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ddooleyddooley
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WastewaterSinglePathogen renamed WastewaterPathogenAgnostic
+ various grdi and Wastewater enum changes
1 parent b582522 commit e0ca01d

11 files changed

+8417
-5899
lines changed

‎web/templates/grdi/schema.json

+1,406-1,288
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‎web/templates/grdi/schema.yaml

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‎web/templates/grdi/schema_core.yaml

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@@ -1,7 +1,7 @@
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id: https://example.com/GRDI
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name: "GRDI"
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description: ""
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version: 9.0.0
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version: 10.0.0
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imports:
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- 'linkml:types'
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prefixes:

‎web/templates/grdi/schema_enums.tsv

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@@ -354,7 +354,7 @@ environmental_site menu Abattoir [ENVO:01000925]
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Artificial wetland [ENVO:03501406]
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Breeding ground [ENVO:03501441]
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Building [ENVO:00000073]
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Barn [EOL:0001898]
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Barn [ENVO:03501257]
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Breeder barn [ENVO:03501383]
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Broiler barn [ENVO:03501386]
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Sheep barn [ENVO:03501385]
@@ -537,11 +537,11 @@ environmental_material menu Air [ENVO:00002005]
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Biosolids [ENVO:00002059]
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Boot [GSSO:012935]
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Boot cover [OBI:0002806]
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Broom [ENVO:03501377]
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Broom [ENVO:03501431]
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Bulk tank [ENVO:03501379]
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Chick box [AGRO:00000678]
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Chick pad [AGRO:00000672]
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Cleaning equipment [ENVO:03501376]
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Cleaning equipment [ENVO:03501430]
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Compost [ENVO:00002170]
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Contaminated water [ENVO:00002186]
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Fecal slurry [ENVO:03501436]
@@ -574,8 +574,9 @@ environmental_material menu Air [ENVO:00002005]
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Agricultural soil [ENVO:00002259]
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Forest soil [ENVO:00002261]
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Straw [ENVO:00003869]
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Canola straw
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Canola straw [FOODON:00004430]
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Oat straw [FOODON:03309878]
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Barley straw [FOODON:00004559]
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Water [CHEBI:15377]
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Drinking water [ENVO:00003064]
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Groundwater [ENVO:01001004]
@@ -632,7 +633,7 @@ anatomical_part menu Carcass [UBERON:0008979]
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Rectum [UBERON:0001052]
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Spleen [UBERON:0002106]
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Urinary bladder [UBERON:0001255]
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Foot [BTO:0000476]
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Foot [UBERON:0002387]
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Head [UBERON:0000033]
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Brain [UBERON:0000955]
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Ear [UBERON:0001690]
@@ -776,9 +777,9 @@ food_product menu Animal feed [ENVO:02000047]
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Chicken meat (ground or minced, regular) [FOODON:03000404]
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Chicken meat (ground or minced, boneless) [FOODON:03000410]
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Chicken nugget [FOODON:00002672]
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Chicken thigh
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Chicken thigh [FOODON:02020219]
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Chicken thigh (skinless) [FOODON:00003331]
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Chicken thigh (skinless, with bone)
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Chicken thigh (skinless, with bone) [FOODON:02020227]
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Chicken thigh (skinless, boneless) [FOODON:03000417]
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Chicken upper thigh [FOODON:03000381]
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Chicken upper thigh (with skin) [FOODON:03000383]
@@ -815,7 +816,8 @@ food_product menu Animal feed [ENVO:02000047]
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Pepperoni [FOODON:03311003]
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Salami [FOODON:03312067]
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Shellfish [FOODON:03411433]
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Shrimp [FOODON:03411237]
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Shrimp [FOODON:03411237]
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Scallop [FOODON:03411489]
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Turkey breast [FOODON:00002690]
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Turkey breast (back off) [FOODON:03000386]
