",
"termAccession": "OBI:0100026"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/C_5438",
"annotationValue": "Oryza sativa",
"termSource": "C",
"termAccession": "http://purl.obolibrary.org/obo/C_5438"
}
},
{
"@id": "#EmptyMaterialAttributeValue",
"category": {
"@id": "#MaterialAttribute/MCO:0000059",
"characteristicType": {
"@id": "MCO:0000059",
"annotationValue": "OD600",
"termSource": "MCO",
"termAccession": "MCO:0000059"
}
}
}
]
},
{
"@id": "#Sample_\u2206suxA",
"name": "\u2206suxA",
"characteristics": [
{
"@id": "#MaterialAttributeValue/organism=Xanthomonas oryzae pv. oryzae PXO99A",
"category": {
"@id": "#MaterialAttribute/OBI:0100026",
"characteristicType": {
"@id": "OBI:0100026",
"annotationValue": "organism",
"termSource": "OBI",
"termAccession": "OBI:0100026"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/NCBITAXON_360094",
"annotationValue": "Xanthomonas oryzae pv. oryzae PXO99A",
"termSource": "NCBITAXON",
"termAccession": "http://purl.obolibrary.org/obo/NCBITAXON_360094"
}
},
{
"@id": "#MaterialAttributeValue/OD600=0,5",
"category": {
"@id": "#MaterialAttribute/MCO:0000059",
"characteristicType": {
"@id": "MCO:0000059",
"annotationValue": "OD600",
"termSource": "MCO",
"termAccession": "MCO:0000059"
}
},
"value": {
"@id": "#UserTerm_0,5",
"annotationValue": "0,5"
}
}
]
},
{
"@id": "#Sample_Oryza_sativa_IR24",
"name": "Oryza sativa IR24",
"characteristics": [
{
"@id": "#MaterialAttributeValue/organism=Oryza sativa",
"category": {
"@id": "#MaterialAttribute/OBI:0100026",
"characteristicType": {
"@id": "OBI:0100026",
"annotationValue": "organism",
"termSource": "OBI",
"termAccession": "OBI:0100026"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/C_5438",
"annotationValue": "Oryza sativa",
"termSource": "C",
"termAccession": "http://purl.obolibrary.org/obo/C_5438"
}
},
{
"@id": "#EmptyMaterialAttributeValue",
"category": {
"@id": "#MaterialAttribute/MCO:0000059",
"characteristicType": {
"@id": "MCO:0000059",
"annotationValue": "OD600",
"termSource": "MCO",
"termAccession": "MCO:0000059"
}
}
}
]
},
{
"@id": "#Sample_\u2206suxB",
"name": "\u2206suxB",
"characteristics": [
{
"@id": "#MaterialAttributeValue/organism=Xanthomonas oryzae pv. oryzae PXO99A",
"category": {
"@id": "#MaterialAttribute/OBI:0100026",
"characteristicType": {
"@id": "OBI:0100026",
"annotationValue": "organism",
"termSource": "OBI",
"termAccession": "OBI:0100026"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/NCBITAXON_360094",
"annotationValue": "Xanthomonas oryzae pv. oryzae PXO99A",
"termSource": "NCBITAXON",
"termAccession": "http://purl.obolibrary.org/obo/NCBITAXON_360094"
}
},
{
"@id": "#MaterialAttributeValue/OD600=0,5",
"category": {
"@id": "#MaterialAttribute/MCO:0000059",
"characteristicType": {
"@id": "MCO:0000059",
"annotationValue": "OD600",
"termSource": "MCO",
"termAccession": "MCO:0000059"
}
},
"value": {
"@id": "#UserTerm_0,5",
"annotationValue": "0,5"
}
}
]
},
{
"@id": "#Sample_Oryza_sativa_Kitaake\t\t",
"name": "Oryza sativa Kitaake\t\t",
"characteristics": [
{
"@id": "#MaterialAttributeValue/organism=Oryza sativa",
"category": {
"@id": "#MaterialAttribute/OBI:0100026",
"characteristicType": {
"@id": "OBI:0100026",
"annotationValue": "organism",
"termSource": "OBI",
"termAccession": "OBI:0100026"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/C_5438",
"annotationValue": "Oryza sativa",
"termSource": "C",
"termAccession": "http://purl.obolibrary.org/obo/C_5438"
}
},
{
"@id": "#EmptyMaterialAttributeValue",
"category": {
"@id": "#MaterialAttribute/MCO:0000059",
"characteristicType": {
"@id": "MCO:0000059",
"annotationValue": "OD600",
"termSource": "MCO",
"termAccession": "MCO:0000059"
}
}
}
]
},
{
"@id": "#Sample_Xoo_wt",
"name": "Xoo wt",
"characteristics": [
{
"@id": "#MaterialAttributeValue/organism=Xanthomonas oryzae pv. oryzae PXO99A",
"category": {
"@id": "#MaterialAttribute/OBI:0100026",
"characteristicType": {
"@id": "OBI:0100026",
"annotationValue": "organism",
"termSource": "OBI",
"termAccession": "OBI:0100026"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/NCBITAXON_360094",
"annotationValue": "Xanthomonas oryzae pv. oryzae PXO99A",
"termSource": "NCBITAXON",
"termAccession": "http://purl.obolibrary.org/obo/NCBITAXON_360094"
}
},
{
"@id": "#MaterialAttributeValue/OD600=0,5",
"category": {
"@id": "#MaterialAttribute/MCO:0000059",
"characteristicType": {
"@id": "MCO:0000059",
"annotationValue": "OD600",
"termSource": "MCO",
"termAccession": "MCO:0000059"
}
},
"value": {
"@id": "#UserTerm_0,5",
"annotationValue": "0,5"
}
}
]
},
{
"@id": "#Sample_Oryza_sativa_Kitaake\t\t",
"name": "Oryza sativa Kitaake\t\t",
"characteristics": [
{
"@id": "#MaterialAttributeValue/organism=Oryza sativa",
"category": {
"@id": "#MaterialAttribute/OBI:0100026",
"characteristicType": {
"@id": "OBI:0100026",
"annotationValue": "organism",
"termSource": "OBI",
"termAccession": "OBI:0100026"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/C_5438",
"annotationValue": "Oryza sativa",
"termSource": "C",
"termAccession": "http://purl.obolibrary.org/obo/C_5438"
}
},
{
"@id": "#EmptyMaterialAttributeValue",
"category": {
"@id": "#MaterialAttribute/MCO:0000059",
"characteristicType": {
"@id": "MCO:0000059",
"annotationValue": "OD600",
"termSource": "MCO",
"termAccession": "MCO:0000059"
}
}
}
]
},
{
"@id": "#Sample_\u2206sux",
"name": "\u2206sux",
"characteristics": [
{
"@id": "#MaterialAttributeValue/organism=Xanthomonas oryzae pv. oryzae PXO99A",
"category": {
"@id": "#MaterialAttribute/OBI:0100026",
"characteristicType": {
"@id": "OBI:0100026",
"annotationValue": "organism",
"termSource": "OBI",
"termAccession": "OBI:0100026"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/NCBITAXON_360094",
"annotationValue": "Xanthomonas oryzae pv. oryzae PXO99A",
"termSource": "NCBITAXON",
"termAccession": "http://purl.obolibrary.org/obo/NCBITAXON_360094"
}
},
{
"@id": "#MaterialAttributeValue/OD600=0,5",
"category": {
"@id": "#MaterialAttribute/MCO:0000059",
"characteristicType": {
"@id": "MCO:0000059",
"annotationValue": "OD600",
"termSource": "MCO",
"termAccession": "MCO:0000059"
}
},
"value": {
"@id": "#UserTerm_0,5",
"annotationValue": "0,5"
}
}
]
},
{
"@id": "#Sample_Oryza_sativa_Kitaake\t\t",
"name": "Oryza sativa Kitaake\t\t",
"characteristics": [
{
"@id": "#MaterialAttributeValue/organism=Oryza sativa",
"category": {
"@id": "#MaterialAttribute/OBI:0100026",
"characteristicType": {
"@id": "OBI:0100026",
"annotationValue": "organism",
"termSource": "OBI",
"termAccession": "OBI:0100026"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/C_5438",
"annotationValue": "Oryza sativa",
"termSource": "C",
"termAccession": "http://purl.obolibrary.org/obo/C_5438"
}
},
{
"@id": "#EmptyMaterialAttributeValue",
"category": {
"@id": "#MaterialAttribute/MCO:0000059",
"characteristicType": {
"@id": "MCO:0000059",
"annotationValue": "OD600",
"termSource": "MCO",
"termAccession": "MCO:0000059"
}
}
}
]
},
{
"@id": "#Sample_\u2206suxC",
"name": "\u2206suxC",
"characteristics": [
{
"@id": "#MaterialAttributeValue/organism=Xanthomonas oryzae pv. oryzae PXO99A",
"category": {
"@id": "#MaterialAttribute/OBI:0100026",
"characteristicType": {
"@id": "OBI:0100026",
"annotationValue": "organism",
"termSource": "OBI",
"termAccession": "OBI:0100026"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/NCBITAXON_360094",
"annotationValue": "Xanthomonas oryzae pv. oryzae PXO99A",
"termSource": "NCBITAXON",
"termAccession": "http://purl.obolibrary.org/obo/NCBITAXON_360094"
}
},
{
"@id": "#MaterialAttributeValue/OD600=0,5",
"category": {
"@id": "#MaterialAttribute/MCO:0000059",
"characteristicType": {
"@id": "MCO:0000059",
"annotationValue": "OD600",
"termSource": "MCO",
"termAccession": "MCO:0000059"
}
},
"value": {
"@id": "#UserTerm_0,5",
"annotationValue": "0,5"
}
}
]
},
{
"@id": "#Sample_Oryza_sativa_Kitaake\t\t",
"name": "Oryza sativa Kitaake\t\t",
"characteristics": [
{
"@id": "#MaterialAttributeValue/organism=Oryza sativa",
"category": {
"@id": "#MaterialAttribute/OBI:0100026",
"characteristicType": {
"@id": "OBI:0100026",
"annotationValue": "organism",
"termSource": "OBI",
"termAccession": "OBI:0100026"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/C_5438",
"annotationValue": "Oryza sativa",
"termSource": "C",
"termAccession": "http://purl.obolibrary.org/obo/C_5438"
