🐝 antibiotics: updating metadata (#3601)

* updating metadata * rearrange * adding per million for tests with ast result * remove per million calculation * resistance * updating snapshot * remove unused module
owid · Nov 24, 2024 · 9f58c4c · 9f58c4c
1 parent 794b052
commit 9f58c4c
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Showing 4 changed files with 31 additions and 20 deletions.
diff --git a/etl/steps/data/garden/antibiotics/2024-10-18/who_glass.meta.yml b/etl/steps/data/garden/antibiotics/2024-10-18/who_glass.meta.yml
@@ -6,7 +6,18 @@ definitions:
         - Global Health
         - Antibiotics
     display:
-      name: << syndrome.capitalize >>
+      name: << syndrome.capitalize() >>
+  syndrome:
+    <%- if syndrome == "BLOOD" %>
+    bloodstream
+    <%- elif syndrome == "STOOL" %>
+    gastrointestinal
+    <%- elif syndrome == "URINE" %>
+    urinary tract
+    <%- elif syndrome == "UROGENITAL" %>
+    gonorrohea
+    <% endif %>
+
 
 
 # Learn more about the available fields:
@@ -19,30 +30,30 @@ tables:
   who_glass:
     variables:
       bcispermillion:
-        title: Bacteriologically confirmed <<syndrome.lower()>> infections per million population
+        title: Samples tested and confirmed to be {definitions.syndrome} infections per million population
         unit: "confirmed infections per million"
         presentation:
-          title_public: Bacteriologically confirmed <<syndrome.lower()>> infections per million population
+          title_public: Samples tested and confirmed to be {definitions.syndrome} infections per million population
       totalspecimenisolates:
-        title: Total specimen isolates of <<syndrome.lower()>> infections
-        unit: "isolates"
+        title: Total specimens collected of {definitions.syndrome} infections
+        unit: "specimens"
         presentation:
-          title_public: Total specimen isolates of <<syndrome.lower()>> infections
+          title_public: Total specimen collected of {definitions.syndrome} infections
       isolspermillion:
-        title: Isolates of <<syndrome.lower()>> infections per million population
-        unit: "isolates per million"
+        title: Samples tested and confirmed to be {definitions.syndrome} infections with antibiotic susceptibility test results per million population
+        unit: "confirmed infections per million"
         presentation:
-          title_public: Isolates of <<syndrome.lower()>> infections per million population
+          title_public: Samples tested and confirmed to be {definitions.syndrome} infections with antibiotic susceptibility test results per million population
       totalspecimenisolateswithast:
-        title: Bacterially confirmed <<syndrome.lower()>> infections per million population with antibiotic susceptibility test results
-        unit: "confirmed infections per million"
+        title: Samples tested and confirmed to be {definitions.syndrome} infections with antibiotic susceptibility test results
+        unit: "confirmed infections"
         presentation:
-          title_public: Bacterially confirmed <<syndrome.lower()>> infections per million population with antibiotic susceptibility test results
+          title_public: Samples tested and confirmed to be {definitions.syndrome} infections with antibiotic susceptibility test results
       astresult:
-        title: Share of bacterial confirmed <<syndrome.lower()>> infections with antibiotic susceptibility test results
+        title: Share of samples tested and confirmed to be {definitions.syndrome} infections with antibiotic susceptibility test results
         unit: "%"
         short_unit: "%"
         display:
           numDecimalPlaces: 1
         presentation:
-          title_public: Share of bacterial confirmed <<syndrome.lower()>> infections with antibiotic susceptibility test results
+          title_public: Share of samples tested and confirmed to be {definitions.syndrome} infections with antibiotic susceptibility test results
diff --git a/etl/steps/data/garden/antibiotics/2024-10-18/who_glass.py b/etl/steps/data/garden/antibiotics/2024-10-18/who_glass.py
@@ -13,7 +13,7 @@ def run(dest_dir: str) -> None:
     #
     # Load meadow dataset.
     ds_meadow = paths.load_dataset("who_glass")
-
+    # Add population dataset.
     # Read table from meadow dataset.
     tb = ds_meadow["who_glass"].reset_index()
 

diff --git a/snapshots/antibiotics/2024-10-18/who_glass.zip.dvc b/snapshots/antibiotics/2024-10-18/who_glass.zip.dvc
@@ -3,7 +3,7 @@
 meta:
   origin:
     # Data product / Snapshot
-    title: Global Antimicrobial Resitsance and Use Surveillance System (GLASS)
+    title: Global Antimicrobial Resistance and Use Surveillance System (GLASS)
     description: |-
       GLASS provides a standardized approach to the collection, analysis, interpretation and sharing of data by countries and seeks to actively support capacity building and monitor the status of existing and new national surveillance systems. Furthermore, GLASS promotes a shift from surveillance approaches based solely on laboratory data to a system that includes epidemiological, clinical, and population-level data. GLASS has been conceived to progressively incorporate data from surveillance of AMR in humans, such as monitoring of resistance and the use of antimicrobial medicines, including AMR in the food chain and in the environment.
     date_published: "2024-09-16"
@@ -14,7 +14,7 @@ meta:
     # Citation
     producer: World Health Organization
     citation_full: |-
-      Global AMR data - Global Antimicrobial Resitsance and Use Surveillance System (GLASS), World Health Organization (2024)
+      Global AMR data - Global Antimicrobial Resistance and Use Surveillance System (GLASS), World Health Organization (2024)
 
     attribution_short: WHO
 
@@ -28,6 +28,6 @@ meta:
       url: https://www.who.int/about/policies/terms-of-use
 
 outs:
-  - md5: 12d197f03c1dc917f7e27662bd2e581b
+  - md5: b1c4d820b37417b77214db814348233f
     size: 55169
     path: who_glass.zip
diff --git a/snapshots/antibiotics/2024-10-18/who_glass_by_antibiotic.zip.dvc b/snapshots/antibiotics/2024-10-18/who_glass_by_antibiotic.zip.dvc
@@ -3,7 +3,7 @@
 meta:
   origin:
     # Data product / Snapshot
-    title: Global Antimicrobial Resitsance and Use Surveillance System (GLASS) - by antibiotic
+    title: Global Antimicrobial Resistance and Use Surveillance System (GLASS) - by antibiotic
     description: |-
       GLASS provides a standardized approach to the collection, analysis, interpretation and sharing of data by countries and seeks to actively support capacity building and monitor the status of existing and new national surveillance systems. Furthermore, GLASS promotes a shift from surveillance approaches based solely on laboratory data to a system that includes epidemiological, clinical, and population-level data. GLASS has been conceived to progressively incorporate data from surveillance of AMR in humans, such as monitoring of resistance and the use of antimicrobial medicines, including AMR in the food chain and in the environment.
     date_published: "2024-09-16"
@@ -14,7 +14,7 @@ meta:
     # Citation
     producer: World Health Organization
     citation_full: |-
-      Global AMR data - Global Antimicrobial Resitsance and Use Surveillance System (GLASS), World Health Organization (2024)
+      Global AMR data - Global Antimicrobial Resistance and Use Surveillance System (GLASS), World Health Organization (2024)
 
     attribution_short: WHO