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cidgoh / GRDI_AMR_One_Health

A data specification for harmonizing One Health AMR pathogen genomics contextual data. The specification provides standardized (ontology-based) fields and terms which are implemented via a spreadsheet collection template, supported by field and reference guides as well as different curation and new term request SOPs.
MIT License
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6.4.2 - release note tracking #18

Closed cmrn-rhi closed 1 year ago

cmrn-rhi commented 1 year ago

Template Fixes:

Specification Changes:

Field Change
antimicrobial_agent_name NEW PICKLIST items: Enrofloxacin [CHEBI:35720], Norfloxacin [CHEBI:100246], Oxolinic acid [CHEBI:138856], Oxytetracycline [CHEBI:27701], Piperacillin [CHEBI:8232], Polymyxin B [ARO:3000454]
<enrofloxacin_fields> NEW enrofloxacin fields: resistance_phenotype, measurement_sign, measurement, testing_standard, testing_standard_version, testing_standard_details,susceptible_breakpoint, intermediate_breakpoint, and resistant_breakpoint.
food_packaging_date NEW field.
food_product_properties NEW PICKLIST items: Food (canned) [FOODON:00002418], Food (dried) [FOODON:03307539], Food (fresh) [FOODON:00002457], and Food (frozen) [FOODON:03302148].
food_quality_date NEW field.
<norfloxacin_fields> NEW norfloxacin fields: resistance_phenotype, measurement_sign, measurement, testing_standard, testing_standard_version, testing_standard_details,susceptible_breakpoint, intermediate_breakpoint, and resistant_breakpoint.
<oxolinic-acid_fields> NEW oxolinic acid fields: resistance_phenotype, measurement_sign, measurement, testing_standard, testing_standard_version, testing_standard_details,susceptible_breakpoint, intermediate_breakpoint, and resistant_breakpoint.
<oxytetracycline_fields> NEW oxytetracycline fields: resistance_phenotype, measurement_sign, measurement, testing_standard, testing_standard_version, testing_standard_details,susceptible_breakpoint, intermediate_breakpoint, and resistant_breakpoint.
<piperacillin_fields> NEW piperacillin fields: resistance_phenotype, measurement_sign, measurement, testing_standard, testing_standard_version, testing_standard_details,susceptible_breakpoint, intermediate_breakpoint, and resistant_breakpoint.
<polymyxin-b_fields> NEW polymyxin b fields: resistance_phenotype, measurement_sign, measurement, testing_standard, testing_standard_version, testing_standard_details,susceptible_breakpoint, intermediate_breakpoint, and resistant_breakpoint.
sequencing_instrument Several GENEPIO term IDs deprecated after rehoming in OBI, see issue #18 for details.

Version Tracking:

Excel Template, Reference Guides, Curation SOP

New Term SOP to be update as well.

cmrn-rhi commented 1 year ago

Deprecated IDs

sequencing_instrument new IDs deprecated IDs
Illumina Genome Analyzer II OBI:0000703 GENEPIO:0100107
Illumina Genome Analyzer IIx OBI:0002000 GENEPIO:0100108
Illumina HiSeq 1000 OBI:0002022 GENEPIO:0100114
Illumina HiSeq 2000 OBI:0002001 GENEPIO:0100116
Illumina HiSeq 2500 OBI:0002002 GENEPIO:0100117
Illumina HiSeq 3000 OBI:0002048 GENEPIO:0100118
Illumina HiSeq 4000 OBI:0002049 GENEPIO:0100119
Illumina MiSeq OBI:0002003 GENEPIO:0100125
Illumina NextSeq 500 OBI:0002021 GENEPIO:0100127
PacBio RS II OBI:0002012 GENEPIO:0100132

Rationale: Ontology for Biomedical Investigations (OBI) was deemed an appropriate domain ontology to home these terms. All sequencing instrument terms are in the process of being created in OBI, imported into GENEPIO, and then deprecated in GENEPIO. More information on this process is available at: https://github.com/cidgoh/GRDI_AMR_One_Health/wiki/Deprecating-&-Normalizing-Specification-Values-&-IDs

cmrn-rhi commented 1 year ago

Released