}
},
{
"@id": "#EmptyMaterialAttributeValue",
"category": {
"@id": "#MaterialAttribute/MCO:0000059",
"characteristicType": {
"@id": "MCO:0000059",
"annotationValue": "OD600",
"termSource": "MCO",
"termAccession": "MCO:0000059"
}
}
}
]
},
{
"@id": "#Sample_\u2206suxA",
"name": "\u2206suxA",
"characteristics": [
{
"@id": "#MaterialAttributeValue/organism=Xanthomonas oryzae pv. oryzae PXO99A",
"category": {
"@id": "#MaterialAttribute/OBI:0100026",
"characteristicType": {
"@id": "OBI:0100026",
"annotationValue": "organism",
"termSource": "OBI",
"termAccession": "OBI:0100026"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/NCBITAXON_360094",
"annotationValue": "Xanthomonas oryzae pv. oryzae PXO99A",
"termSource": "NCBITAXON",
"termAccession": "http://purl.obolibrary.org/obo/NCBITAXON_360094"
}
},
{
"@id": "#MaterialAttributeValue/OD600=0,5",
"category": {
"@id": "#MaterialAttribute/MCO:0000059",
"characteristicType": {
"@id": "MCO:0000059",
"annotationValue": "OD600",
"termSource": "MCO",
"termAccession": "MCO:0000059"
}
},
"value": {
"@id": "#UserTerm_0,5",
"annotationValue": "0,5"
}
}
]
},
{
"@id": "#Sample_Oryza_sativa_Kitaake\t\t",
"name": "Oryza sativa Kitaake\t\t",
"characteristics": [
{
"@id": "#MaterialAttributeValue/organism=Oryza sativa",
"category": {
"@id": "#MaterialAttribute/OBI:0100026",
"characteristicType": {
"@id": "OBI:0100026",
"annotationValue": "organism",
"termSource": "OBI",
"termAccession": "OBI:0100026"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/C_5438",
"annotationValue": "Oryza sativa",
"termSource": "C",
"termAccession": "http://purl.obolibrary.org/obo/C_5438"
}
},
{
"@id": "#EmptyMaterialAttributeValue",
"category": {
"@id": "#MaterialAttribute/MCO:0000059",
"characteristicType": {
"@id": "MCO:0000059",
"annotationValue": "OD600",
"termSource": "MCO",
"termAccession": "MCO:0000059"
}
}
}
]
},
{
"@id": "#Sample_\u2206suxB",
"name": "\u2206suxB",
"characteristics": [
{
"@id": "#MaterialAttributeValue/organism=Xanthomonas oryzae pv. oryzae PXO99A",
"category": {
"@id": "#MaterialAttribute/OBI:0100026",
"characteristicType": {
"@id": "OBI:0100026",
"annotationValue": "organism",
"termSource": "OBI",
"termAccession": "OBI:0100026"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/NCBITAXON_360094",
"annotationValue": "Xanthomonas oryzae pv. oryzae PXO99A",
"termSource": "NCBITAXON",
"termAccession": "http://purl.obolibrary.org/obo/NCBITAXON_360094"
}
},
{
"@id": "#MaterialAttributeValue/OD600=0,5",
"category": {
"@id": "#MaterialAttribute/MCO:0000059",
"characteristicType": {
"@id": "MCO:0000059",
"annotationValue": "OD600",
"termSource": "MCO",
"termAccession": "MCO:0000059"
}
},
"value": {
"@id": "#UserTerm_0,5",
"annotationValue": "0,5"
}
}
]
},
{
"@id": "#Sample_Oryzae_sativa_Nipponbare",
"name": "Oryzae sativa Nipponbare",
"characteristics": [
{
"@id": "#MaterialAttributeValue/organism=Oryza sativa",
"category": {
"@id": "#MaterialAttribute/OBI:0100026",
"characteristicType": {
"@id": "OBI:0100026",
"annotationValue": "organism",
"termSource": "OBI",
"termAccession": "OBI:0100026"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/C_5438",
"annotationValue": "Oryza sativa",
"termSource": "C",
"termAccession": "http://purl.obolibrary.org/obo/C_5438"
}
},
{
"@id": "#EmptyMaterialAttributeValue",
"category": {
"@id": "#MaterialAttribute/MCO:0000059",
"characteristicType": {
"@id": "MCO:0000059",
"annotationValue": "OD600",
"termSource": "MCO",
"termAccession": "MCO:0000059"
}
}
}
]
},
{
"@id": "#Sample_Xoo_wt",
"name": "Xoo wt",
"characteristics": [
{
"@id": "#MaterialAttributeValue/organism=Xanthomonas oryzae pv. oryzae PXO99A",
"category": {
"@id": "#MaterialAttribute/OBI:0100026",
"characteristicType": {
"@id": "OBI:0100026",
"annotationValue": "organism",
"termSource": "OBI",
"termAccession": "OBI:0100026"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/NCBITAXON_360094",
"annotationValue": "Xanthomonas oryzae pv. oryzae PXO99A",
"termSource": "NCBITAXON",
"termAccession": "http://purl.obolibrary.org/obo/NCBITAXON_360094"
}
},
{
"@id": "#MaterialAttributeValue/OD600=0,5",
"category": {
"@id": "#MaterialAttribute/MCO:0000059",
"characteristicType": {
"@id": "MCO:0000059",
"annotationValue": "OD600",
"termSource": "MCO",
"termAccession": "MCO:0000059"
}
},
"value": {
"@id": "#UserTerm_0,5",
"annotationValue": "0,5"
}
}
]
},
{
"@id": "#Sample_Oryzae_sativa_Nipponbare",
"name": "Oryzae sativa Nipponbare",
"characteristics": [
{
"@id": "#MaterialAttributeValue/organism=Oryza sativa",
"category": {
"@id": "#MaterialAttribute/OBI:0100026",
"characteristicType": {
"@id": "OBI:0100026",
"annotationValue": "organism",
"termSource": "OBI",
"termAccession": "OBI:0100026"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/C_5438",
"annotationValue": "Oryza sativa",
"termSource": "C",
"termAccession": "http://purl.obolibrary.org/obo/C_5438"
}
},
{
"@id": "#EmptyMaterialAttributeValue",
"category": {
"@id": "#MaterialAttribute/MCO:0000059",
"characteristicType": {
"@id": "MCO:0000059",
"annotationValue": "OD600",
"termSource": "MCO",
"termAccession": "MCO:0000059"
}
}
}
]
},
{
"@id": "#Sample_\u2206sux",
"name": "\u2206sux",
"characteristics": [
{
"@id": "#MaterialAttributeValue/organism=Xanthomonas oryzae pv. oryzae PXO99A",
"category": {
"@id": "#MaterialAttribute/OBI:0100026",
"characteristicType": {
"@id": "OBI:0100026",
"annotationValue": "organism",
"termSource": "OBI",
"termAccession": "OBI:0100026"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/NCBITAXON_360094",
"annotationValue": "Xanthomonas oryzae pv. oryzae PXO99A",
"termSource": "NCBITAXON",
"termAccession": "http://purl.obolibrary.org/obo/NCBITAXON_360094"
}
},
{
"@id": "#MaterialAttributeValue/OD600=0,5",
"category": {
"@id": "#MaterialAttribute/MCO:0000059",
"characteristicType": {
"@id": "MCO:0000059",
"annotationValue": "OD600",
"termSource": "MCO",
"termAccession": "MCO:0000059"
}
},
"value": {
"@id": "#UserTerm_0,5",
"annotationValue": "0,5"
}
}
]
},
{
"@id": "#Sample_Oryzae_sativa_Nipponbare",
"name": "Oryzae sativa Nipponbare",
"characteristics": [
{
"@id": "#MaterialAttributeValue/organism=Oryza sativa",
"category": {
"@id": "#MaterialAttribute/OBI:0100026",
"characteristicType": {
"@id": "OBI:0100026",
"annotationValue": "organism",
"termSource": "OBI",
"termAccession": "OBI:0100026"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/C_5438",
"annotationValue": "Oryza sativa",
"termSource": "C",
"termAccession": "http://purl.obolibrary.org/obo/C_5438"
}
},
{
"@id": "#EmptyMaterialAttributeValue",
"category": {
"@id": "#MaterialAttribute/MCO:0000059",
"characteristicType": {
"@id": "MCO:0000059",
"annotationValue": "OD600",
"termSource": "MCO",
"termAccession": "MCO:0000059"
}
}
}
]
},
{
"@id": "#Sample_\u2206suxC",
"name": "\u2206suxC",
"characteristics": [
{
"@id": "#MaterialAttributeValue/organism=Xanthomonas oryzae pv. oryzae exposure",
"category": {
"@id": "#MaterialAttribute/OBI:0100026",
"characteristicType": {
"@id": "OBI:0100026",
"annotationValue": "organism",
"termSource": "OBI",
"termAccession": "OBI:0100026"
}
},
"value": {
"@id": "https://bioregistry.io/PECO:0007257",
"annotationValue": "Xanthomonas oryzae pv. oryzae exposure",
"termSource": "PECO",
"termAccession": "https://bioregistry.io/PECO:0007257"
}
},
{
"@id": "#MaterialAttributeValue/OD600=0,5",
"category": {
"@id": "#MaterialAttribute/MCO:0000059",
"characteristicType": {
"@id": "MCO:0000059",
"annotationValue": "OD600",
"termSource": "MCO",
"termAccession": "MCO:0000059"
}
},
"value": {
"@id": "#UserTerm_0,5",
"annotationValue": "0,5"
}
}
]
},
{
"@id": "#Sample_Oryzae_sativa_Nipponbare",
"name": "Oryzae sativa Nipponbare",
"characteristics": [
{
"@id": "#MaterialAttributeValue/organism=Oryza sativa",
"category": {
"@id": "#MaterialAttribute/OBI:0100026",
"characteristicType": {
"@id": "OBI:0100026",
"annotationValue": "organism",
"termSource": "OBI",
"termAccession": "OBI:0100026"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/C_5438",
"annotationValue": "Oryza sativa",
"termSource": "C",
"termAccession": "http://purl.obolibrary.org/obo/C_5438"
}
},
{
"@id": "#EmptyMaterialAttributeValue",
"category": {
"@id": "#MaterialAttribute/MCO:0000059",
"characteristicType": {
"@id": "MCO:0000059",
"annotationValue": "OD600",
