CD2H gitForager

Egon Willighagen

Login: egonw

Company: @BiGCAT-UM

Location: Maastricht, The Netherlands

Bio: Open scientist teaching and doing research at the Faculty of Health, Medicine, and Life Sciences at Maastricht University. ORCID: 0000-0001-7542-0286

Blog: https://chem-bla-ics.blogspot.com/

Member of

Repositories

5stardata.info: Information around TimBL's 5 star Open Data plan
acsrdf2010: owl:thing's for the ACS RDF symposium in August 2010 in Boston
ACS-Twitter-Visualization: Visualize ACS tweets using a tag cloud
ambit: null
ambit2-all: Copy of the ambit2-all repository on SourceForge, for development not ready for master/trunk yet.
ambit.js: JavaScript library for interaction with AMBIT instances.
ambit-mirror: GitHub read-only mirror of AMBIT
ami: null
AZOrange: AstraZeneca add-ons to Orange.
biblatex-biomedcentral: null
bioclipse2wdchem: Bioclipse scripts for Wikidata:WikiProject Chemistry
bioclipse.ambit: AMBIT plugin for Bioclipse
bioclipse.bigcatedu: null
bioclipse.bioinformatics: The Bioinformatics feature of Bioclipse 2
bioclipse.bridgedb: Bioclipse BridgeDB integration
bioclipse.brunn: Brunn is a laboratory information system for Bioclipse 2.
bioclipse.cheminformatics: Bioclipse2 Cheminformatics.
bioclipse.cir: Bioclipse plugin for the Chemical Identifier Resolver
bioclipse.core: Bioclipse2 Core.
bioclipse.ds: Bioclipe2 Decision Support.
bioclipse.experimental: Bioclipse2 Experimental features
bioclipse.icebear: Bioclipse Isbj�rn
bioclipse.ons: Open Notebook Science Solubility Project
bioclipse.openphacts: Bioclipse Open PHACTS
bioclipse.opentox: OpenTox functionality for Bioclipse.
bioclipse.oscar: Oscar plugin for Bioclipse
bioclipse.rdf: Bioclipse2 RDF.
bioclipse.sb: Systems Biology support in Bioclipse
bioclipse.social: Bioclipse Social - Linking Bioclipse to the Social Web.
bioclipse.statistics: Bioclipse2 Statistics.
bioclipse.textmining: null
bioclipse.wikidata: Wikidata plugin for Bioclipse.
bioclipse.wikipathways: Bioclipse plugins for WikiPathways and PathVisio
biomarkers: Biomarker collection.
biostar-central: BiosStar
blueobelisk.debian: Debian meta package for Blue Obelisk software.
blueobelisk.userscript: Blue Obelisk Userscripts
bodr: Blue Obelisk Data Repository - your one stop place of element and isotope data.
bopaper: null
BridgeDb: null
bridgedbjs: JS client for BridgeDb.org ID mapping framework webservices
BridgeDbR: BIoconductor R package for BridgeDb
BSL-explained: A lot of Bioclipse Scripting Language examples
cacm-article: null
cb: Source code for the Chemical blogspace website
cdk: The Chemistry Development Kit
cdk-build-util: Collection of auxiliary developer utilities used by the Chemistry Development Kit.
cdkcmd: CDK command line utilities
CDKitty: The Chemistry Development Kit Google Wave Robot
CDkLabBook: null
cdk-migration: Repository with the Migration chapter of my CDK book.
cdkr: Integrating R and the CDK
cdk-taverna: CDK-Taverna for Taverna 2.x
cdk-taverna-2: null
chapterBCOT: Book Chapter: "Interactive Predictive Toxicology with Bioclipse and OpenTox"
chembl.rdf: Scripts to create RDF for ChEMBL.
chembl-rdf-paper: ChEMBL-RDF paper
chemcompoundbox: Chemical Compound Box
chemicalblogspace: Automatically exported from code.google.com/p/openreview
cheminfbenchmark: Cheminformatics Benchmark Toolkit
cheminformatics.classics: Cheminformatics Classics
chemojava: Automatically exported from code.google.com/p/chemojava
chempaint: Chemical Structure plugin for PathVisio
ci-advent-2017: Archive of Compound Interest Christmas Advent 2017
cinfony: Git clone of the cinfony source code repository.
citation.js: Citation.js converts formats like BibTeX, Wikidata JSON and ContentMine JSON to CSL-JSON to convert to other formats like APA, Vancouver and back to BibTeX.
citedin: CitedIn
citeulike: Copy of the SVN CiteULike repository to host any possible patches by my hand. I am not a main author of CiteULike.
citeulike-export: BibTeX exports of the 'egonw' account on CiteULike.
citeuliker: R Client library for CiteULike.
civic-api-docs: Beautiful static documentation for your API
Client.Java: A Triple Pattern Fragments client for Java (Jena)
cml-schema: Schema repository for the Chemical Markup Language.
cmnanotox: ContentMining of Nanotoxicity literature - an open notebook science project
collaborative.cheminformatics: LaTeX sources for the book chapter.
completeness: null
conferenceR: R package to support tweeting at conferences.
