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4.2.1 - release note tracking #9

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cmrn-rhi opened this issue Nov 9, 2022 · 5 comments
Closed

4.2.1 - release note tracking #9

cmrn-rhi opened this issue Nov 9, 2022 · 5 comments
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@cmrn-rhi
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cmrn-rhi commented Nov 9, 2022 •
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Template Fixes:

  • Added the following fields to the Strain and Isolate Information and Merged tabs:
    • ceftazidime_testing_standard
    • ceftazidime_testing_standard_version
    • ceftazidime_testing_standard_details
    • ceftazidime_susceptible_breakpoint
    • ceftazidime_intermediate_breakpoint
    • ceftazidime_resistant_breakpoint
    • ceftazidime-clavulanic_acid_resistance_phenotype
    • ceftazidime-clavulanic_acid_measurement_sign
    • ceftazidime-clavulanic_acid_measurement
  • Purpose_of_sequencing field now draws from the purpose_of_sequencing picklist instead of the purpose_of_sampling picklist. No impact users at this time since both lists contained the same entities.

Specification Changes:

Field Change
animal_source_of_food FOODON:03411563 label updated from "Poultry" to "Poultry or game bird"
food_product "Meat scrap" FOODON:03309475 removed due to synonymy with "Meat trim" FOODON:03309475 which was already present in this list.
environmental_material "Bulk tank" ENVO:03501407 removed (incorrect ID assignment) and new ID has been requested. "Animal manure" ENVO:00003031 ID changed to AGRO:00000079. "Poultry litter" ENVO:00003860 ID changed to AGRO:00000080
host (food production name) FOODON:03411563 label updated from "Poultry" to "Poultry or game bird". "Whether" changed to "Wether sheep" FOODON:00004306
organism Still discussing with workgroup.
taxonomic_identification_process New recommended field GENEPIO:0100583 and associated picklist added.
taxonomic_identification_process_details New free text recommended field GENEPIO:0100584 added.

Specification Changes - Reference Guide Only:

Field Change
food_product "Chicken meat (ground or minced, extra lean)" FOODON:03000392 ID corrected to FOODON:03000396.
@cmrn-rhi
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cmrn-rhi commented Nov 15, 2022 •
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Confirmed with Andrew Scott that Ceftazidime and Ceftazidime + Clavulanic acid group were the fields missing.

Following added to spec under organisms:

  • Citrobacter freundii [NCBITaxon:546]
  • Salmonella enterica subsp. arizonae [NCBITaxon:59203]
  • Klebsiella oxytoca [NCBITaxon:571]
  • Klebsiella pneumoniae subsp pneumoniae [NCBITaxon:72407]
  • Klebsiella pneumoniae subsp ozaenae [NCBITaxon:574]
  • Enterobacter cloacae [NCBITaxon:550]

@cmrn-rhi
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Also added "Salmonella enterica" [NCBITaxon:28901] to provide a more general term people can use. Still need to discuss the addition of other general organism classes and addressing the "non-listeria monocytogenes listeria" class request.

@cmrn-rhi
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Updates to organisms based on AMR-GRDI Workgroup meeting (2022-11-14):

New Terms:

