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Merge pull request #425 from cidgoh/grdi-update
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GRDI template update
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@kennethbruskiewicz
kennethbruskiewicz committed Dec 8, 2023
2 parents c6fa6e3 + 7af754a commit c6e938e
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185 changes: 142 additions & 43 deletions web/templates/grdi/schema.json
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Original file line number Diff line number Diff line change
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"name": "GRDI",
"description": "",
"id": "https://example.com/GRDI",
"version": "8.8.4",
"version": "8.9.8",
"prefixes": {
"linkml": {
"prefix_prefix": "linkml",
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}
},
"enums": {
"null value menu": {
"name": "null value menu",
"from_schema": "https://example.com/GRDI",
"permissible_values": {
"Not Applicable [GENEPIO:0001619]": {
"text": "Not Applicable [GENEPIO:0001619]"
},
"Missing [GENEPIO:0001618]": {
"text": "Missing [GENEPIO:0001618]"
},
"Not Collected [GENEPIO:0001620]": {
"text": "Not Collected [GENEPIO:0001620]"
},
"Not Provided [GENEPIO:0001668]": {
"text": "Not Provided [GENEPIO:0001668]"
},
"Restricted Access [GENEPIO:0001810]": {
"text": "Restricted Access [GENEPIO:0001810]"
}
}
},
"sample_collected_by menu": {
"name": "sample_collected_by menu",
"from_schema": "https://example.com/GRDI",
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"Technical replicate [OBI:0000249]": {
"text": "Technical replicate [OBI:0000249]"
},
"Isolated from single source": {
"text": "Isolated from single source"
"Isolated from single source [GENEPIO:0100926]": {
"text": "Isolated from single source [GENEPIO:0100926]"
}
}
},
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"Artificial wetland [ENVO:03501406]": {
"text": "Artificial wetland [ENVO:03501406]"
},
"Breeding ground": {
"text": "Breeding ground"
"Breeding ground [ENVO:03501441]": {
"text": "Breeding ground [ENVO:03501441]"
},
"Building [ENVO:00000073]": {
"text": "Building [ENVO:00000073]"
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"Farm [ENVO:00000078]": {
"text": "Farm [ENVO:00000078]"
},
"Beef farm": {
"text": "Beef farm",
"Beef farm [ENVO:03501443]": {
"text": "Beef farm [ENVO:03501443]",
"is_a": "Farm [ENVO:00000078]"
},
"Breeder farm [ENVO:03501384]": {
Expand All @@ -1378,8 +1399,8 @@
"text": "Feedlot [ENVO:01000627]",
"is_a": "Farm [ENVO:00000078]"
},
"Beef cattle feedlot": {
"text": "Beef cattle feedlot",
"Beef cattle feedlot [ENVO:03501444]": {
"text": "Beef cattle feedlot [ENVO:03501444]",
"is_a": "Feedlot [ENVO:01000627]"
},
"Fish farm [ENVO:00000294]": {
Expand Down Expand Up @@ -1419,8 +1440,8 @@
"Marine environment [ENVO:01000320]": {
"text": "Marine environment [ENVO:01000320]"
},
"Benthic zone": {
