egonw

@Grab(group='org.bridgedb', module='org.bridgedb.bio', version='3.1.1')

import java.util.ArrayList
import java.util.List
import java.util.Map
import java.util.HashMap

import java.nio.file.Path
import java.nio.file.Files

egonw

SELECT DISTINCT ?entity ?entityLabel ?propertyLabel ?valueLabel ?retracted ?retractedLabel WITH {
  SELECT DISTINCT ?entity ?p ?statement ?retracted WHERE {
    ?retracted wdt:P31 wd:Q45182324 .
    ?entity ?p ?statement .
    ?statement prov:wasDerivedFrom / pr:P248 ?retracted .
  }
} AS %STATEMENTS WHERE {
  INCLUDE %STATEMENTS
  ?p ^wikibase:claim ?property .
  ?statement ?ps ?value .

egonw

Pathways without any tag: 74. Details:
http://classic.wikipathways.org/instance/WP3104_r118203 'Mevalonate pathway (Arabidopsis thaliana)' 
http://classic.wikipathways.org/instance/WP3029_r118242 'Vitamin E biosynthesis (Arabidopsis thaliana)' 
http://classic.wikipathways.org/instance/WP3113_r118262 'Gibberellin biosynthesis III (early C-13 hydroxylation) (Arabidopsis thaliana)' 
http://classic.wikipathways.org/instance/WP3024_r116502 'Formation of ternary complex, then 43S complex (Oryza sativa)' 
http://classic.wikipathways.org/instance/WP3066_r118243 'Glutamine biosynthesis I (Arabidopsis thaliana)' 
http://classic.wikipathways.org/instance/WP3083_r118610 'Gamma-glutamyl cycle (Zea mays)' 
http://classic.wikipathways.org/instance/WP3003_r118295 'Cap-dependent translation initiation (Oryza sativa)' 
http://classic.wikipathways.org/instance/WP3087_r118265 'GDP-L-fucose biosynthesis I from GDP-D-mannose (Arabidopsis thaliana)' 
http://classic.wikipathways.org/instance/WP3035_r118280 'IAA biosynthesis VI via i

egonw

PREFIX target: <http://www.wikidata.org/entity/Q76>

SELECT DISTINCT ?source ?sourceLabel WHERE {
  VALUES ?refType { pr:P248 pr:P854 }
  target: ?propp ?statement .
  ?statement prov:wasDerivedFrom ?reference .
  ?reference ?refType ?source .
  SERVICE wikibase:label { bd:serviceParam wikibase:language "[AUTO_LANGUAGE],en". }
}

egonw

SELECT DISTINCT ?np ?chembl WHERE {
  ?np wdt:P703 [] ; wdt:P592 ?chembl .
}

egonw

2023 stuff for CiTO annotations

Some files related to some data curation I did yesterday to add some 200~ish CiTO annotations to Wikidata. The data is CCZero, from https://doi.org/10.5281/zenodo.6885109

There are two files here:

• cits_cleaned.csv derived from the cits.csv from the Zenodo data
• quickstatements.groovy that takes cits_cleaned.csv as input and creates QuickStatements

egonw

{
  "@context": "https://schema.org/",
  "@type": "CreativeWork",
  "name": "PC_DUSTINESS Template",
  "description": "The Dustiness with small drum data entry template is published at 10.2787/505397 under CC BY-SA 4.0 license.",
  "license": "https://creativecommons.org/licenses/by-sa/4.0/",
  "keywords": "dustiness, NM-110, NM-200",
  "url": "https://search.data.enanomapper.net/projects/enanomapper/datatemplates/pchem/index.html?template=PC_DUSTINESS",
  "archivedAt": "http://dx.doi.org/10.2787/505397",
  "provider": {

egonw

#defaultView:BarChart
SELECT ?year (count(distinct ?citing_work) as ?count) ?workLabel WITH {
  SELECT (count(distinct ?citing_work) as ?totalCount) ?work WHERE {
    ?work wdt:P50 / wdt:P496 "0000-0001-7542-0286" .
    ?citing_work wdt:P2860 ?work .
  } group by ?work
    order by DESC(?totalCount)
    limit 10
} AS %PAPERS WHERE {
  INCLUDE %PAPERS

egonw

# tool: scholia
#defaultView:Graph
PREFIX target: <http://www.wikidata.org/entity/Q211171>

SELECT ?class ?classLabel ?otherclass ?otherclassLabel ?rgb WITH {
  SELECT DISTINCT ?class ?otherclass ?rgb WHERE {
    { VALUES ?class_ { target: }
      { ?otherclass_ wdt:P279 ?class_ . BIND( "3182BD" AS ?rgb) BIND(?class_ AS ?class) BIND(?otherclass_ AS ?otherclass) }
      UNION
      { ?otherclass_ wdt:P31 ?class_ . BIND( "E6550D" AS ?rgb) BIND(?class_ AS ?class) BIND(?otherclass_ AS ?otherclass) }

egonw

SELECT (SUBSTR(STR(?wikidata),32) AS ?qid)
  (CONCAT("\"\"\"", ?inchikey_, "\"\"\"") AS ?inchikey)
  (CONCAT("\"\"\"", ?inchi_, "\"\"\"") AS ?inchi)
  (CONCAT("\"\"\"", ?chemform_, "\"\"\"") AS ?chemform)
  (CONCAT("\"\"\"", ?smiles_, "\"\"\"") AS ?smiles)
  (CONCAT(str(?mass_), "U483261") AS ?mass)
WHERE {
  VALUES ?inchikey_ { "WSYNAKWAAXYNMW-DEOSSOPVSA-N" "PTCHLTYDAIWNSD-SSDOTTSWSA-N" "GAZIIOYXDWTTMC-GFCCVEGCSA-N" "CIUYPOUJRYWLDF-QFIPXVFZSA-N" "HAGZRCCJXLGJTR-BDAKNGLRSA-N" }
  ?wikidata wdt:P235 ?inchikey_ ;
            wdt:P234 ?inchi_ ;