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Turkey breast (skinless) [FOODON:03000372]
@@ -846,6 +848,8 @@ food_product menu Animal feed [ENVO:02000047]
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Nuts and seed products
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Almond (whole or parts) [FOODON:03000218]
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Almond (whole) [FOODON:00003523]
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Barley seed [FOODON:00003394]
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Canola seed [FOODON:00004560]
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Chia seed powder [FOODON:00003925]
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Chia seed (whole or parts) [FOODON:03000241]
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Flaxseed powder [FOODON:00004276]
@@ -955,6 +959,9 @@ animal_source_of_food menu Cow [NCBITaxon:9913]
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Chicken [NCBITaxon:9031]
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Turkey [NCBITaxon:9103]
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Sheep [NCBITaxon:9940]
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Shellfish [FOODON:03411433]
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Scallop [NCBITaxon:6566]
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Shrimp [FOODON:03411237
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food_product_production_stream menu Beef cattle production stream [FOODON:03000452]
@@ -1036,9 +1043,11 @@ host (common name) menu Bird [NCBITaxon:8782]
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Turkey [NCBITaxon:9103]
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Fish [FOODON:03411222]
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Rainbow Trout [NCBITaxon:8022]
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Sablefish [NCBITaxon:229290]
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Salmon [FOODON:00003473]
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Atlantic Salmon [NCBITaxon:8030]
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Chinook salmon [NCBITaxon:74940]
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Coho Salmon [NCBITaxon:8019]
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Mammal [FOODON:03411134]
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Companion animal [FOODON:03000300]
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Cow [NCBITaxon:9913]
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Blue Mussel [NCBITaxon:6550]
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host (scientific name) menu Bos taurus [NCBITaxon:9913]
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host (scientific name) menu Anoplopoma fimbria [NCBITaxon:229290]
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Bos taurus [NCBITaxon:9913]
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Crassostrea virginica [NCBITaxon:6565]
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Gallus gallus [NCBITaxon:9031]
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Grus americana [NCBITaxon:9117]
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Larus marinus [NCBITaxon:8912]
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Meleagris gallopavo [NCBITaxon:9103]
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Mytilus edulis [NCBITaxon:6550]
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Oncorhynchus kisutch [NCBITaxon:8019]
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Oncorhynchus mykiss [NCBITaxon:8022]
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Oncorhynchus tshawytscha [NCBITaxon:74940]
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Ovis aries [NCBITaxon:9940]
@@ -1216,6 +1227,7 @@ organism menu Acinetobacter [NCBITaxon:469]
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Pantoea [NCBITaxon:53335]
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Pantoea ananatis [NCBITaxon:553]
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Photobacterium [NCBITaxon:657]
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Photobacterium indicum[NCBITaxon:81447]
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Photobacterium sp. [NCBITaxon:660]
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Providencia [NCBITaxon:586]
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Providencia rettgeri [NCBITaxon:587]
@@ -1228,6 +1240,7 @@ organism menu Acinetobacter [NCBITaxon:469]
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Pseudomonas sp. [NCBITaxon:306]
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Psychrobacter [NCBITaxon:497]
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Psychrobacter faecalis [NCBITaxon:180588]
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Psychrobacter nivimaris [NCBITaxon:281738]
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Psychrobacter sp. [NCBITaxon:56811]
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Rahnella [NCBITaxon:34037]
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Rahnella aquatilis [NCBITaxon:34038]
@@ -1241,6 +1254,7 @@ organism menu Acinetobacter [NCBITaxon:469]
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Shewanella [NCBITaxon:22]
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Shewanella pealeana [NCBITaxon:70864]
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Shewanella putrefaciens [NCBITaxon:24]
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Shewanella oncorhynchi [NCBITaxon:2726434]
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Shewanella sp. [NCBITaxon:50422]
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Staphylococcus [NCBITaxon:1279]
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Staphylococcus aureus [NCBITaxon:1280]
@@ -1270,6 +1284,7 @@ sequenced_by menu Public Health Agency of Canada (PHAC) [GENEPIO:0100551]
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Health Canada (HC) [GENEPIO:0100554]
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Environment and Climate Change Canada (ECCC) [GENEPIO:0100555]
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Fisheries and Oceans Canada (DFO) [GENEPIO:0100556]
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McGill University [GENEPIO:0101083]
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12741289