"termSource": "MCO",
"termAccession": "MCO:0000059"
}
}
}
]
},
{
"@id": "#Sample_\u2206suxA",
"name": "\u2206suxA",
"characteristics": [
{
"@id": "#MaterialAttributeValue/organism=Xanthomonas oryzae pv. oryzae PXO99A",
"category": {
"@id": "#MaterialAttribute/OBI:0100026",
"characteristicType": {
"@id": "OBI:0100026",
"annotationValue": "organism",
"termSource": "OBI",
"termAccession": "OBI:0100026"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/NCBITAXON_360094",
"annotationValue": "Xanthomonas oryzae pv. oryzae PXO99A",
"termSource": "NCBITAXON",
"termAccession": "http://purl.obolibrary.org/obo/NCBITAXON_360094"
}
},
{
"@id": "#MaterialAttributeValue/OD600=0,5",
"category": {
"@id": "#MaterialAttribute/MCO:0000059",
"characteristicType": {
"@id": "MCO:0000059",
"annotationValue": "OD600",
"termSource": "MCO",
"termAccession": "MCO:0000059"
}
},
"value": {
"@id": "#UserTerm_0,5",
"annotationValue": "0,5"
}
}
]
},
{
"@id": "#Sample_Oryzae_sativa_Nipponbare",
"name": "Oryzae sativa Nipponbare",
"characteristics": [
{
"@id": "#MaterialAttributeValue/organism=Oryza sativa",
"category": {
"@id": "#MaterialAttribute/OBI:0100026",
"characteristicType": {
"@id": "OBI:0100026",
"annotationValue": "organism",
"termSource": "OBI",
"termAccession": "OBI:0100026"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/C_5438",
"annotationValue": "Oryza sativa",
"termSource": "C",
"termAccession": "http://purl.obolibrary.org/obo/C_5438"
}
},
{
"@id": "#EmptyMaterialAttributeValue",
"category": {
"@id": "#MaterialAttribute/MCO:0000059",
"characteristicType": {
"@id": "MCO:0000059",
"annotationValue": "OD600",
"termSource": "MCO",
"termAccession": "MCO:0000059"
}
}
}
]
},
{
"@id": "#Sample_\u2206suxB",
"name": "\u2206suxB",
"characteristics": [
{
"@id": "#MaterialAttributeValue/organism=Xanthomonas oryzae pv. oryzae PXO99A",
"category": {
"@id": "#MaterialAttribute/OBI:0100026",
"characteristicType": {
"@id": "OBI:0100026",
"annotationValue": "organism",
"termSource": "OBI",
"termAccession": "OBI:0100026"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/NCBITAXON_360094",
"annotationValue": "Xanthomonas oryzae pv. oryzae PXO99A",
"termSource": "NCBITAXON",
"termAccession": "http://purl.obolibrary.org/obo/NCBITAXON_360094"
}
},
{
"@id": "#MaterialAttributeValue/OD600=0,5",
"category": {
"@id": "#MaterialAttribute/MCO:0000059",
"characteristicType": {
"@id": "MCO:0000059",
"annotationValue": "OD600",
"termSource": "MCO",
"termAccession": "MCO:0000059"
}
},
"value": {
"@id": "#UserTerm_0,5",
"annotationValue": "0,5"
}
}
]
}
],
"outputs": [
{
"@id": "#Sample_Oryza_sativa_IR24_Xoo_wt",
"name": "Oryza sativa IR24_Xoo wt"
},
{
"@id": "#Sample_Oryza_sativa_IR24_Xoo_wt",
"name": "Oryza sativa IR24_Xoo wt"
},
{
"@id": "#Sample_Oryza_sativa_IR24_\u2206sux",
"name": "Oryza sativa IR24_\u2206sux"
},
{
"@id": "#Sample_Oryza_sativa_IR24_\u2206sux",
"name": "Oryza sativa IR24_\u2206sux"
},
{
"@id": "#Sample_Oryza_sativa_IR24_\u2206suxC",
"name": "Oryza sativa IR24_\u2206suxC"
},
{
"@id": "#Sample_Oryza_sativa_IR24_\u2206suxC",
"name": "Oryza sativa IR24_\u2206suxC"
},
{
"@id": "#Sample_Oryza_sativa_IR24_\u2206suxA",
"name": "Oryza sativa IR24_\u2206suxA"
},
{
"@id": "#Sample_Oryza_sativa_IR24_\u2206suxA",
"name": "Oryza sativa IR24_\u2206suxA"
},
{
"@id": "#Sample_Oryza_sativa_IR24_\u2206suxB",
"name": "Oryza sativa IR24_\u2206suxB"
},
{
"@id": "#Sample_Oryza_sativa_IR24_\u2206suxB",
"name": "Oryza sativa IR24_\u2206suxB"
},
{
"@id": "#Sample_Oryza_sativa_Kitaake_Xoo_wt",
"name": "Oryza sativa Kitaake_Xoo wt"
},
{
"@id": "#Sample_Oryza_sativa_Kitaake_Xoo_wt",
"name": "Oryza sativa Kitaake_Xoo wt"
},
{
"@id": "#Sample_Oryza_sativa_Kitaake_\u2206sux",
"name": "Oryza sativa Kitaake_\u2206sux"
},
{
"@id": "#Sample_Oryza_sativa_Kitaake_\u2206sux",
"name": "Oryza sativa Kitaake_\u2206sux"
},
{
"@id": "#Sample_Oryza_sativa_Kitaake_\u2206suxC",
"name": "Oryza sativa Kitaake_\u2206suxC"
},
{
"@id": "#Sample_Oryza_sativa_Kitaake_\u2206suxC",
"name": "Oryza sativa Kitaake_\u2206suxC"
},
{
"@id": "#Sample_Oryza_sativa_Kitaake_\u2206suxA",
"name": "Oryza sativa Kitaake_\u2206suxA"
},
{
"@id": "#Sample_Oryza_sativa_Kitaake_\u2206suxA",
"name": "Oryza sativa Kitaake_\u2206suxA"
},
{
"@id": "#Sample_Oryza_sativa_Kitaake_\u2206suxB",
"name": "Oryza sativa Kitaake_\u2206suxB"
},
{
"@id": "#Sample_Oryza_sativa_Kitaake_\u2206suxB",
"name": "Oryza sativa Kitaake_\u2206suxB"
},
{
"@id": "#Sample_Oryzae_sativa_Nipponbare_Xoo_wt",
"name": "Oryzae sativa Nipponbare_Xoo wt"
},
{
"@id": "#Sample_Oryzae_sativa_Nipponbare_Xoo_wt",
"name": "Oryzae sativa Nipponbare_Xoo wt"
},
{
"@id": "#Sample_Oryzae_sativa_Nipponbare_\u2206sux",
"name": "Oryzae sativa Nipponbare_\u2206sux"
},
{
"@id": "#Sample_Oryzae_sativa_Nipponbare_\u2206sux",
"name": "Oryzae sativa Nipponbare_\u2206sux"
},
{
"@id": "#Sample_Oryzae_sativa_Nipponbare_\u2206suxC",
"name": "Oryzae sativa Nipponbare_\u2206suxC"
},
{
"@id": "#Sample_Oryzae_sativa_Nipponbare_\u2206suxC",
"name": "Oryzae sativa Nipponbare_\u2206suxC"
},
{
"@id": "#Sample_Oryzae_sativa_Nipponbare_\u2206suxA",
"name": "Oryzae sativa Nipponbare_\u2206suxA"
},
{
"@id": "#Sample_Oryzae_sativa_Nipponbare_\u2206suxA",
"name": "Oryzae sativa Nipponbare_\u2206suxA"
},
{
"@id": "#Sample_Oryzae_sativa_Nipponbare_\u2206suxB",
"name": "Oryzae sativa Nipponbare_\u2206suxB"
},
{
"@id": "#Sample_Oryzae_sativa_Nipponbare_\u2206suxB",
"name": "Oryzae sativa Nipponbare_\u2206suxB"
}
]
},
{
"@id": "#Process_lesion_measurement",
"name": "lesion measurement",
"executesProtocol": {
"@id": "#Protocol_clippingassay.docx",
"name": "clippingassay.docx",
"parameters": [
{
"@id": "#ProtocolParameter/NCIT:C25207",
"parameterName": {
"@id": "NCIT:C25207",
"annotationValue": "Time",
"termSource": "NCIT",
"termAccession": "NCIT:C25207"
}
}
]
},
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NCIT:C25207",
"parameterName": {
"@id": "NCIT:C25207",
"annotationValue": "Time",
"termSource": "NCIT",
"termAccession": "NCIT:C25207"
}
},
"value": {
"@id": "#UserTerm_12_DAI",
"annotationValue": "12 DAI"
}
}
],
"inputs": [
{
"@id": "#Sample_Oryza_sativa_IR24_Xoo_wt",
"name": "Oryza sativa IR24_Xoo wt"
},
{
"@id": "#Sample_Oryza_sativa_IR24_\u2206sux",
"name": "Oryza sativa IR24_\u2206sux"
},
{
"@id": "#Sample_Oryza_sativa_IR24_\u2206suxC",
"name": "Oryza sativa IR24_\u2206suxC"
},
{
"@id": "#Sample_Oryza_sativa_IR24_\u2206suxA",
"name": "Oryza sativa IR24_\u2206suxA"
},
{
"@id": "#Sample_Oryza_sativa_IR24_\u2206suxB",
"name": "Oryza sativa IR24_\u2206suxB"
},
{
"@id": "#Sample_Oryza_sativa_IR24_\u2206suxB",
"name": "Oryza sativa IR24_\u2206suxB"
},
{
"@id": "#Sample_Oryza_sativa_Kitaake_Xoo_wt",
"name": "Oryza sativa Kitaake_Xoo wt"
},
{
"@id": "#Sample_Oryza_sativa_Kitaake_\u2206sux",
"name": "Oryza sativa Kitaake_\u2206sux"
},
{
"@id": "#Sample_Oryza_sativa_Kitaake_\u2206suxC",
"name": "Oryza sativa Kitaake_\u2206suxC"
},
{
"@id": "#Sample_Oryza_sativa_Kitaake_\u2206suxA",
"name": "Oryza sativa Kitaake_\u2206suxA"
},
{
"@id": "#Sample_Oryza_sativa_Kitaake_\u2206suxB",
"name": "Oryza sativa Kitaake_\u2206suxB"
},
{
"@id": "#Sample_Oryza_sativa_Kitaake_\u2206suxC",
"name": "Oryza sativa Kitaake_\u2206suxC"
},
{
"@id": "#Sample_Oryzae_sativa_Nipponbare_Xoo_wt",
"name": "Oryzae sativa Nipponbare_Xoo wt"
},
{
"@id": "#Sample_Oryzae_sativa_Nipponbare_\u2206sux",
"name": "Oryzae sativa Nipponbare_\u2206sux"
},
{
"@id": "#Sample_Oryzae_sativa_Nipponbare_\u2206suxC",
"name": "Oryzae sativa Nipponbare_\u2206suxC"
},
{
"@id": "#Sample_Oryzae_sativa_Nipponbare_\u2206suxA",
"name": "Oryzae sativa Nipponbare_\u2206suxA"
},
{
"@id": "#Sample_Oryzae_sativa_Nipponbare_\u2206suxB",
"name": "Oryzae sativa Nipponbare_\u2206suxB"
}
],
"outputs": [
{
"@id": "assays/Clipping/dataset/Inoculation_data_IR24.xlsx",
"name": "assays/Clipping/dataset/Inoculation data_IR24.xlsx",
"type": "Raw Data File"
},
{
"@id": "assays/Clipping/dataset/Inoculation_data_IR24.xlsx",
"name": "assays/Clipping/dataset/Inoculation data_IR24.xlsx",
"type": "Raw Data File"
},
{
"@id": "assays/Clipping/dataset/Inoculation_data_IR24.xlsx",
"name": "assays/Clipping/dataset/Inoculation data_IR24.xlsx",
"type": "Raw Data File"
},
{
"@id": "assays/Clipping/dataset/Inoculation_data_IR24.xlsx",
"name": "assays/Clipping/dataset/Inoculation data_IR24.xlsx",