"text": "Benthic zone",
"Benthic zone [ENVO:03501440]": {
"text": "Benthic zone [ENVO:03501440]",
"is_a": "Marine environment [ENVO:01000320]"
},
"Pelagic zone [ENVO:00000208]": {
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"River [ENVO:00000022]": {
"text": "River [ENVO:00000022]"
},
"Roost (bird)": {
"text": "Roost (bird)"
"Roost (bird) [ENVO:03501439]": {
"text": "Roost (bird) [ENVO:03501439]"
},
"Rural area [ENVO:01000772]": {
"text": "Rural area [ENVO:01000772]"
},
"Slough": {
"text": "Slough"
"Slough [ENVO:03501438]": {
"text": "Slough [ENVO:03501438]"
},
"Stream [ENVO:00000023]": {
"text": "Stream [ENVO:00000023]"
Expand All @@ -1483,8 +1504,8 @@
"Truck [ENVO:01000602]": {
"text": "Truck [ENVO:01000602]"
},
"Urban area": {
"text": "Urban area"
"Urban area [ENVO:03501437]": {
"text": "Urban area [ENVO:03501437]"
},
"Water surface [ENVO:01001191]": {
"text": "Water surface [ENVO:01001191]"
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"Contaminated water [ENVO:00002186]": {
"text": "Contaminated water [ENVO:00002186]"
},
"Fecal slurry": {
"text": "Fecal slurry",
"Fecal slurry [ENVO:03501436]": {
"text": "Fecal slurry [ENVO:03501436]",
"is_a": "Contaminated water [ENVO:00002186]"
},
"Fluid from meat rinse [GENEPIO:0004323]": {
Expand All @@ -1883,8 +1904,8 @@
"text": "Effluent [ENVO:03501407]",
"is_a": "Contaminated water [ENVO:00002186]"
},
"Influent": {
"text": "Influent",
"Influent [ENVO:03501442]": {
"text": "Influent [ENVO:03501442]",
"is_a": "Contaminated water [ENVO:00002186]"
},
"Surface runoff [ENVO:03501408]": {
Expand Down Expand Up @@ -2049,16 +2070,16 @@
"Feces [UBERON:0001988]": {
"text": "Feces [UBERON:0001988]"
},
"Fecal composite": {
"text": "Fecal composite",
"Fecal composite [GENEPIO:0004512]": {
"text": "Fecal composite [GENEPIO:0004512]",
"is_a": "Feces [UBERON:0001988]"
},
"Feces (fresh)": {
"text": "Feces (fresh)",
"Feces (fresh) [GENEPIO:0004512]": {
"text": "Feces (fresh) [GENEPIO:0004512]",
"is_a": "Feces [UBERON:0001988]"
},
"Feces (environmental)": {
"text": "Feces (environmental)",
"Feces (environmental) [GENEPIO:0004514]": {
"text": "Feces (environmental) [GENEPIO:0004514]",
"is_a": "Feces [UBERON:0001988]"
},
"Meconium [UBERON:0007109]": {
Expand Down Expand Up @@ -2248,8 +2269,8 @@
"text": "Mesenteric lymph node [UBERON:0002509]",
"is_a": "Lymph node [UBERON:0000029]"
},
"Mantle (bird)": {
"text": "Mantle (bird)"
"Mantle (bird) [GENEPIO:0100927]": {
"text": "Mantle (bird) [GENEPIO:0100927]"
},
"Neck [UBERON:0000974]": {
"text": "Neck [UBERON:0000974]"
Expand Down Expand Up @@ -3426,8 +3447,8 @@
"Auger (earth auger) [AGRO:00000405]": {
"text": "Auger (earth auger) [AGRO:00000405]"
},
"Box corer": {
"text": "Box corer"
"Box corer [GENEPIO:0100928]": {
"text": "Box corer [GENEPIO:0100928]"
},
"Container [OBI:0000967]": {
"text": "Container [OBI:0000967]"