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purpose_of_sequencing menu Cluster/Outbreak investigation [GENEPIO:0100001]
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DNBSEQ-G50 [GENEPIO:0100150]
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13391354

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sequencing_assay_type menu Amplicon sequencing assay [OBI:0002767]
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16S ribosomal gene sequencing assay [OBI:0002763]
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Whole genome sequencing assay [OBI:0002117]
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Whole metagenome sequencing assay [OBI:0002623]
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Whole virome sequencing assay [OBI:0002768]
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sequence_submitted_by menu Public Health Agency of Canada (PHAC) [GENEPIO:0100551]
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Canadian Food Inspection Agency (CFIA) [GENEPIO:0100552]
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Agriculture and Agri-Food Canada (AAFC) [GENEPIO:0100553]
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Health Canada (HC) [GENEPIO:0100554]
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Environment and Climate Change Canada (ECCC) [GENEPIO:0100555]
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Fisheries and Oceans Canada (DFO) [GENEPIO:0100556]
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McGill University [GENEPIO:0101083]
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attribute_package menu Pathogen.cl [GENEPIO:0001835]

‎web/templates/grdi/schema_slots.tsv

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@@ -106,6 +106,7 @@ Multiple alternative isolate IDs can be provided, separated by semi-colons." GHI
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Sequence information GENEPIO:0100472 sequencing_project_name WhitespaceMinimizedString The name of the project/initiative/program for which sequencing was performed. Provide the name of the project and/or the project ID here. If the information is unknown or cannot be provided, leave blank or provide a null value. AMR-GRDI (PA-1356)
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Sequence information GENEPIO:0100473 sequencing_platform sequencing_platform menu null value menu The platform technology used to perform the sequencing. Provide the name of the company that created the sequencing instrument by selecting a value from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value. Illumina [GENEPIO:0001923]
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Sequence information GENEPIO:0001452 sequencing_instrument sequencing_instrument menu null value menu The model of the sequencing instrument used. Provide the model sequencing instrument by selecting a value from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value. Illumina HiSeq 2500 [GENEPIO:0100117]
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Sequence information GENEPIO:0100997 sequencing_assay_type sequencing_assay_type menu The overarching sequencing methodology that was used to determine the sequence of a biomaterial. Example Guidance: Provide the name of the DNA or RNA sequencing technology used in your study. If unsure refer to the protocol documentation, or provide a null value. whole genome sequencing assay [OBI:0002117]
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Sequence information GENEPIO:0001450 library_preparation_kit WhitespaceMinimizedString The name of the DNA library preparation kit used to generate the library being sequenced. Provide the name of the library preparation kit used. Nextera XT
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Sequence information GENEPIO:0001454 sequencing_protocol WhitespaceMinimizedString The protocol or method used for sequencing. Provide the name and version of the procedure or protocol used for sequencing. You can also provide a link to a protocol online. https://www.protocols.io/view/ncov-2019-sequencing-protocol-bbmuik6w?version_warning=no
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Sequence information GENEPIO:0001476 r1_fastq_filename WhitespaceMinimizedString The user-specified filename of the r1 FASTQ file. Provide the r1 FASTQ filename. ABC123_S1_L001_R1_001.fastq.gz

‎web/templates/menu.json

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@@ -78,8 +78,8 @@
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"status": "published",
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"display": true
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},
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"WastewaterSinglePathogen": {
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"name": "WastewaterSinglePathogen",
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"WastewaterPathogenAgnostic": {
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"name": "WastewaterPathogenAgnostic",
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"status": "published",
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"display": true
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}

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