"type": "Raw Data File"
},
{
"@id": "assays/Clipping/dataset/Inoculation_data_IR24.xlsx",
"name": "assays/Clipping/dataset/Inoculation data_IR24.xlsx",
"type": "Raw Data File"
},
{
"@id": "assays/Clipping/dataset/Inoculation_data_IR24.xlsx",
"name": "assays/Clipping/dataset/Inoculation data_IR24.xlsx",
"type": "Raw Data File"
},
{
"@id": "assays/Clipping/dataset/Inoculation_data_Kitaake.xlsx",
"name": "assays/Clipping/dataset/Inoculation data_Kitaake.xlsx",
"type": "Raw Data File"
},
{
"@id": "assays/Clipping/dataset/Inoculation_data_Kitaake.xlsx",
"name": "assays/Clipping/dataset/Inoculation data_Kitaake.xlsx",
"type": "Raw Data File"
},
{
"@id": "assays/Clipping/dataset/Inoculation_data_Kitaake.xlsx",
"name": "assays/Clipping/dataset/Inoculation data_Kitaake.xlsx",
"type": "Raw Data File"
},
{
"@id": "assays/Clipping/dataset/Inoculation_data_Kitaake.xlsx",
"name": "assays/Clipping/dataset/Inoculation data_Kitaake.xlsx",
"type": "Raw Data File"
},
{
"@id": "assays/Clipping/dataset/Inoculation_data_Kitaake.xlsx",
"name": "assays/Clipping/dataset/Inoculation data_Kitaake.xlsx",
"type": "Raw Data File"
},
{
"@id": "assays/Clipping/dataset/Inoculation_data_Kitaake.xlsx",
"name": "assays/Clipping/dataset/Inoculation data_Kitaake.xlsx",
"type": "Raw Data File"
},
{
"@id": "assays/Clipping/dataset/sucrose_gene_on_Nip_V2.xlsx",
"name": "assays/Clipping/dataset/sucrose gene on Nip_V2.xlsx",
"type": "Raw Data File"
},
{
"@id": "assays/Clipping/dataset/sucrose_gene_on_Nip_V2.xlsx",
"name": "assays/Clipping/dataset/sucrose gene on Nip_V2.xlsx",
"type": "Raw Data File"
},
{
"@id": "assays/Clipping/dataset/sucrose_gene_on_Nip_V2.xlsx",
"name": "assays/Clipping/dataset/sucrose gene on Nip_V2.xlsx",
"type": "Raw Data File"
},
{
"@id": "assays/Clipping/dataset/sucrose_gene_on_Nip_V2.xlsx",
"name": "assays/Clipping/dataset/sucrose gene on Nip_V2.xlsx",
"type": "Raw Data File"
},
{
"@id": "assays/Clipping/dataset/sucrose_gene_on_Nip_V2.xlsx",
"name": "assays/Clipping/dataset/sucrose gene on Nip_V2.xlsx",
"type": "Raw Data File"
}
]
}
]
},
{
"filename": "assays/Growth Curves/isa.assay.xlsx",
"@id": "assays/Growth_Curves/",
"measurementType": {
"@id": "http://purl.obolibrary.org/obo/MCO_0000059",
"annotationValue": "OD600",
"termSource": "MCO",
"termAccession": "http://purl.obolibrary.org/obo/MCO_0000059"
},
"technologyType": {
"@id": "#UserTerm_Photospectrometer",
"annotationValue": "Photospectrometer"
},
"technologyPlatform": "Tecan",
"dataFiles": [
{
"@id": "assays/Growth_Curves/dataset/RawData",
"name": "assays/Growth Curves/dataset/RawData",
"type": "Raw Data File"
},
{
"@id": "assays/Growth_Curves/dataset/RawData/\u2206sux_raw",
"name": "assays/Growth Curves/dataset/RawData/\u2206sux_raw",
"type": "Raw Data File"
},
{
"@id": "assays/Growth_Curves/dataset/RawData/\u2206suxA_raw",
"name": "assays/Growth Curves/dataset/RawData/\u2206suxA_raw",
"type": "Raw Data File"
},
{
"@id": "assays/Growth_Curves/dataset/RawData/\u2206suxB_raw",
"name": "assays/Growth Curves/dataset/RawData/\u2206suxB_raw",
"type": "Raw Data File"
},
{
"@id": "assays/Growth_Curves/dataset/RawData/\u2206suxC_raw",
"name": "assays/Growth Curves/dataset/RawData/\u2206suxC_raw",
"type": "Raw Data File"
},
{
"@id": "assays/Growth_Curves/dataset/RawData/\u2206suxR_raw",
"name": "assays/Growth Curves/dataset/RawData/\u2206suxR_raw",
"type": "Raw Data File"
},
{
"@id": "assays/Growth_Curves/dataset/AnalyzedData/\u2206sux_analyzed/\u2206sux(203-205)_summary.xlsx",
"name": "assays/Growth Curves/dataset/AnalyzedData/\u2206sux_analyzed/\u2206sux(203-205)_summary.xlsx",
"type": "Raw Data File"
},
{
"@id": "assays/Growth_Curves/dataset/AnalyzedData/\u2206suxR_analyzed/suxR.tif",
"name": "assays/Growth Curves/dataset/AnalyzedData/\u2206suxR_analyzed/suxR.tif",
"type": "Raw Data File"
},
{
"@id": "assays/Growth_Curves/dataset/AnalyzedData/\u2206suxC_analyzed/suxC.tif",
"name": "assays/Growth Curves/dataset/AnalyzedData/\u2206suxC_analyzed/suxC.tif",
"type": "Raw Data File"
},
{
"@id": "assays/Growth_Curves/dataset/AnalyzedData/\u2206suxB_analyzed/suxB.tif",
"name": "assays/Growth Curves/dataset/AnalyzedData/\u2206suxB_analyzed/suxB.tif",
"type": "Raw Data File"
},
{
"@id": "assays/Growth_Curves/dataset/AnalyzedData/\u2206suxA_analyzed/suxA.tif",
"name": "assays/Growth Curves/dataset/AnalyzedData/\u2206suxA_analyzed/suxA.tif",
"type": "Raw Data File"
},
{
"@id": "assays/Growth_Curves/dataset/RawData/wt_raw",
"name": "assays/Growth Curves/dataset/RawData/wt_raw",
"type": "Raw Data File"
},
{
"@id": "assays/Growth_Curves/dataset/AnalyzedData/wt_analyzed/wt.tif",
"name": "assays/Growth Curves/dataset/AnalyzedData/wt_analyzed/wt.tif",
"type": "Raw Data File"
}
],
"materials": {},
"unitCategories": [
{
"@id": "https://bioregistry.io/UO:0000027",
"annotationValue": "degree celsius",
"termSource": "UO",
"termAccession": "https://bioregistry.io/UO:0000027"
},
{
"@id": "https://bioregistry.io/NCIT:C28251",
"annotationValue": "Millimeter",
"termSource": "NCIT",
"termAccession": "https://bioregistry.io/NCIT:C28251"
},
{
"@id": "https://bioregistry.io/NCIT:C25529",
"annotationValue": "Hour",
"termSource": "NCIT",
"termAccession": "https://bioregistry.io/NCIT:C25529"
}
],
"processSequence": [
{
"@id": "#Process_Growth_curves",
"name": "Growth curves",
"executesProtocol": {
"@id": "#Protocol_Growth-Assay-in-12-well-plates.pdf",
"name": "Growth-Assay-in-12-well-plates.pdf",
"parameters": [
{
"@id": "#ProtocolParameter/EFO:0001702",
"parameterName": {
"@id": "EFO:0001702",
"annotationValue": "temperature",
"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
{
"@id": "#ProtocolParameter/NCIT:C64646",
"parameterName": {
"@id": "NCIT:C64646",
"annotationValue": "Amplitude",
"termSource": "NCIT",
"termAccession": "NCIT:C64646"
}
},
{
"@id": "#ProtocolParameter/NCIT:C25207",
"parameterName": {
"@id": "NCIT:C25207",
"annotationValue": "Time",
"termSource": "NCIT",
"termAccession": "NCIT:C25207"
}
}
]
},
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/EFO:0001702",
"parameterName": {
"@id": "EFO:0001702",
"annotationValue": "temperature",
"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
"value": 28,
"unit": {
"@id": "https://bioregistry.io/UO:0000027",
"annotationValue": "degree celsius",
"termSource": "UO",
"termAccession": "https://bioregistry.io/UO:0000027"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C64646",
"parameterName": {
"@id": "NCIT:C64646",
"annotationValue": "Amplitude",
"termSource": "NCIT",
"termAccession": "NCIT:C64646"
}
},
"value": 3,
"unit": {
"@id": "https://bioregistry.io/NCIT:C28251",
"annotationValue": "Millimeter",
"termSource": "NCIT",
"termAccession": "https://bioregistry.io/NCIT:C28251"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C25207",
"parameterName": {
"@id": "NCIT:C25207",
"annotationValue": "Time",
"termSource": "NCIT",
"termAccession": "NCIT:C25207"
}
},
"value": 24,
"unit": {
"@id": "https://bioregistry.io/NCIT:C25529",
"annotationValue": "Hour",
"termSource": "NCIT",
"termAccession": "https://bioregistry.io/NCIT:C25529"
}
}
],
"inputs": [
{
"@id": "#Source_Xoo_wt",
"name": "Xoo wt"
},
{
"@id": "#Source_\u2206sux",
"name": "\u2206sux"
},
{
"@id": "#Source_\u2206suxA",
"name": "\u2206suxA"
},
{
"@id": "#Source_\u2206suxB",
"name": "\u2206suxB"
},
{
"@id": "#Source_\u2206suxC",
"name": "\u2206suxC"
},
{
"@id": "#Source_\u2206suxR",
"name": "\u2206suxR"
}
],
"outputs": [
{
"@id": "assays/Growth_Curves/dataset/RawData",
"name": "assays/Growth Curves/dataset/RawData",
"type": "Raw Data File"
},
{
"@id": "assays/Growth_Curves/dataset/RawData/\u2206sux_raw",
"name": "assays/Growth Curves/dataset/RawData/\u2206sux_raw",
"type": "Raw Data File"
},
{
"@id": "assays/Growth_Curves/dataset/RawData/\u2206suxA_raw",
"name": "assays/Growth Curves/dataset/RawData/\u2206suxA_raw",
"type": "Raw Data File"
},
{
"@id": "assays/Growth_Curves/dataset/RawData/\u2206suxB_raw",
"name": "assays/Growth Curves/dataset/RawData/\u2206suxB_raw",
"type": "Raw Data File"
},
{
"@id": "assays/Growth_Curves/dataset/RawData/\u2206suxC_raw",
"name": "assays/Growth Curves/dataset/RawData/\u2206suxC_raw",
"type": "Raw Data File"
},
{
"@id": "assays/Growth_Curves/dataset/RawData/\u2206suxR_raw",
"name": "assays/Growth Curves/dataset/RawData/\u2206suxR_raw",
"type": "Raw Data File"
}
]
},
{