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"Filter [GENEPIO:0100103]": {
"text": "Filter [GENEPIO:0100103]"
},
"PONAR grab sampler": {
"text": "PONAR grab sampler"
"PONAR grab sampler [GENEPIO:0100929]": {
"text": "PONAR grab sampler [GENEPIO:0100929]"
},
"Scoop [GENEPIO:0002125]": {
"text": "Scoop [GENEPIO:0002125]"
},
"Soil sample probe": {
"text": "Soil sample probe"
"Soil sample probe [GENEPIO:0100930]": {
"text": "Soil sample probe [GENEPIO:0100930]"
},
"Spatula [NCIT:C149941]": {
"text": "Spatula [NCIT:C149941]"
Expand Down Expand Up @@ -3517,8 +3538,8 @@
"text": "Air filtration [GENEPIO:0100031]",
"is_a": "Filtration [OBI:0302885]"
},
"Water filtration": {
"text": "Water filtration",
"Water filtration [GENEPIO:0100931]": {
"text": "Water filtration [GENEPIO:0100931]",
"is_a": "Filtration [OBI:0302885]"
},
"Lavage [OBI:0600044]": {
Expand All @@ -3541,14 +3562,14 @@
"Rinsing for specimen collection [GENEPIO_0002116]": {
"text": "Rinsing for specimen collection [GENEPIO_0002116]"
},
"Scooping": {
"text": "Scooping"
"Scooping [GENEPIO:0100932]": {
"text": "Scooping [GENEPIO:0100932]"
},
"Sediment collection": {
"text": "Sediment collection"
"Sediment collection [GENEPIO:0100933]": {
"text": "Sediment collection [GENEPIO:0100933]"
},
"Soil coring": {
"text": "Soil coring"
"Soil coring [GENEPIO:0100934]": {
"text": "Soil coring [GENEPIO:0100934]"
}
}
},
Expand Down Expand Up @@ -4050,6 +4071,14 @@
"text": "Aeromonas hydrophila [NCBITaxon:644]",
"is_a": "Aeromonas [NCBITaxon:642]"
},
"Aeromonas rivipollensis [NCBITaxon:948519]": {
"text": "Aeromonas rivipollensis [NCBITaxon:948519]",
"is_a": "Aeromonas [NCBITaxon:642]"
},
"Aeromonas salmonicida [NCBITaxon:645]": {
"text": "Aeromonas salmonicida [NCBITaxon:645]",
"is_a": "Aeromonas [NCBITaxon:642]"
},
"Campylobacter [NCBITaxon:194]": {
"text": "Campylobacter [NCBITaxon:194]"
},
Expand All @@ -4076,6 +4105,10 @@
"text": "Citrobacter freundii [NCBITaxon:546]",
"is_a": "Citrobacter [NCBITaxon:544]"
},
"Citrobacter gillenii [NCBITaxon:67828]": {
"text": "Citrobacter gillenii [NCBITaxon:67828]",
"is_a": "Citrobacter [NCBITaxon:544]"
},
"Clostridioides [NCBITaxon:1870884]": {
"text": "Clostridioides [NCBITaxon:1870884]"
},
Expand All @@ -4090,6 +4123,10 @@
"text": "Clostridium perfringens [NCBITaxon:1502]",
"is_a": "Clostridium [NCBITaxon:1485]"
},
"Clostridium sporogenes [NCBITaxon:1509]": {
"text": "Clostridium sporogenes [NCBITaxon:1509]",
"is_a": "Clostridium [NCBITaxon:1485]"
},
"Comamonas [NCBITaxon:283]": {
"text": "Comamonas [NCBITaxon:283]"
},
Expand Down Expand Up @@ -4218,6 +4255,17 @@
"text": "Escherichia fergusonii [NCBITaxon:564]",
"is_a": "Escherichia [NCBITaxon:561]"
},
"Exiguobacterium [NCBITaxon:33986]": {
"text": "Exiguobacterium [NCBITaxon:33986]"
},
"Exiguobacterium oxidotolerans [NCBITaxon:223958]": {
"text": "Exiguobacterium oxidotolerans [NCBITaxon:223958]",
"is_a": "Exiguobacterium [NCBITaxon:33986]"
