egonw

for iri in $(wget -q --header "accept:text/csv" "https://query.wikidata.org/sparql?query=SELECT DISTINCT ?iri WHERE { [] wdt:P5305 ?iri }" -O -|grep -oP '^http[\S]+')
do
  echo "isql $port $user $password exec='LOAD SERVICE <$iri> DATA;'";
done

egonw

Elevator Pitch: Wikidata für langjährige Wikipedianer_innen

Du arbeitest bei Wikipedia mit, oder? Okay, stell dir vor:

Im südostasiatischen Hinterhuglhapfing wurde eine neue Volkszählung durchgeführt. Artikel in der bairischen Wikipedia für alle Orte in der Region wurden schon vor Jahren angelegt – wer aktualisiert jetzt die Einwohnerzahlen?

Oder: Eine schwedische Wikipedianerin war in Feuerland im Urlaub und hat einheimische Insektenarten fotografiert. Wie landen die Fotos jetzt in den entsprechenden Wikipedia-Artikeln in fünfzehn Sprachversionen?

egonw

WendyAnneWarr #gcc2018mainz GCC next year will be  nov 3-5 2019 in Mainz
WendyAnneWarr #gcc2018mainz nowStefan Kast does closing comments.
WendyAnneWarr #gcc2018mainz AZ’s design make test analysis DMTA will take some time  to implement
WendyAnneWarr #gcc2018mainz first thing to do at AZ was to clean up the data and make knowledge base including @Reaxys etc. An automation platform prototype was built during 2017.
WendyAnneWarr #gcc2018mainz Tyrchan. Working with Marwin Segler. https://t.co/yAnt0PQFQn
MichaelKGilson #gcc2018mainz Tyrchan... Empirical eval of drug design by AI in Astra Zeneca projects. Observes will need automated synthesis and rxn prediction for this to really work.
    --> MichaelKGilson Already doing automated synthesis. Next couple years expect to integrate with the AI.
WendyAnneWarr #gcc2018mainz Tyrchan presents filtering down of AI-generated compounds. Don’t like to show his slides since Work unpublished but I guess that this one is OK https://t.co/opWYT3Exw5
WendyAnneWarr #gcc2018mainz 

egonw

#include <stdio.h>
#include <stdlib.h>
#include <stdint.h>
#ifdef _MSC_VER
#include <intrin.h> /* for rdtscp and clflush */
#pragma optimize("gt",on)
#else
#include <x86intrin.h> /* for rdtscp and clflush */
#endif

egonw

#!/usr/bin/env python
from sys import stdin, stdout
import csv

rdr = csv.reader(stdin, delimiter='\t')
wrt = csv.writer(stdout, delimiter='\t')

vals = []
rows = []
for row in rdr:

egonw

#QUERY <http://sparql.wikipathways.org>

PREFIX wdt: <http://www.wikidata.org/prop/direct/>
PREFIX wd: <http://www.wikidata.org/entity/>
PREFIX p: <http://www.wikidata.org/prop/>
PREFIX wikibase: <http://wikiba.se/ontology#>
PREFIX bd: <http://www.bigdata.com/rdf#>

SELECT DISTINCT str(?inchikeyLit) as ?inchikey str(?pathwayIDLit) as ?pathwayID WHERE {
 SERVICE <https://query.wikidata.org/bigdata/namespace/wdq/sparql> {

egonw

all: sql2rdf.jar
	curl -s "http://ebi.edu.au/ftp/databases/chembl/ChEMBLdb/releases/chembl_15/chembl_15_mysql.tar.gz" |\
	tar  xOvzf -  chembl_15_mysql/chembl_15.mysqldump.sql |\
	java -cp sql2rdf.jar SQLToRDF

sql2rdf.jar : SQL2RDF.jj
	javacc SQL2RDF.jj ## tested with javacc 5.0
	javac SQLToRDF.java
	jar cvf $@ *.class
	

egonw

<?php

$params = array(
	'client' => 'lipids', // or 'locus', for Arabidopis
	'app' => 'lipids', // or 'locus', for Arabidopis
	'mimetype' => 'text/html', 
	'contents' => file_get_contents('article.html'),// read the article HTML from a separate file
);

$curl = curl_init('http://tryit.elsevier.com/oms/OpenMinerService');

egonw

/*******************************************************************************
 * Bioclipse-script to iteratively build a molecule in JChemPaint
 * Author: Ola Spjuth
 * Author: Egon Willighagen
 ******************************************************************************/

//Start with a carbon and open in JCP
mol=cdk.fromSMILES("C")
mol2=cdk.generate2dCoordinates(mol)
ui.open(mol2)

egonw

var dbName = "exampleScriptDB";
 
if ( structuredb.allDatabaseNames().contains(dbName) ) {
  structuredb.deleteDatabase(dbName);
}

structuredb.createDatabase(dbName);

smiles = new Array("Cc1ccccc1", "CCO", "O=O");
names = new Array("toluene", "beer", "air");