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(v0.7.1.9024) eucast_rules() fix, new MOs

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dr. M.S. (Matthijs) Berends
2019-08-06 14:39:22 +02:00
parent 85b62aaf8f
commit 3a1f960f89
23 changed files with 252 additions and 411 deletions
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12
data-raw/eucast_rules.tsv
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@ -1,4 +1,14 @@
if_mo_property like_is_one_of this_value and_these_antibiotics have_these_values then_change_these_antibiotics to_value reference.rule reference.rule_group
# ---------------------------------------------------------------------------------------------------
# For editing this EUCAST reference file, these values can all be used for target antibiotics:
# all_betalactams, aminoglycosides, carbapenems, cephalosporins, cephalosporins_without_CAZ, fluoroquinolones,
# glycopeptides, macrolides, minopenicillins, polymyxins, streptogramins, tetracyclines, ureidopenicillins
# and all separate EARS-Net letter codes like AMC. They can be separated by comma: 'AMC, fluoroquinolones'.
# The if_mo_property column can be any column name from the AMR::microorganisms data set, or "genus_species" or "gramstain".
# The like.is.one_of column must contain one of: like, is, one_of ('like' will read the first column as regular expression)
# The EUCAST guideline contains references to the 'Burkholderia cepacia complex'. All species in this group can be found in: LiPuma J, Curr Opin Pulm Med. 2005 Nov;11(6):528-33. (PMID 16217180).
# >>>>> IF YOU WANT TO IMPORT THIS FILE INTO YOUR OWN SOFTWARE, HAVE THE FIRST 10 LINES SKIPPED <<<<<
# ---------------------------------------------------------------------------------------------------
if_mo_property like.is.one_of this_value and_these_antibiotics have_these_values then_change_these_antibiotics to_value reference.rule reference.rule_group
order is Enterobacteriales AMP S AMX S Enterobacteriales (Order) Breakpoints
order is Enterobacteriales AMP I AMX I Enterobacteriales (Order) Breakpoints
order is Enterobacteriales AMP R AMX R Enterobacteriales (Order) Breakpoints

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