Egon Willighagen egonw
egonw
/ extractBioschemas.groovy
Created
February 12, 2025 19:11
Extract chemical from a Beilstein Journal of Organic Chemistry article
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| // Copyright (c) 2022-2024 Egon Willighagen <egon.willighagen@gmail.com> | |
| // | |
| // How to cite: https://joss.theoj.org/papers/10.21105/joss.02558 | |
| // | |
| // GPL v3 | |
| @Grab(group='io.github.egonw.bacting', module='managers-rdf', version='1.0.4') | |
| @Grab(group='io.github.egonw.bacting', module='managers-ui', version='1.0.4') | |
| @Grab(group='io.github.egonw.bacting', module='net.bioclipse.managers.jsoup', version='1.0.4') |
egonw
/ createNewTemplate.groovy
Created
December 29, 2024 11:34
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| @Grab(group='org.nanopub', module='nanopub', version='1.66') | |
| import org.nanopub.Nanopub; | |
| import org.nanopub.NanopubCreator; | |
| import org.nanopub.NanopubUtils; | |
| import org.eclipse.rdf4j.model.impl.SimpleValueFactory; | |
| import org.eclipse.rdf4j.model.vocabulary.FOAF; | |
| import org.eclipse.rdf4j.model.vocabulary.RDF; | |
| import org.eclipse.rdf4j.model.vocabulary.RDFS; | |
| import org.eclipse.rdf4j.model.vocabulary.SKOS; |
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| @Grab(group='org.nanopub', module='nanopub', version='1.66') | |
| import org.nanopub.Nanopub; | |
| import org.nanopub.NanopubCreator; | |
| import org.nanopub.NanopubUtils; | |
| import org.eclipse.rdf4j.model.impl.SimpleValueFactory; | |
| import org.eclipse.rdf4j.model.vocabulary.FOAF; | |
| import org.eclipse.rdf4j.model.vocabulary.RDF; | |
| import org.eclipse.rdf4j.model.vocabulary.RDFS; | |
| import org.eclipse.rdf4j.model.vocabulary.SKOS; |
egonw
/ WP2223.diff
Last active
September 2, 2024 05:09
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| diff --git a/WP2223.gpml b/WP2223.gpml.new | |
| index 8d01090..d2897db 100644 | |
| --- a/WP2223.gpml | |
| +++ b/WP2223.gpml.new | |
| @@ -1,183 +1,187 @@ | |
| <?xml version="1.0" encoding="UTF-8"?> | |
| <Pathway xmlns="http://pathvisio.org/GPML/2013a" Name="LIN-12/Notch Lateral Signaling" Data-Source="WikiPathways" Version="WP2223_r135294" Author="[Kyook, MaintBot, RaatsS, Khanspers]" Last-Modified="20240815205238" Organism="Caenorhabditis elegans"> | |
| <Comment Source="WikiPathways-description">Lateral signaling targets and negative regulation of LET-23 signaling. The LIN-12/Notch pathway plays two related roles in vulval development; to prevent adjacent induced vulval precursor cells (VPCs) from both becoming 1° VPCs and to induce VPCs adjacent to the 1°VPC to take a 2° cell fate. | |
| -See figure 14 in http://www.wormbook.org/chapters/www_vulvaldev/vulvaldev.pdf. | |
| -</Comment> |
egonw
/ willighagen_cito.rq
Created
August 11, 2024 15:15
Wikidata SPARQL query to how the citation network between my articles
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| # tool: scholia | |
| #defaultView:Graph | |
| PREFIX target: <http://www.wikidata.org/entity/Q124174475> | |
| SELECT | |
| ?citing_work ?citing_workLabel ?rgb | |
| ?cited_work ?cited_workLabel | |
| WITH { | |
| SELECT (COUNT(*) AS ?count) ?citing_work WHERE { |
egonw
/ createQS.groovy
Created
August 7, 2024 08:21
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| @Grab(group='io.github.egonw.bacting', module='managers-ui', version='1.0.0') | |
| @Grab(group='io.github.egonw.bacting', module='net.bioclipse.managers.wikidata', version='1.0.0') | |
| import java.util.*; | |
| import java.text.SimpleDateFormat; | |
| workspaceRoot = "." | |
| ui = new net.bioclipse.managers.UIManager(workspaceRoot); | |
| wikidata = new net.bioclipse.managers.WikidataManager(workspaceRoot); |
egonw
/ WriteSDF.groovy
Created
May 1, 2024 19:06
Groovy script using SPARQL to retrieve polymers with CXSMILES from Wikidata (CCZero), generates coordinates, and then writes an SD file.
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| // CC-BY 4.0 International. (c) 2024 Egon Willighagen | |
| @Grab(group='io.github.egonw.bacting', module='managers-ui', version='0.5.2') | |
| @Grab(group='io.github.egonw.bacting', module='managers-rdf', version='0.5.2') | |
| @Grab(group='org.openscience.cdk', module='cdk-smiles', version='2.9') | |
| @Grab(group='org.openscience.cdk', module='cdk-silent', version='2.9') | |
| @Grab(group='org.openscience.cdk', module='cdk-ctab', version='2.9') | |
| @Grab(group='org.openscience.cdk', module='cdk-sdg', version='2.9') | |
| import org.openscience.cdk.smiles.SmilesParser; |
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| prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> | |
| prefix np: <http://www.nanopub.org/nschema#> | |
| prefix npa: <http://purl.org/nanopub/admin/> | |
| prefix npx: <http://purl.org/nanopub/x/> | |
| prefix xsd: <http://www.w3.org/2001/XMLSchema#> | |
| prefix dct: <http://purl.org/dc/terms/> | |
| select ?np ?label ?subj ?citationrel ?obj ?date where { | |
| graph npa:graph { | |
| ?np npa:hasValidSignatureForPublicKey ?pubkey . |
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| #defaultView:Map | |
| SELECT ?osc ?oscLabel ?location WHERE { | |
| ?osc wdt:P1344 wd:Q104785223 . | |
| { | |
| ?osc wdt:P625 ?location . | |
| } UNION { | |
| ?osc wdt:P159 / wdt:P625 ?location . | |
| } | |
| SERVICE wikibase:label { bd:serviceParam wikibase:language "[AUTO_LANGUAGE],en". } | |
| } |
egonw
/ foo.groovy
Created
March 17, 2024 13:47
Script to convert https://nanocommons.github.io/specifications/nanomile/ content (somewhat cleaned up) to ERM Identifier DB content
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| new File("/tmp/foo.tsv").eachLine { line -> | |
| fields = line.split('\t') | |
| nanomileid = fields[0] | |
| ermid = fields[1] | |
| ermidShort = ermid.split(':')[1] | |
| content = """--- | |
| title: "Material: ${ermidShort}" | |
| type: ChemicalSubstance | |
| id: ${ermidShort} | |
| tag: ${ermid} |
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