"@id": "#Process_Growth_curves_analysis_0",
"name": "Growth curves analysis_0",
"executesProtocol": {
"@id": "#Protocol_AnalyzedData/\u2206sux_analyzed",
"name": "AnalyzedData/\u2206sux_analyzed"
},
"inputs": [
{
"@id": "assays/Growth_Curves/dataset/RawData/\u2206sux_raw",
"name": "assays/Growth Curves/dataset/RawData/\u2206sux_raw",
"type": "Raw Data File"
}
],
"outputs": [
{
"@id": "assays/Growth_Curves/dataset/AnalyzedData/\u2206sux_analyzed/\u2206sux(203-205)_summary.xlsx",
"name": "assays/Growth Curves/dataset/AnalyzedData/\u2206sux_analyzed/\u2206sux(203-205)_summary.xlsx",
"type": "Raw Data File"
}
]
},
{
"@id": "#Process_Growth_curves_analysis_1",
"name": "Growth curves analysis_1",
"executesProtocol": {
"@id": "#Protocol_AnalyzedData/\u2206suxR_analyzed",
"name": "AnalyzedData/\u2206suxR_analyzed"
},
"inputs": [
{
"@id": "assays/Growth_Curves/dataset/RawData/\u2206suxR_raw",
"name": "assays/Growth Curves/dataset/RawData/\u2206suxR_raw",
"type": "Raw Data File"
}
],
"outputs": [
{
"@id": "assays/Growth_Curves/dataset/AnalyzedData/\u2206suxR_analyzed/suxR.tif",
"name": "assays/Growth Curves/dataset/AnalyzedData/\u2206suxR_analyzed/suxR.tif",
"type": "Raw Data File"
}
]
},
{
"@id": "#Process_Growth_curves_analysis_2",
"name": "Growth curves analysis_2",
"executesProtocol": {
"@id": "#Protocol_AnalyzedData/\u2206suxC_analyzed",
"name": "AnalyzedData/\u2206suxC_analyzed"
},
"inputs": [
{
"@id": "assays/Growth_Curves/dataset/RawData/\u2206suxC_raw",
"name": "assays/Growth Curves/dataset/RawData/\u2206suxC_raw",
"type": "Raw Data File"
}
],
"outputs": [
{
"@id": "assays/Growth_Curves/dataset/AnalyzedData/\u2206suxC_analyzed/suxC.tif",
"name": "assays/Growth Curves/dataset/AnalyzedData/\u2206suxC_analyzed/suxC.tif",
"type": "Raw Data File"
}
]
},
{
"@id": "#Process_Growth_curves_analysis_3",
"name": "Growth curves analysis_3",
"executesProtocol": {
"@id": "#Protocol_AnalyzedData/\u2206suxB_analyzed",
"name": "AnalyzedData/\u2206suxB_analyzed"
},
"inputs": [
{
"@id": "assays/Growth_Curves/dataset/RawData/\u2206suxB_raw",
"name": "assays/Growth Curves/dataset/RawData/\u2206suxB_raw",
"type": "Raw Data File"
}
],
"outputs": [
{
"@id": "assays/Growth_Curves/dataset/AnalyzedData/\u2206suxB_analyzed/suxB.tif",
"name": "assays/Growth Curves/dataset/AnalyzedData/\u2206suxB_analyzed/suxB.tif",
"type": "Raw Data File"
}
]
},
{
"@id": "#Process_Growth_curves_analysis_4",
"name": "Growth curves analysis_4",
"executesProtocol": {
"@id": "#Protocol_AnalyzedData/\u2206suxA_analyzed",
"name": "AnalyzedData/\u2206suxA_analyzed"
},
"inputs": [
{
"@id": "assays/Growth_Curves/dataset/RawData/\u2206suxA_raw",
"name": "assays/Growth Curves/dataset/RawData/\u2206suxA_raw",
"type": "Raw Data File"
}
],
"outputs": [
{
"@id": "assays/Growth_Curves/dataset/AnalyzedData/\u2206suxA_analyzed/suxA.tif",
"name": "assays/Growth Curves/dataset/AnalyzedData/\u2206suxA_analyzed/suxA.tif",
"type": "Raw Data File"
}
]
},
{
"@id": "#Process_Growth_curves_analysis_5",
"name": "Growth curves analysis_5",
"executesProtocol": {
"@id": "#Protocol_AnalyzedData/wt_analyzed",
"name": "AnalyzedData/wt_analyzed"
},
"inputs": [
{
"@id": "assays/Growth_Curves/dataset/RawData/wt_raw",
"name": "assays/Growth Curves/dataset/RawData/wt_raw",
"type": "Raw Data File"
}
],
"outputs": [
{
"@id": "assays/Growth_Curves/dataset/AnalyzedData/wt_analyzed/wt.tif",
"name": "assays/Growth Curves/dataset/AnalyzedData/wt_analyzed/wt.tif",
"type": "Raw Data File"
}
]
}
]
},
{
"filename": "assays/Motility/isa.assay.xlsx",
"@id": "assays/Motility/",
"measurementType": {
"@id": "https://bioregistry.io/EFO:0002908",
"annotationValue": "motility assay",
"termSource": "EFO",
"termAccession": "https://bioregistry.io/EFO:0002908"
},
"technologyType": {
"@id": "https://bioregistry.io/NCIT:C16215",
"annotationValue": "Soft Agar Assay",
"termSource": "NCIT",
"termAccession": "https://bioregistry.io/NCIT:C16215"
},
"dataFiles": [
{
"@id": "assays/Motility/dataset/RawData/Swimming/Swimming_wt.xlsx",
"name": "assays/Motility/dataset/RawData/Swimming/Swimming_wt.xlsx",
"type": "Raw Data File"
},
{
"@id": "assays/Motility/dataset/RawData/Swimming/Swimming_\u2206sux.xlsx",
"name": "assays/Motility/dataset/RawData/Swimming/Swimming_\u2206sux.xlsx",
"type": "Raw Data File"
},
{
"@id": "assays/Motility/dataset/RawData/Swarming",
"name": "assays/Motility/dataset/RawData/Swarming",
"type": "Raw Data File"
},
{
"@id": "assays/Motility/dataset/AnalyzedData/Swimming_summary.xlsx",
"name": "assays/Motility/dataset/AnalyzedData/Swimming_summary.xlsx",
"type": "Raw Data File"
},
{
"@id": "assays/Motility/dataset/RawData/Swarming/Swarming_\u2206sux.xlsx",
"name": "assays/Motility/dataset/RawData/Swarming/Swarming_\u2206sux.xlsx",
"type": "Raw Data File"
},
{
"@id": "assays/Motility/dataset/RawData/Swarming/Swarming_wt.xlsx",
"name": "assays/Motility/dataset/RawData/Swarming/Swarming_wt.xlsx",
"type": "Raw Data File"
},
{
"@id": "assays/Motility/dataset/AnalyzedData/Swarming_summary.xlsx",
"name": "assays/Motility/dataset/AnalyzedData/Swarming_summary.xlsx",
"type": "Raw Data File"
}
],
"materials": {},
"processSequence": [
{
"@id": "#Process_Motility_0",
"name": "Motility_0",
"executesProtocol": {
"@id": "#Protocol_Protocol_Swimming-Assay-for-Xoo.pdf",
"name": "Protocol_Swimming-Assay-for-Xoo.pdf",
"parameters": [
{
"@id": "#ProtocolParameter/NCIT:C60819",
"parameterName": {
"@id": "NCIT:C60819",
"annotationValue": "Assay",
"termSource": "NCIT",
"termAccession": "NCIT:C60819"
}
}
]
},
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NCIT:C60819",
"parameterName": {
"@id": "NCIT:C60819",
"annotationValue": "Assay",
"termSource": "NCIT",
"termAccession": "NCIT:C60819"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/C_1E56D0A8",
"annotationValue": "swimming",
"termSource": "C",
"termAccession": "http://purl.obolibrary.org/obo/C_1E56D0A8"
}
}
],
"inputs": [
{
"@id": "#Source_Xoo_wt",
"name": "Xoo wt"
},
{
"@id": "#Source_\u2206sux",
"name": "\u2206sux"
}
],
"outputs": [
{
"@id": "assays/Motility/dataset/RawData/Swimming/Swimming_wt.xlsx",
"name": "assays/Motility/dataset/RawData/Swimming/Swimming_wt.xlsx",
"type": "Raw Data File"
},
{
"@id": "assays/Motility/dataset/RawData/Swimming/Swimming_\u2206sux.xlsx",
"name": "assays/Motility/dataset/RawData/Swimming/Swimming_\u2206sux.xlsx",
"type": "Raw Data File"
}
]
},
{
"@id": "#Process_Motility_1",
"name": "Motility_1",
"executesProtocol": {
"@id": "#Protocol_Protocol_Swarming-Assay-for-Xoo.pdf",
"name": "Protocol_Swarming-Assay-for-Xoo.pdf",
"parameters": [
{
"@id": "#ProtocolParameter/NCIT:C60819",
"parameterName": {
"@id": "NCIT:C60819",
"annotationValue": "Assay",
"termSource": "NCIT",
"termAccession": "NCIT:C60819"
}
}
]
},
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NCIT:C60819",
"parameterName": {
"@id": "NCIT:C60819",
"annotationValue": "Assay",
"termSource": "NCIT",
"termAccession": "NCIT:C60819"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/C_7546",
"annotationValue": "swarming",
"termSource": "C",
"termAccession": "http://purl.obolibrary.org/obo/C_7546"
}
}
],
"inputs": [
{
"@id": "#Source_Xoo_wt",
"name": "Xoo wt"
},
{
"@id": "#Source_\u2206sux",
"name": "\u2206sux"
}
],
"outputs": [
{
"@id": "assays/Motility/dataset/RawData/Swarming",
"name": "assays/Motility/dataset/RawData/Swarming",
"type": "Raw Data File"
},
{
"@id": "assays/Motility/dataset/RawData/Swarming",
"name": "assays/Motility/dataset/RawData/Swarming",
"type": "Raw Data File"
}
]
},
{
"@id": "#Process_Motility_Analysis_0",
"name": "Motility Analysis_0",
"executesProtocol": {
"@id": "#Protocol_Protocol_Swimming-Assay-for-Xoo.pdf",
"name": "Protocol_Swimming-Assay-for-Xoo.pdf"
},
"inputs": [
{
"@id": "assays/Motility/dataset/RawData/Swimming/Swimming_\u2206sux.xlsx",
"name": "assays/Motility/dataset/RawData/Swimming/Swimming_\u2206sux.xlsx",
"type": "Raw Data File"
},
{
"@id": "assays/Motility/dataset/RawData/Swimming/Swimming_wt.xlsx",
"name": "assays/Motility/dataset/RawData/Swimming/Swimming_wt.xlsx",
"type": "Raw Data File"
}
],
"outputs": [
{
"@id": "assays/Motility/dataset/AnalyzedData/Swimming_summary.xlsx",
"name": "assays/Motility/dataset/AnalyzedData/Swimming_summary.xlsx",
"type": "Raw Data File"
},
{
"@id": "assays/Motility/dataset/AnalyzedData/Swimming_summary.xlsx",