  • Acinetobacter sp. [NCBITaxon:472]
  • Citrobacter freundii [NCBITaxon:546]
  • Comamonas [NCBITaxon:283]
  • Comamonas aquatica [NCBITaxon:225991]
  • Enterobacter cancerogenus [NCBITaxon:69218]
  • Enterobacter cloacae [NCBITaxon:550]
  • Enterobacter hormaechei [NCBITaxon:158836]
  • Lelliottia amnigena [NCBITaxon:61646]
  • Pluralibacter gergoviae [NCBITaxon:61647]
  • Salmonella enterica subsp. arizonae [NCBITaxon:59203]
  • Klebsiella oxytoca [NCBITaxon:571]
  • Klebsiella pneumoniae subsp. pneumoniae [NCBITaxon:72407]
  • Klebsiella pneumoniae subsp. ozaenae [NCBITaxon:574]
  • Kosakonia [NCBITaxon:1330547]
  • Leclercia [NCBITaxon:83654]
  • Listeria [NCBITaxon:1637]
  • Ochrobactrum [NCBITaxon:528]
  • Providencia [NCBITaxon:586]
  • Providencia rettgeri [NCBITaxon:587]
  • Rahnella [NCBITaxon:34037]
  • Rahnella aquatilis [NCBITaxon:34038]
  • Raoultella [NCBITaxon:160674]
  • Salmonella enterica [NCBITaxon:28901]
  • Salmonella enterica subsp. arizonae [NCBITaxon:59203]
  • Vibrio [NCBITaxon:662]

Changed Terms:

  • Klebsiella pneumoniae [NCIT:C86457] -> [NCBITaxon:573]
  • Salmonella enterica subsp enterica -> Salmonella enterica subsp. enterica

Removed Terms:

  • Acinetobacter baumannii NIPH 60 NCBITaxon:1217647
  • Acinetobacter baumannii NIPH 80 NCBITaxon:1217629
  • Acinetobacter sp. Ag2 NCBITaxon:1646532
  • Citrobacter freundii GTC 09479 NCBITaxon:1288347
  • Citrobacter sp. KTE32 NCBITaxon:1169350
  • Citrobacter sp. MGH105 NCBITaxon:1686380
  • Comamonas aquatica DA1877 NCBITaxon:1457173
  • Enterobacter cloacae complex sp. 43444
  • Enterobacter cloacae complex sp. GN03164
  • Enterobacter cloacae str. Hanford NCBITaxon:1340854
  • Enterobacter cloacae UCI 49 NCBITaxon:1400154
  • Enterobacter hormaechei subsp. steigerwaltii NCBITaxon:299766
  • Enterobacter sp. BIDMC93 NCBITaxon:1686396
  • Enterobacter sp. SA187 NCBITaxon:1914861
  • Escherichia coli 1047 NCBITaxon:1411693
  • Escherichia coli 1365 NCBITaxon:1411697
  • Escherichia coli 2-011-08_S4_C1 NCBITaxon:1444201
  • Escherichia coli 2-156-04_S3_C2 NCBITaxon:1444150
  • Escherichia coli 2-210-07_S3_C1 NCBITaxon:1444122
  • Escherichia coli 2-316-03_S3_C1 NCBITaxon:1444124
  • Escherichia coli 3-105-05_S4_C3 NCBITaxon:1444278
  • Escherichia coli 3-267-03_S1_C2 NCBITaxon:1444085
  • Escherichia coli 3006 NCBITaxon:1005565
  • Escherichia coli 38.16 NCBITaxon:1411698
  • Escherichia coli 5-172-05_S4_C3 NCBITaxon:1444269
  • Escherichia coli 541-1 NCBITaxon:752786
  • Escherichia coli 6-537-08_S4_C2 NCBITaxon:1444257
  • Escherichia coli 7-233-03_S4_C1 NCBITaxon:1444213
  • Escherichia coli APEC O78 NCBITaxon:1274814
  • Escherichia coli C353_09 NCBITaxon:1126898
  • Escherichia coli chi7122 NCBITaxon:475609
  • Escherichia coli E1140 NCBITaxon:1453472
  • Escherichia coli FBP1 NCBITaxon:1412837
  • Escherichia coli FCP1 NCBITaxon:1412839
  • Escherichia coli HVH 150 (4-3258106) NCBITaxon:1281083
  • Escherichia coli HVH 22 (4-2258986) NCBITaxon:1280973
  • Escherichia coli HVH 79 (4-2512823) NCBITaxon:1281017
  • Escherichia coli HVH 83 (4-2051087) NCBITaxon:1281020
  • Escherichia coli IAI1 NCBITaxon:585034
  • Escherichia coli IMT8073 NCBITaxon:1337997
  • Escherichia coli KOEGE 3 (4a) NCBITaxon:1281153
  • Escherichia coli KOEGE 40 (102a) NCBITaxon:1281159
  • Escherichia coli KTE100 NCBITaxon:1182699
  • Escherichia coli KTE13 NCBITaxon:1169318
  • Escherichia coli KTE146 NCBITaxon:1182725
  • Escherichia coli KTE184 NCBITaxon:1181730
  • Escherichia coli KTE196 NCBITaxon:1181742
  • Escherichia coli KTE222 NCBITaxon:1181768
  • Escherichia coli KTE47 NCBITaxon:1182654
  • Escherichia coli MS499 NCBITaxon:1450517
  • Escherichia coli N1 NCBITaxon:1005567
  • Escherichia coli O103:H11 str. 04-3023 NCBITaxon:1446501
  • Escherichia coli O5:K4(L):H4 str. ATCC 23502 NCBITaxon:1268238
  • Escherichia coli O69:H11 str. 07-3763 NCBITaxon:1446751
  • Escherichia coli UMEA 3336-1 NCBITaxon:1281243
  • Escherichia coli UMEA 3671-1 NCBITaxon:1281260
  • Escherichia coli UMEA 3805-1 NCBITaxon:1281270
  • Escherichia fergusonii ATCC 35469 NCBITaxon:585054
  • Klebsiella oxytoca MGH 28 NCBITaxon:1328429
  • Pseudomonas sp. HMSC064G05 NCBITaxon:1715204
  • Pseudomonas sp. HMSC067F09 NCBITaxon:1739343
  • Rahnella sp. Y9602 NCBITaxon:1873497
  • Serratia sp. 14-2641 NCBITaxon:1841657