},
"Exiguobacterium sp. [NCBITaxon:44751]": {
"text": "Exiguobacterium sp. [NCBITaxon:44751]",
"is_a": "Exiguobacterium [NCBITaxon:33986]"
},
"Klebsiella [NCBITaxon:570]": {
"text": "Klebsiella [NCBITaxon:570]"
},
Expand Down Expand Up @@ -4245,6 +4293,13 @@
"text": "Klebsiella pneumoniae subsp. ozaenae [NCBITaxon:574]",
"is_a": "Klebsiella [NCBITaxon:570]"
},
"Kluyvera [NCBITaxon:579]": {
"text": "Kluyvera [NCBITaxon:579]"
},
"Kluyvera intermedia [NCBITaxon:61648]": {
"text": "Kluyvera intermedia [NCBITaxon:61648]",
"is_a": "Kluyvera [NCBITaxon:579]"
},
"Kosakonia [NCBITaxon:1330547]": {
"text": "Kosakonia [NCBITaxon:1330547]"
},
Expand Down Expand Up @@ -4276,13 +4331,27 @@
"text": "Pantoea ananatis [NCBITaxon:553]",
"is_a": "Pantoea [NCBITaxon:53335]"
},
"Photobacterium [NCBITaxon:657]": {
"text": "Photobacterium [NCBITaxon:657]"
},
"Photobacterium sp. [NCBITaxon:660]": {
"text": "Photobacterium sp. [NCBITaxon:660]",
"is_a": "Photobacterium [NCBITaxon:657]"
},
"Providencia [NCBITaxon:586]": {
"text": "Providencia [NCBITaxon:586]"
},
"Providencia rettgeri [NCBITaxon:587]": {
"text": "Providencia rettgeri [NCBITaxon:587]",
"is_a": "Providencia [NCBITaxon:586]"
},
"Pseudoalteromonas [NCBITaxon:53246]": {
"text": "Pseudoalteromonas [NCBITaxon:53246]"
},
"Pseudoalteromonas tetraodonis [NCBITaxon:43659]": {
"text": "Pseudoalteromonas tetraodonis [NCBITaxon:43659]",
"is_a": "Pseudoalteromonas [NCBITaxon:53246]"
},
"Pseudomonas [NCBITaxon:286]": {
"text": "Pseudomonas [NCBITaxon:286]"
},
Expand All @@ -4298,6 +4367,21 @@
"text": "Pseudomonas soli [NCBITaxon:1306993]",
"is_a": "Pseudomonas [NCBITaxon:286]"
},
"Pseudomonas sp. [NCBITaxon:306]": {
"text": "Pseudomonas sp. [NCBITaxon:306]",
"is_a": "Pseudomonas [NCBITaxon:286]"
},
"Psychrobacter [NCBITaxon:497]": {
"text": "Psychrobacter [NCBITaxon:497]"
},
"Psychrobacter faecalis [NCBITaxon:180588]": {
"text": "Psychrobacter faecalis [NCBITaxon:180588]",
"is_a": "Psychrobacter [NCBITaxon:497]"
},
"Psychrobacter sp. [NCBITaxon:56811]": {
"text": "Psychrobacter sp. [NCBITaxon:56811]",
"is_a": "Psychrobacter [NCBITaxon:497]"
},
"Rahnella [NCBITaxon:34037]": {
"text": "Rahnella [NCBITaxon:34037]"
},
Expand Down Expand Up @@ -4330,6 +4414,21 @@
"Serratia [NCBITaxon:613]": {
"text": "Serratia [NCBITaxon:613]"
},
"Shewanella [NCBITaxon:22]": {
"text": "Shewanella [NCBITaxon:22]"
},
"Shewanella pealeana [NCBITaxon:70864]": {
"text": "Shewanella pealeana [NCBITaxon:70864]",
"is_a": "Shewanella [NCBITaxon:22]"
},
"Shewanella putrefaciens [NCBITaxon:24]": {
"text": "Shewanella putrefaciens [NCBITaxon:24]",
"is_a": "Shewanella [NCBITaxon:22]"
},
"Shewanella sp. [NCBITaxon:50422]": {
"text": "Shewanella sp. [NCBITaxon:50422]",
"is_a": "Shewanella [NCBITaxon:22]"
},
"Staphylococcus [NCBITaxon:1279]": {
"text": "Staphylococcus [NCBITaxon:1279]"
},
Expand Down
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