"name": "assays/Motility/dataset/AnalyzedData/Swimming_summary.xlsx",
"type": "Raw Data File"
}
]
},
{
"@id": "#Process_Motility_Analysis_1",
"name": "Motility Analysis_1",
"executesProtocol": {
"@id": "#Protocol_Protocol_Swarming-Assay-for-Xoo.pdf",
"name": "Protocol_Swarming-Assay-for-Xoo.pdf"
},
"inputs": [
{
"@id": "assays/Motility/dataset/RawData/Swarming/Swarming_\u2206sux.xlsx",
"name": "assays/Motility/dataset/RawData/Swarming/Swarming_\u2206sux.xlsx",
"type": "Raw Data File"
},
{
"@id": "assays/Motility/dataset/RawData/Swarming/Swarming_wt.xlsx",
"name": "assays/Motility/dataset/RawData/Swarming/Swarming_wt.xlsx",
"type": "Raw Data File"
}
],
"outputs": [
{
"@id": "assays/Motility/dataset/AnalyzedData/Swarming_summary.xlsx",
"name": "assays/Motility/dataset/AnalyzedData/Swarming_summary.xlsx",
"type": "Raw Data File"
},
{
"@id": "assays/Motility/dataset/AnalyzedData/Swarming_summary.xlsx",
"name": "assays/Motility/dataset/AnalyzedData/Swarming_summary.xlsx",
"type": "Raw Data File"
}
]
}
]
},
{
"filename": "assays/qRT-PCR/isa.assay.xlsx",
"@id": "assays/qRT-PCR/",
"measurementType": {
"@id": "https://bioregistry.io/NCIT:C185299",
"annotationValue": "Transcript Variant",
"termSource": "NCIT",
"termAccession": "https://bioregistry.io/NCIT:C185299"
},
"technologyType": {
"@id": "http://purl.obolibrary.org/obo/GENEPIO_0001959",
"annotationValue": "RT-PCR method",
"termSource": "GENEPIO",
"termAccession": "http://purl.obolibrary.org/obo/GENEPIO_0001959"
},
"dataFiles": [
{
"@id": "assays/qRT-PCR/dataset/qRT-PCR_14022024/raw_data/suxA",
"name": "assays/qRT-PCR/dataset/qRT-PCR_14022024/raw data/suxA",
"type": "Raw Data File"
},
{
"@id": "assays/qRT-PCR/dataset/qRT-PCR_14022024/raw_data/suxB",
"name": "assays/qRT-PCR/dataset/qRT-PCR_14022024/raw data/suxB",
"type": "Raw Data File"
},
{
"@id": "assays/qRT-PCR/dataset/qRT-PCR_14022024/raw_data/suxC",
"name": "assays/qRT-PCR/dataset/qRT-PCR_14022024/raw data/suxC",
"type": "Raw Data File"
},
{
"@id": "assays/qRT-PCR/dataset/qRT-PCR_14022024/raw_data/suxR",
"name": "assays/qRT-PCR/dataset/qRT-PCR_14022024/raw data/suxR",
"type": "Raw Data File"
},
{
"@id": "assays/qRT-PCR/dataset/qRT-PCR_07082023/raw_data/suxA",
"name": "assays/qRT-PCR/dataset/qRT-PCR_07082023/raw data/suxA",
"type": "Raw Data File"
},
{
"@id": "assays/qRT-PCR/dataset/qRT-PCR_07082023/raw_data/suxB",
"name": "assays/qRT-PCR/dataset/qRT-PCR_07082023/raw data/suxB",
"type": "Raw Data File"
},
{
"@id": "assays/qRT-PCR/dataset/qRT-PCR_07082023/raw_data/suxC",
"name": "assays/qRT-PCR/dataset/qRT-PCR_07082023/raw data/suxC",
"type": "Raw Data File"
},
{
"@id": "assays/qRT-PCR/dataset/qRT-PCR_07082023/raw_data/suxR",
"name": "assays/qRT-PCR/dataset/qRT-PCR_07082023/raw data/suxR",
"type": "Raw Data File"
},
{
"@id": "assays/qRT-PCR/dataset/qRT-PCR_07082023/\u2206ct_sux_genes",
"name": "assays/qRT-PCR/dataset/qRT-PCR_07082023/\u2206ct sux genes",
"type": "Raw Data File"
},
{
"@id": "assays/qRT-PCR/dataset/qRT-PCR_14022024/14022024_\u2206ct_sux_genes",
"name": "assays/qRT-PCR/dataset/qRT-PCR_14022024/14022024_\u2206ct sux genes",
"type": "Raw Data File"
}
],
"materials": {},
"processSequence": [
{
"@id": "#Process_qRT-PCR_0",
"name": "qRT-PCR_0",
"executesProtocol": {
"@id": "#Protocol_qRT-PCR_07082023/2023-07-17-qPCR-of-suxA.pdf",
"name": "qRT-PCR_07082023/2023-07-17-qPCR-of-suxA.pdf",
"parameters": [
{
"@id": "#ProtocolParameter/SO:0000704",
"parameterName": {
"@id": "SO:0000704",
"annotationValue": "gene",
"termSource": "SO",
"termAccession": "SO:0000704"
}
}
]
},
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/SO:0000704",
"parameterName": {
"@id": "SO:0000704",
"annotationValue": "gene",
"termSource": "SO",
"termAccession": "SO:0000704"
}
},
"value": {
"@id": "#UserTerm_suxA",
"annotationValue": "suxA"
}
}
],
"inputs": [
{
"@id": "#Source_Xoo_wt",
"name": "Xoo wt"
}
],
"outputs": [
{
"@id": "assays/qRT-PCR/dataset/qRT-PCR_14022024/raw_data/suxA",
"name": "assays/qRT-PCR/dataset/qRT-PCR_14022024/raw data/suxA",
"type": "Raw Data File"
}
]
},
{
"@id": "#Process_qRT-PCR_1",
"name": "qRT-PCR_1",
"executesProtocol": {
"@id": "#Protocol_qRT-PCR_07082023/2023-07-19-qPCR-of-suxB.pdf",
"name": "qRT-PCR_07082023/2023-07-19-qPCR-of-suxB.pdf",
"parameters": [
{
"@id": "#ProtocolParameter/SO:0000704",
"parameterName": {
"@id": "SO:0000704",
"annotationValue": "gene",
"termSource": "SO",
"termAccession": "SO:0000704"
}
}
]
},
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/SO:0000704",
"parameterName": {
"@id": "SO:0000704",
"annotationValue": "gene",
"termSource": "SO",
"termAccession": "SO:0000704"
}
},
"value": {
"@id": "#UserTerm_suxB",
"annotationValue": "suxB"
}
}
],
"inputs": [
{
"@id": "#Source_Xoo_wt",
"name": "Xoo wt"
}
],
"outputs": [
{
"@id": "assays/qRT-PCR/dataset/qRT-PCR_14022024/raw_data/suxB",
"name": "assays/qRT-PCR/dataset/qRT-PCR_14022024/raw data/suxB",
"type": "Raw Data File"
}
]
},
{
"@id": "#Process_qRT-PCR_2",
"name": "qRT-PCR_2",
"executesProtocol": {
"@id": "#Protocol_qRT-PCR_07082023/2023-08-03-qPCR-of-suxC.pdf",
"name": "qRT-PCR_07082023/2023-08-03-qPCR-of-suxC.pdf",
"parameters": [
{
"@id": "#ProtocolParameter/SO:0000704",
"parameterName": {
"@id": "SO:0000704",
"annotationValue": "gene",
"termSource": "SO",
"termAccession": "SO:0000704"
}
}
]
},
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/SO:0000704",
"parameterName": {
"@id": "SO:0000704",
"annotationValue": "gene",
"termSource": "SO",
"termAccession": "SO:0000704"
}
},
"value": {
"@id": "#UserTerm_suxC",
"annotationValue": "suxC"
}
}
],
"inputs": [
{
"@id": "#Source_Xoo_wt",
"name": "Xoo wt"
}
],
"outputs": [
{
"@id": "assays/qRT-PCR/dataset/qRT-PCR_14022024/raw_data/suxC",
"name": "assays/qRT-PCR/dataset/qRT-PCR_14022024/raw data/suxC",
"type": "Raw Data File"
}
]
},
{
"@id": "#Process_qRT-PCR_3",
"name": "qRT-PCR_3",
"executesProtocol": {
"@id": "#Protocol_qRT-PCR_07082023/2023-08-07-qPCR-of-suxR.pdf",
"name": "qRT-PCR_07082023/2023-08-07-qPCR-of-suxR.pdf",
"parameters": [
{
"@id": "#ProtocolParameter/SO:0000704",
"parameterName": {
"@id": "SO:0000704",
"annotationValue": "gene",
"termSource": "SO",
"termAccession": "SO:0000704"
}
}
]
},
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/SO:0000704",
"parameterName": {
"@id": "SO:0000704",
"annotationValue": "gene",
"termSource": "SO",
"termAccession": "SO:0000704"
}
},
"value": {
"@id": "#UserTerm_suxR",
"annotationValue": "suxR"
}
}
],
"inputs": [
{
"@id": "#Source_Xoo_wt",
"name": "Xoo wt"
}
],
"outputs": [
{
"@id": "assays/qRT-PCR/dataset/qRT-PCR_14022024/raw_data/suxR",
"name": "assays/qRT-PCR/dataset/qRT-PCR_14022024/raw data/suxR",
"type": "Raw Data File"
}
]
},
{
"@id": "#Process_qRT-PCR_4",
"name": "qRT-PCR_4",
"executesProtocol": {
"@id": "#Protocol_qRT-PCR_14022024/qPCR_14.02.2024_I_Analysis.xlsx",
"name": "qRT-PCR_14022024/qPCR_14.02.2024_I_Analysis.xlsx",
"parameters": [
{
"@id": "#ProtocolParameter/SO:0000704",
"parameterName": {
"@id": "SO:0000704",
"annotationValue": "gene",
"termSource": "SO",
"termAccession": "SO:0000704"
}
}
]
},
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/SO:0000704",
"parameterName": {
"@id": "SO:0000704",
"annotationValue": "gene",
"termSource": "SO",
"termAccession": "SO:0000704"
}
},
"value": {
"@id": "#UserTerm_suxA",
"annotationValue": "suxA"
}
}
],
"inputs": [
{
"@id": "#Source_Xoo_wt",
"name": "Xoo wt"
}
],
"outputs": [
{
"@id": "assays/qRT-PCR/dataset/qRT-PCR_14022024/raw_data/suxA",
"name": "assays/qRT-PCR/dataset/qRT-PCR_14022024/raw data/suxA",
"type": "Raw Data File"
}
]
},
{
"@id": "#Process_qRT-PCR_5",
"name": "qRT-PCR_5",
"executesProtocol": {
"@id": "#Protocol_qRT-PCR_14022024/qPCR_14.02.2024_I_Analysis.xlsx",
"name": "qRT-PCR_14022024/qPCR_14.02.2024_I_Analysis.xlsx",
"parameters": [
{
"@id": "#ProtocolParameter/SO:0000704",
"parameterName": {
"@id": "SO:0000704",
"annotationValue": "gene",
"termSource": "SO",
"termAccession": "SO:0000704"
}
}
]
},
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/SO:0000704",
"parameterName": {
"@id": "SO:0000704",
"annotationValue": "gene",
"termSource": "SO",
"termAccession": "SO:0000704"
}
},
"value": {
"@id": "#UserTerm_suxB",
"annotationValue": "suxB"
}
}
],
"inputs": [
{
"@id": "#Source_Xoo_wt",
"name": "Xoo wt"
}
],
"outputs": [
{
"@id": "assays/qRT-PCR/dataset/qRT-PCR_14022024/raw_data/suxB",