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cmrn-rhi commented Nov 16, 2022 •
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Other field changes:

environmental_site

  • Research farm [ENVO:03501417]; new ID
  • Manure digester facility [ENVO:03501422]; new ID and definition
  • Manure lagoon (Anaerobic lagoon) [ENVO:03501423]; new ID and definition

weather_type

  • Cloudy/Overcast [ENVO:03501418]; new ID and definition
  • Partially cloudy [ENVO:03501419]; new ID and definition
  • Drizzle [ENVO:03501420]; new ID and definition

environmental_material

  • Fluid from meat rinse[GENEPIO:0004323]; new ID
  • Freezer [ENVO:03501415]; new ID and definition
  • Freezer handle [ENVO:03501414]; new ID and definition
  • Manure digester equipment [ENVO:03501424]; new ID and definition

anatomical_part

  • Swine carcass [FOODON:03311719]; new definition

food_product

  • Brassica carinata meal [FOODON:00004310]; new ID and definition
  • Sausage (whole) [FOODON:03315904]; new label and definition
  • Corn cob (whole or parts) [FOODON:03310791]; new label and definition
  • Greens (raw) [FOODON:03310765]; new definition

food_product_properties

  • Italian-style food product [FOODON:00004321]; new label, ID, and definition

collection_device

  • Culture plate [GENEPIO:0004318]; new ID and definition
  • Vacuum device [GENEPIO:0002127]; new definition

collection_method

  • Fecal grab [GENEPIO:0004326]; new ID

host (common name)

  • Companion animal [FOODON:03000300]; new ID

host (food production name)

  • Fish egg [FOODON_00004319]; new ID and definition
  • Fry (fish) [FOODON_00004318]; new ID and definition
  • Juvenile fish [FOODON_00004317]; new ID and definition

sequencing_platform

  • BGI Genomics [GENEPIO:0004324]; new ID
  • MGI [GENEPIO:0004325]; new ID

@cmrn-rhi cmrn-rhi mentioned this issue Nov 16, 2022
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@cmrn-rhi
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Released v4.2.1

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