View curation1.groovy
// Copyright (C) 2017 Egon Willighagen
// MIT license
// see https://www.wikidata.org/wiki/Wikidata:WikiProject_Chemistry/Tools#Chemical_compound_without_InChI
/* results (2017-10-29):
Number of missing InChIs: 2098
InChI too long: 1736
With undefined stereo: 348
View calcuateMZs.groovy
bioclipse.requireVersion("2.7.0")
// download all GPML files for a species, and save those in /WikiPathways/data/
// first, calculate m/z values for everything in Wikidata
referenceFile = "/WikiPathways/mz_smiles.tsv"
mzData = new java.util.HashMap()
new File(bioclipse.fullPath(referenceFile)).eachLine { line ->
tokens = line.tokenize( '\t' )
if (tokens[0] != "compound") {
wkid = tokens[0].substring(31)
View bbl processor
/**
* LaTeX .bbl output.
*
* (Code contributed by Egon Willighagen, based on the prototype.text code.)
*/
CSL.Output.Formats.prototype.latex = {
"text_escape": function (text) {
if (!text) {
text = "";
}
View cites
{
pico2008wikipathways,
Hanumappa2013,
Ratnam2014,
Fabregat2016,
Kanehisa2017,
Swainston2016,
Cerami2010,
Kamburov2013,
jennen2010biotransformation,
View gist:553e1329936135699c641e3c32750c27
@article{Rijswijk2017,
author = {van Rijswijk, Merlijn and Beirnaert, Charlie and Caron, Christophe and Cascante, Marta and Dominguez, Victoria and Dunn, Warwick B. and Ebbels, Timothy M. D. and Giacomoni, Franck and Gonzalez-Beltran, Alejandra and Hankemeier, Thomas and Haug, Kenneth and Izquierdo-Garcia, Jose L. and Jimenez, Rafael C. and Jourdan, Fabien and Kale, Namrata and Klapa, Maria I. and Kohlbacher, Oliver and Koort, Kairi and Kultima, Kim and Le Corguill\'{e}, Gildas and Moschonas, Nicholas K. and Neumann, Steffen and O'Donovan, Claire and Reczko, Martin and Rocca-Serra, Philippe and Rosato, Antonio and Salek, Reza M. and Sansone, Susanna-Assunta and Satagopam, Venkata and Schober, Daniel and Shimmo, Ruth and Spicer, Rachel A. and Spjuth, Ola and Th\'{e}venot, Etienne A. and Viant, Mark R. and Weber, Ralf J. M. and Willighagen, Egon L. and Zanetti, Gianluigi and Steinbeck, Christoph},
day = {6},
NOdoi = {10.12688/f1000research.12342.1},
issn = {2046-1402},
journal = {F1000Resear
View nms.ttl
@prefix void: <http://rdfs.org/ns/void#> .
@prefix owl: <http://www.w3.org/2002/07/owl#> .
@prefix enm: <http://purl.enanomapper.org/onto/> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix npo: <http://purl.bioontology.org/ontology/npo#> .
@prefix sso: <http://semanticscience.org/resource/> .
@prefix cito: <http://purl.org/net/cito/> .
@prefix bao: <http://www.bioassayontology.org/bao#> .
@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
View README.txt
# INSTALL STUFF
$ curl -s https://deb.nodesource.com/gpgkey/nodesource.gpg.key | sudo apt-key add -
$ sudo nano /etc/apt/sources.list.d/nodesource.list
deb https://deb.nodesource.com/node_6.x stretch main
# deb-src https://deb.nodesource.com/node_6.x stretch main
$ sudo npm install --global getpapers
View All Reactome pathways in WikiPathways
PREFIX cur: <http://vocabularies.wikipathways.org/wp#Curation:>
SELECT DISTINCT ?pathway (str(?titleLit) as ?title)
WHERE {
?pathway wp:ontologyTag cur:Reactome_Approved ;
dc:title ?titleLit .
}
View gist:518d7f6a0e6cf52c9840042d037e9e9a
SELECT DISTINCT ?item ?date_modified WHERE {
VALUES ?item {
wd:Q410688 wd:Q410689
}
?item schema:dateModified ?date_modified .
FILTER (?date_modified > "2017-05-29"^^xsd:dateTime)
}
View wikidata.rq
SELECT ?mol ?molLabel ?InChIKey ?CAS ?ChemSpider ?CID ?ChEBI ?HMDB WHERE {
?mol wdt:P235 ?InChIKey .
OPTIONAL { ?mol wdt:P231 ?CAS }
OPTIONAL { ?mol wdt:P661 ?ChemSpider }
OPTIONAL { ?mol wdt:P662 ?CID }
OPTIONAL { ?mol wdt:P683 ?ChEBI }
OPTIONAL { ?mol wdt:P2057 ?HMDB }
FILTER (regex(str(?InChIKey), "^YTFVRYKNXDADBI-"))
SERVICE wikibase:label { bd:serviceParam wikibase:language "en". }
}