"name": "assays/qRT-PCR/dataset/qRT-PCR_14022024/raw data/suxB",
"type": "Raw Data File"
}
]
},
{
"@id": "#Process_qRT-PCR_6",
"name": "qRT-PCR_6",
"executesProtocol": {
"@id": "#Protocol_qRT-PCR_14022024/qPCR_14.02.2024_I_Analysis.xlsx",
"name": "qRT-PCR_14022024/qPCR_14.02.2024_I_Analysis.xlsx",
"parameters": [
{
"@id": "#ProtocolParameter/SO:0000704",
"parameterName": {
"@id": "SO:0000704",
"annotationValue": "gene",
"termSource": "SO",
"termAccession": "SO:0000704"
}
}
]
},
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/SO:0000704",
"parameterName": {
"@id": "SO:0000704",
"annotationValue": "gene",
"termSource": "SO",
"termAccession": "SO:0000704"
}
},
"value": {
"@id": "#UserTerm_suxC",
"annotationValue": "suxC"
}
}
],
"inputs": [
{
"@id": "#Source_Xoo_wt",
"name": "Xoo wt"
}
],
"outputs": [
{
"@id": "assays/qRT-PCR/dataset/qRT-PCR_14022024/raw_data/suxC",
"name": "assays/qRT-PCR/dataset/qRT-PCR_14022024/raw data/suxC",
"type": "Raw Data File"
}
]
},
{
"@id": "#Process_qRT-PCR_7",
"name": "qRT-PCR_7",
"executesProtocol": {
"@id": "#Protocol_qRT-PCR_14022024/qPCR_14.02.2024_I_Analysis.xlsx",
"name": "qRT-PCR_14022024/qPCR_14.02.2024_I_Analysis.xlsx",
"parameters": [
{
"@id": "#ProtocolParameter/SO:0000704",
"parameterName": {
"@id": "SO:0000704",
"annotationValue": "gene",
"termSource": "SO",
"termAccession": "SO:0000704"
}
}
]
},
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/SO:0000704",
"parameterName": {
"@id": "SO:0000704",
"annotationValue": "gene",
"termSource": "SO",
"termAccession": "SO:0000704"
}
},
"value": {
"@id": "#UserTerm_suxR",
"annotationValue": "suxR"
}
}
],
"inputs": [
{
"@id": "#Source_Xoo_wt",
"name": "Xoo wt"
}
],
"outputs": [
{
"@id": "assays/qRT-PCR/dataset/qRT-PCR_14022024/raw_data/suxR",
"name": "assays/qRT-PCR/dataset/qRT-PCR_14022024/raw data/suxR",
"type": "Raw Data File"
}
]
},
{
"@id": "#Process_qRT-PCR_analysis_0",
"name": "qRT-PCR analysis_0",
"executesProtocol": {
"@id": "#Protocol_qRT-PCR_07082023/\u2206ct_sux_genes/sucrase_summary.xlsx",
"name": "qRT-PCR_07082023/\u2206ct sux genes/sucrase_summary.xlsx"
},
"inputs": [
{
"@id": "assays/qRT-PCR/dataset/qRT-PCR_07082023/raw_data/suxA",
"name": "assays/qRT-PCR/dataset/qRT-PCR_07082023/raw data/suxA",
"type": "Raw Data File"
},
{
"@id": "assays/qRT-PCR/dataset/qRT-PCR_07082023/raw_data/suxB",
"name": "assays/qRT-PCR/dataset/qRT-PCR_07082023/raw data/suxB",
"type": "Raw Data File"
},
{
"@id": "assays/qRT-PCR/dataset/qRT-PCR_07082023/raw_data/suxC",
"name": "assays/qRT-PCR/dataset/qRT-PCR_07082023/raw data/suxC",
"type": "Raw Data File"
},
{
"@id": "assays/qRT-PCR/dataset/qRT-PCR_07082023/raw_data/suxR",
"name": "assays/qRT-PCR/dataset/qRT-PCR_07082023/raw data/suxR",
"type": "Raw Data File"
}
],
"outputs": [
{
"@id": "assays/qRT-PCR/dataset/qRT-PCR_07082023/\u2206ct_sux_genes",
"name": "assays/qRT-PCR/dataset/qRT-PCR_07082023/\u2206ct sux genes",
"type": "Raw Data File"
},
{
"@id": "assays/qRT-PCR/dataset/qRT-PCR_07082023/\u2206ct_sux_genes",
"name": "assays/qRT-PCR/dataset/qRT-PCR_07082023/\u2206ct sux genes",
"type": "Raw Data File"
},
{
"@id": "assays/qRT-PCR/dataset/qRT-PCR_07082023/\u2206ct_sux_genes",
"name": "assays/qRT-PCR/dataset/qRT-PCR_07082023/\u2206ct sux genes",
"type": "Raw Data File"
},
{
"@id": "assays/qRT-PCR/dataset/qRT-PCR_07082023/\u2206ct_sux_genes",
"name": "assays/qRT-PCR/dataset/qRT-PCR_07082023/\u2206ct sux genes",
"type": "Raw Data File"
}
]
},
{
"@id": "#Process_qRT-PCR_analysis_1",
"name": "qRT-PCR analysis_1",
"executesProtocol": {
"@id": "#Protocol_qRT-PCR_14022024/14022024_\u2206ct_sux_genes/dct_2_4_6_8hours.pptx",
"name": "qRT-PCR_14022024/14022024_\u2206ct sux genes/dct_2_4_6_8hours.pptx"
},
"inputs": [
{
"@id": "assays/qRT-PCR/dataset/qRT-PCR_14022024/raw_data/suxA",
"name": "assays/qRT-PCR/dataset/qRT-PCR_14022024/raw data/suxA",
"type": "Raw Data File"
},
{
"@id": "assays/qRT-PCR/dataset/qRT-PCR_14022024/raw_data/suxB",
"name": "assays/qRT-PCR/dataset/qRT-PCR_14022024/raw data/suxB",
"type": "Raw Data File"
},
{
"@id": "assays/qRT-PCR/dataset/qRT-PCR_14022024/raw_data/suxC",
"name": "assays/qRT-PCR/dataset/qRT-PCR_14022024/raw data/suxC",
"type": "Raw Data File"
},
{
"@id": "assays/qRT-PCR/dataset/qRT-PCR_14022024/raw_data/suxR",
"name": "assays/qRT-PCR/dataset/qRT-PCR_14022024/raw data/suxR",
"type": "Raw Data File"
}
],
"outputs": [
{
"@id": "assays/qRT-PCR/dataset/qRT-PCR_14022024/14022024_\u2206ct_sux_genes",
"name": "assays/qRT-PCR/dataset/qRT-PCR_14022024/14022024_\u2206ct sux genes",
"type": "Raw Data File"
},
{
"@id": "assays/qRT-PCR/dataset/qRT-PCR_14022024/14022024_\u2206ct_sux_genes",
"name": "assays/qRT-PCR/dataset/qRT-PCR_14022024/14022024_\u2206ct sux genes",
"type": "Raw Data File"
},
{
"@id": "assays/qRT-PCR/dataset/qRT-PCR_14022024/14022024_\u2206ct_sux_genes",
"name": "assays/qRT-PCR/dataset/qRT-PCR_14022024/14022024_\u2206ct sux genes",
"type": "Raw Data File"
},
{
"@id": "assays/qRT-PCR/dataset/qRT-PCR_14022024/14022024_\u2206ct_sux_genes",
"name": "assays/qRT-PCR/dataset/qRT-PCR_14022024/14022024_\u2206ct sux genes",
"type": "Raw Data File"
}
]
}
]
}
],
"factors": [
{
"@id": "#Factor/Factor [Time]",
"factorName": "Factor [Time]",
"factorType": {
"@id": "NCIT:C25207",
"annotationValue": "Time",
"termSource": "NCIT",
"termAccession": "NCIT:C25207"
}
}
],
"characteristicCategories": [
{
"@id": "#MaterialAttribute/#UserTerm_Input_[Sample_Name]",
"characteristicType": {
"@id": "#UserTerm_Input_[Sample_Name]",
"annotationValue": "Input [Sample Name]"
}
}
],
"unitCategories": [
{
"@id": "https://bioregistry.io/UO:0000032",
"annotationValue": "hour",
"termSource": "UO",
"termAccession": "https://bioregistry.io/UO:0000032"
}
]
},
{
"@id": "studies/PLACEHOLDER_STUDY_DNS_Assay/",
"filename": "studies/PLACEHOLDER_STUDY_DNS Assay/isa.study.xlsx",
"identifier": "PLACEHOLDER_STUDY_DNS Assay",
"people": [
{
"@id": "#Nora_Z\u00f6llner",
"firstName": "Nora",
"lastName": "Z\u00f6llner",
"comments": [
{
"name": "performer (ARC:00000168) DNS Assay",
"value": "DNS Assay"
}
]
}
],
"assays": [
{
"filename": "assays/DNS Assay/isa.assay.xlsx",
"@id": "assays/DNS_Assay/",
"measurementType": {
"@id": "http://purl.obolibrary.org/obo/CHEBI_53648",
"annotationValue": "3,5-dinitrosalicylic acid",
"termSource": "CHEBI",
"termAccession": "http://purl.obolibrary.org/obo/CHEBI_53648"
},
"technologyType": {
"@id": "http://purl.obolibrary.org/obo/CHEBI_67126",
"annotationValue": "colorimetric reagent",
"termSource": "CHEBI",
"termAccession": "http://purl.obolibrary.org/obo/CHEBI_67126"
},
"technologyPlatform": "Tecan",
"dataFiles": [
{
"@id": "assays/DNS_Assay/dataset/SuxB_KM.xlsx",
"name": "assays/DNS Assay/dataset/SuxB_KM.xlsx",
"type": "Raw Data File"
}
],
"materials": {
"samples": [
{
"@id": "#Sample_SuxB",
"name": "SuxB"
}
]
},
"processSequence": [
{
"@id": "#Process_DNS_Assay_0",
"name": "DNS Assay_0",
"executesProtocol": {
"@id": "#Protocol_Colorimetric-Invertase-Assay.pdf",
"name": "Colorimetric-Invertase-Assay.pdf",
"description": "Method 1_20241213_151246.xlsx",
"parameters": [
{
"@id": "#ProtocolParameter/NCIT:C60819",
"parameterName": {
"@id": "NCIT:C60819",
"annotationValue": "Assay",
"termSource": "NCIT",
"termAccession": "NCIT:C60819"
}
}
]
},
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NCIT:C60819",
"parameterName": {
"@id": "NCIT:C60819",
"annotationValue": "Assay",
"termSource": "NCIT",
"termAccession": "NCIT:C60819"
}
},
"value": {
"@id": "https://bioregistry.io/CHEBI:53648",
"annotationValue": "3,5-dinitrosalicylic acid",
"termSource": "CHEBI",
"termAccession": "https://bioregistry.io/CHEBI:53648"
}
}
],
"inputs": [
{
"@id": "#Sample_SuxB",
"name": "SuxB"
}
],
"outputs": [
{
"@id": "assays/DNS_Assay/dataset/SuxB_KM.xlsx",
"name": "assays/DNS Assay/dataset/SuxB_KM.xlsx",
"type": "Raw Data File"
}
]
},
{
"@id": "#Process_DNS_Assay_1",
"name": "DNS Assay_1",
"executesProtocol": {
"@id": "#Protocol_Colorimetric-Invertase-Assay.pdf",
"name": "Colorimetric-Invertase-Assay.pdf",
"description": "Method 1_20241213_153520.xlsx",
"parameters": [
{
"@id": "#ProtocolParameter/NCIT:C60819",
"parameterName": {
"@id": "NCIT:C60819",
"annotationValue": "Assay",
"termSource": "NCIT",
"termAccession": "NCIT:C60819"
}
}
]
},
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NCIT:C60819",
