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Added 'type of chemical entity (Q113145171)' #274

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Merged
DeniseSl22 merged 5 commits into from
Jan 29, 2026
Merged

Added 'type of chemical entity (Q113145171)' #274

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38bdd3b
Added 'type of chemical entity (Q113145171)'
DeniseSl22 Jan 29, 2026
e80cb7c
Update API endpoint for Wikidata queries and error detection
DeniseSl22 Jan 29, 2026
9d047d9
Added wdt:P31 individually
DeniseSl22 Jan 29, 2026
21eeb74
Added wdt:P31 individually to avoid loosing data
DeniseSl22 Jan 29, 2026
d3fa935
Added wdt:p31 directly to avoid loosing data
DeniseSl22 Jan 29, 2026
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12 changes: 9 additions & 3 deletions .github/workflows/wikidata.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -72,11 +72,11 @@ jobs:

echo 'Accessing the Wikidata data'
## Download outdated IDs for chemicals qLever Style
curl -H "Accept: text/tab-separated-values" --data-urlencode query@datasources/wikidata/queries/chemicalAllRedirects.rq -G https://qlever.cs.uni-freiburg.de/api/wikidata -o datasources/wikidata/recentData/metabolites.tsv
curl -H "Accept: text/tab-separated-values" --data-urlencode query@datasources/wikidata/queries/chemicalAllRedirects.rq -G https://qlever.dev/api/wikidata -o datasources/wikidata/recentData/metabolites.tsv
## Download outdated IDs for genes qLever Style
curl -H "Accept: text/tab-separated-values" --data-urlencode query@datasources/wikidata/queries/geneHumanAllRedirects.rq -G https://qlever.cs.uni-freiburg.de/api/wikidata -o datasources/wikidata/recentData/gene.tsv
curl -H "Accept: text/tab-separated-values" --data-urlencode query@datasources/wikidata/queries/geneHumanAllRedirects.rq -G https://qlever.dev/api/wikidata -o datasources/wikidata/recentData/gene.tsv
## Download outdated IDs for proteins qLever Style
curl -H "Accept: text/tab-separated-values" --data-urlencode query@datasources/wikidata/queries/proteinHumanAllRedirects.rq -G https://qlever.cs.uni-freiburg.de/api/wikidata -o datasources/wikidata/recentData/protein.tsv
curl -H "Accept: text/tab-separated-values" --data-urlencode query@datasources/wikidata/queries/proteinHumanAllRedirects.rq -G https://qlever.dev/api/wikidata -o datasources/wikidata/recentData/protein.tsv


##Check new data, fail job if query timeout has occured
Expand All @@ -89,6 +89,12 @@ jobs:
head -n 20 "$File"
#echo "DOWNLOAD_FILE=true" >>$GITHUB_ENV
fail_file="${fail_file} $File"
elif grep -q "html" "$File"; then
echo "Data grab error occurred for file: " "$File"
echo "Wikidata data will not be updated"
head -n 20 "$File"
#echo "DOWNLOAD_FILE=true" >>$GITHUB_ENV
fail_file="${fail_file} $File"
else
echo "No Query Timeout detected for file: " "$File"
fi
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15 changes: 15 additions & 0 deletions datasources/wikidata/queries/chemicalAllRedirects.rq
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Expand Up @@ -10,19 +10,34 @@ WHERE
{
{ ?primaryID p:P31/ps:P31 wd:Q11173 }
UNION
{ ?primaryID wdt:P31 wd:Q11173 }
UNION
{ ?primaryID p:P31/ps:P31 wd:Q36496 }
UNION
{ ?primaryID wdt:P31 wd:Q36496 }
UNION
{ ?primaryID p:P31/ps:P31 wd:Q79529 }
UNION
{ ?primaryID wdt:P31 wd:Q79529 }
UNION
{ ?primaryID p:P31/ps:P31 wd:Q55662747 }
UNION
{ ?primaryID wdt:P31 wd:Q55662747 }
UNION
{ ?primaryID p:P31/ps:31 wd:Q113145171 }
UNION
{ ?primaryID wdt:P31 wd:Q113145171 }
UNION
{ ?primaryID p:P279/ps:P279 wd:Q11173 }
UNION
{ ?primaryID p:P279/ps:P279 wd:Q36496 }
UNION
{ ?primaryID p:P279/ps:P279 wd:Q79529 }
UNION
{ ?primaryID p:P279/ps:P279 wd:Q55662747 }
UNION
{ ?primaryID p:P279/ps:P279 wd:Q113145171 }


OPTIONAL{?secondaryID owl:sameAs ?primaryID.}
OPTIONAL{?primaryID rdfs:label ?name.
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2 changes: 2 additions & 0 deletions datasources/wikidata/queries/geneHumanAllRedirects.rq
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Original file line number Diff line number Diff line change
Expand Up @@ -10,6 +10,8 @@ WHERE
{
{ ?primaryID p:P31/ps:P31 wd:Q7187 }
UNION
{ ?primaryID wdt:P31 wd:Q7187 }
UNION
{ ?primaryID p:P279/ps:P279 wd:Q7187 }

?primaryID wdt:P703 wd:Q15978631.
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2 changes: 2 additions & 0 deletions datasources/wikidata/queries/proteinHumanAllRedirects.rq
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Original file line number Diff line number Diff line change
Expand Up @@ -10,6 +10,8 @@ WHERE
{
{ ?primaryID p:P31/ps:P31 wd:Q8054 }
UNION
{ ?primaryID wdt:P31 wd:Q8054 }
UNION
{ ?primaryID p:P279/ps:P279 wd:Q8054 }

?primaryID wdt:P703 wd:Q15978631.
Expand Down