"parameterName": {
"@id": "NCIT:C60819",
"annotationValue": "Assay",
"termSource": "NCIT",
"termAccession": "NCIT:C60819"
}
},
"value": {
"@id": "https://bioregistry.io/CHEBI:53648",
"annotationValue": "3,5-dinitrosalicylic acid",
"termSource": "CHEBI",
"termAccession": "https://bioregistry.io/CHEBI:53648"
}
}
],
"inputs": [
{
"@id": "#Sample_SuxB",
"name": "SuxB"
}
],
"outputs": [
{
"@id": "assays/DNS_Assay/dataset/SuxB_KM.xlsx",
"name": "assays/DNS Assay/dataset/SuxB_KM.xlsx",
"type": "Raw Data File"
}
]
},
{
"@id": "#Process_DNS_Assay_2",
"name": "DNS Assay_2",
"executesProtocol": {
"@id": "#Protocol_Colorimetric-Invertase-Assay.pdf",
"name": "Colorimetric-Invertase-Assay.pdf",
"description": "Method 1_20241213_162634.xlsx",
"parameters": [
{
"@id": "#ProtocolParameter/NCIT:C60819",
"parameterName": {
"@id": "NCIT:C60819",
"annotationValue": "Assay",
"termSource": "NCIT",
"termAccession": "NCIT:C60819"
}
}
]
},
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NCIT:C60819",
"parameterName": {
"@id": "NCIT:C60819",
"annotationValue": "Assay",
"termSource": "NCIT",
"termAccession": "NCIT:C60819"
}
},
"value": {
"@id": "https://bioregistry.io/CHEBI:53648",
"annotationValue": "3,5-dinitrosalicylic acid",
"termSource": "CHEBI",
"termAccession": "https://bioregistry.io/CHEBI:53648"
}
}
],
"inputs": [
{
"@id": "#Sample_SuxB",
"name": "SuxB"
}
],
"outputs": [
{
"@id": "assays/DNS_Assay/dataset/SuxB_KM.xlsx",
"name": "assays/DNS Assay/dataset/SuxB_KM.xlsx",
"type": "Raw Data File"
}
]
},
{
"@id": "#Process_DNS_Assay_3",
"name": "DNS Assay_3",
"executesProtocol": {
"@id": "#Protocol_Colorimetric-Invertase-Assay.pdf",
"name": "Colorimetric-Invertase-Assay.pdf",
"description": "Method 1_20241213_164820.xlsx",
"parameters": [
{
"@id": "#ProtocolParameter/NCIT:C60819",
"parameterName": {
"@id": "NCIT:C60819",
"annotationValue": "Assay",
"termSource": "NCIT",
"termAccession": "NCIT:C60819"
}
}
]
},
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NCIT:C60819",
"parameterName": {
"@id": "NCIT:C60819",
"annotationValue": "Assay",
"termSource": "NCIT",
"termAccession": "NCIT:C60819"
}
},
"value": {
"@id": "https://bioregistry.io/CHEBI:53648",
"annotationValue": "3,5-dinitrosalicylic acid",
"termSource": "CHEBI",
"termAccession": "https://bioregistry.io/CHEBI:53648"
}
}
],
"inputs": [
{
"@id": "#Sample_SuxB",
"name": "SuxB"
}
],
"outputs": [
{
"@id": "assays/DNS_Assay/dataset/SuxB_KM.xlsx",
"name": "assays/DNS Assay/dataset/SuxB_KM.xlsx",
"type": "Raw Data File"
}
]
},
{
"@id": "#Process_DNS_Assay_4",
"name": "DNS Assay_4",
"executesProtocol": {
"@id": "#Protocol_Colorimetric-Invertase-Assay.pdf",
"name": "Colorimetric-Invertase-Assay.pdf",
"description": "Method 1_20241216_163243.xlsx",
"parameters": [
{
"@id": "#ProtocolParameter/NCIT:C60819",
"parameterName": {
"@id": "NCIT:C60819",
"annotationValue": "Assay",
"termSource": "NCIT",
"termAccession": "NCIT:C60819"
}
}
]
},
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NCIT:C60819",
"parameterName": {
"@id": "NCIT:C60819",
"annotationValue": "Assay",
"termSource": "NCIT",
"termAccession": "NCIT:C60819"
}
},
"value": {
"@id": "https://bioregistry.io/CHEBI:53648",
"annotationValue": "3,5-dinitrosalicylic acid",
"termSource": "CHEBI",
"termAccession": "https://bioregistry.io/CHEBI:53648"
}
}
],
"inputs": [
{
"@id": "#Sample_SuxB",
"name": "SuxB"
}
],
"outputs": [
{
"@id": "assays/DNS_Assay/dataset/SuxB_KM.xlsx",
"name": "assays/DNS Assay/dataset/SuxB_KM.xlsx",
"type": "Raw Data File"
}
]
}
]
}
]
},
{
"@id": "studies/PLACEHOLDER_STUDY_RNAseq_Visualization/",
"filename": "studies/PLACEHOLDER_STUDY_RNAseq_Visualization/isa.study.xlsx",
"identifier": "PLACEHOLDER_STUDY_RNAseq_Visualization",
"people": [
{
"@id": "jacob.sharkey@hhu.de",
"firstName": "Jacob",
"lastName": "Sharkey",
"midInitials": "E",
"email": "jacob.sharkey@hhu.de",
"affiliation": "Heinrich Heine University D\u00fcsseldorf, Institute for Molecular Physiology",
"comments": [
{
"name": "performer (ARC:00000168) RNAseq_Visualization",
"value": "RNAseq_Visualization"
}
]
}
],
"assays": [
{
"filename": "assays/RNAseq_Visualization/isa.assay.xlsx",
"@id": "assays/RNAseq_Visualization/",
"technologyPlatform": "R (CHEBI:8735)",
"dataFiles": [
{
"@id": "assays/RNAseq_Visualization/dataset/invitro_RNAseq_analysis/RNAseq_Visuals/2hourvolcano3D.html",
"name": "assays/RNAseq_Visualization/dataset/invitro_RNAseq_analysis/RNAseq_Visuals/2hourvolcano3D.html",
"type": "Raw Data File"
},
{
"@id": "assays/RNAseq_Visualization/dataset/invitro_RNAseq_analysis/RNAseq_Visuals/4hourvolcano3D.html",
"name": "assays/RNAseq_Visualization/dataset/invitro_RNAseq_analysis/RNAseq_Visuals/4hourvolcano3D.html",
"type": "Raw Data File"
},
{
"@id": "assays/RNAseq_Visualization/dataset/invitro_RNAseq_analysis/RNAseq_Visuals/6hourvolcano3D.html",
"name": "assays/RNAseq_Visualization/dataset/invitro_RNAseq_analysis/RNAseq_Visuals/6hourvolcano3D.html",
"type": "Raw Data File"
},
{
"@id": "assays/RNAseq_Visualization/dataset/invitro_RNAseq_analysis/RNAseq_Visuals/PCA.png",
"name": "assays/RNAseq_Visualization/dataset/invitro_RNAseq_analysis/RNAseq_Visuals/PCA.png",
"type": "Raw Data File"
},
{
"@id": "assays/RNAseq_Visualization/dataset/read_counts/1.count/gene_count.xls",
"name": "assays/RNAseq_Visualization/dataset/read_counts/1.count/gene_count.xls",
"type": "Raw Data File"
},
{
"@id": "assays/RNAseq_Visualization/dataset/invitro_RNAseq_analysis/RNAseq_Data",
"name": "assays/RNAseq_Visualization/dataset/invitro_RNAseq_analysis/RNAseq_Data",
"type": "Raw Data File"
}
],
"materials": {},
"processSequence": [
{
"@id": "#Process_Visualization_0",
"name": "Visualization_0",
"executesProtocol": {
"@id": "#Protocol_Volcano3D_Zoellner14.Rmd",
"name": "Volcano3D_Zoellner14.Rmd"
},
"inputs": [
{
"@id": "#Source_read_counts/1.count/gene_count.xls",
"name": "read_counts/1.count/gene_count.xls"
},
{
"@id": "#Source_read_counts/1.count/gene_count.xls",
"name": "read_counts/1.count/gene_count.xls"
},
{
"@id": "#Source_read_counts/1.count/gene_count.xls",
"name": "read_counts/1.count/gene_count.xls"
}
],
"outputs": [
{
"@id": "assays/RNAseq_Visualization/dataset/invitro_RNAseq_analysis/RNAseq_Visuals/2hourvolcano3D.html",
"name": "assays/RNAseq_Visualization/dataset/invitro_RNAseq_analysis/RNAseq_Visuals/2hourvolcano3D.html",
"type": "Raw Data File"
},
{
"@id": "assays/RNAseq_Visualization/dataset/invitro_RNAseq_analysis/RNAseq_Visuals/4hourvolcano3D.html",
"name": "assays/RNAseq_Visualization/dataset/invitro_RNAseq_analysis/RNAseq_Visuals/4hourvolcano3D.html",
"type": "Raw Data File"
},
{
"@id": "assays/RNAseq_Visualization/dataset/invitro_RNAseq_analysis/RNAseq_Visuals/6hourvolcano3D.html",
"name": "assays/RNAseq_Visualization/dataset/invitro_RNAseq_analysis/RNAseq_Visuals/6hourvolcano3D.html",
"type": "Raw Data File"
}
]
},
{
"@id": "#Process_Visualization_1",
"name": "Visualization_1",
"executesProtocol": {
"@id": "#Protocol_PCA_Zoellner6.Rmd",
"name": "PCA_Zoellner6.Rmd"
},
"inputs": [
{
"@id": "#Source_read_counts/1.count/gene_count.xls",
"name": "read_counts/1.count/gene_count.xls"
}
],
"outputs": [
{
"@id": "assays/RNAseq_Visualization/dataset/invitro_RNAseq_analysis/RNAseq_Visuals/PCA.png",
"name": "assays/RNAseq_Visualization/dataset/invitro_RNAseq_analysis/RNAseq_Visuals/PCA.png",
"type": "Raw Data File"
}
]
},
{
"@id": "#Process_DEG_tables",
"name": "DEG tables",
"executesProtocol": {
"@id": "#Protocol_Volcano3D_Zoellner14.Rmd",
"name": "Volcano3D_Zoellner14.Rmd",
"parameters": [
{
"@id": "#ProtocolParameter/#UserTerm_DEG_analysis",
"parameterName": {
"@id": "#UserTerm_DEG_analysis",
"annotationValue": "DEG analysis"
}
}
]
},
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_DEG_analysis",
"parameterName": {
"@id": "#UserTerm_DEG_analysis",
"annotationValue": "DEG analysis"
}
},
"value": {
"@id": "#UserTerm_EdgeR",
"annotationValue": "EdgeR"
}
}
],
"inputs": [
{
"@id": "assays/RNAseq_Visualization/dataset/read_counts/1.count/gene_count.xls",
"name": "assays/RNAseq_Visualization/dataset/read_counts/1.count/gene_count.xls",
"type": "Raw Data File"
}
],
"outputs": [
{
"@id": "assays/RNAseq_Visualization/dataset/invitro_RNAseq_analysis/RNAseq_Data",
"name": "assays/RNAseq_Visualization/dataset/invitro_RNAseq_analysis/RNAseq_Data",
"type": "Raw Data File"
}
]
}
]
}
]
}
]
}