container-galaxy-k8s-runtime: PhenoMeNal runtime for Galaxy running inside a container orchestrator
contentmine.github.io: ContentMine installation instructions website
contentmine.org: The static site
create-bridgedb-lycocyc: null
create-bridgedb-metabolites: Create BridgeDB identity mapping files from HMDB, ChEBI, and Wikidata
Creative-Commons-Markdown: Markdown-formatted Creative Commons licenses
csrml-schema: null
ctr-cdk-groovy: CDK/Groovy answers to the Chemical Toolkit Rosetta
cytopenphacts: null
cytoscape-wikipathways-app: WikiPathways app for Cytoscape to open and access pathways from WikiPathways
d3sparql: JavaScript library for executing SPARQL query and transforming resulted JSON for visualization in D3.js
dbXP_BioclipsePlugin: dbXP Plugin for Bioclipse
dbXP_JavaClient: Java client for dbXP
de.ipbhalle.msbi: IPB-Halle.DE Open Source Metabolomics Software
docker-semanticmediawiki: Ubuntu SemanticMediaWiki container with fully automated install see http://www.semantic-mediawiki.org/
DreamDirections: null
Drug_Disease_Target_Mapping: Finding overlap in targets from disease and drugs.
dvn: dvn: Access to the Dataverse Network API from R
edamontology: EDAM is an ontology of bioinformatics types of data including identifiers, data formats, operations and topics.
effectopedia-patches: Fork of Effectopedia's SVN branch, for my patches.
egonw.github.com: Personal Homepage
ELIXIR-Tox: Repository to organize the further development of the Community Proposal to ELIXIR.
enmrdf: Repository with nanomaterial information in RDF format.
enmSummaries: Engineered NanoMaterial Summaries
events: Materials related to events I might attend, and to talks I am giving
examples-ambit: How to call AMBIT modules
examples-cdk: Example projects, making use of The Chemistry Development Kit
fdptest: null
fopworkshop: FAIR, Open , and Proprietary data workshop
FutureTDM: Materials of FutureTDM project
fvtworkshop: Workshopmateriaal
gcwiki-r-client: Gold Compound Wiki R client demo
genalg: null
git2r: R bindings to the libgit2 library
gosf2github: migrates tickets to GH from SF
groovy.cdk: Website with code examples from the "Groovy Cheminformatics with the Chemistry Development Kit" book.
groovy-citeulike: Groovy CiteULike scripts.
groovy-jcp: Groovy CDK-JChemPaint
GSCF-RClient: R client to connect to GSCF
gtd: Git-based ToDo tool.
hdt-java: HDT Java library and tools.
histwpnanopubs: Code to generate historical WikiPathways nanopubs
ideogram: Chromosome visualization with D3.js
inchi-cdk-bioclipse: Sources of the InChI-CDK-Bioclipse manuscript.
index-submit-form: Google Drive Spreadsheet template for submitting nanomaterial metadata for indexing purposes.
interactive-pvjs: null
jabref: Graphical Java application for managing bibtex (.bib) databases
java-rdfa: RDFa Parser for java
jnchem: Java library to extract data from the Nature Chemistry journal.
jqudt: Java library for working with the QUDT ontology and data using it.
knime-chemspider: Source code for a ChemSpider query API plugin for KNIME.
knime-wikipathways: KNIME nodes for WikiPathways.
knime-wikipathways-updatesite: KNIME Update Site for the WikiPathways feature
label2datanode: A PathVisio plugin to convert a GPML Label into a GPML DataNode.
larsgw.github.io: null
lavoisier: Oxygen is to breathing and lungs what lavoisier is to molecules and databases.
lilikoi: null
loom: The Loom
lucene-indexer: Library to create the WP lucene index
manifesto: Code is Science - a manifesto for anyone who deals with code in a scientific scenario
medea_bmc_article: LaTeX sources for the J. Chem. Inf. article on Medea
MetaboLights: MetaboLights is a database for Metabolomics experiments and derived information. The database is cross-species, cross-technique and covers metabolite structures and their reference spectra as well as their biological roles, locations and concentrations, and experimental data from metabolic experiments.
MetaboliteOntologyMapper: null
metawinterschool-bigcat: #metawinterschool contribution by BiGCaT
models: Scripts to make QSAR models.
moldbvalidator: Molecules Database Validator
mscpils: Course Material for Programming in the Life Sciences
mtbls2: Development of Arabidopsis dataset for www.ebi.ac.uk/metabolights
myfoafexplorer: Automatically exported from code.google.com/p/myfoafexplorer
nanojava: Java library for descriptor calculation for (nano)materials.
nardb2014index: NAR Database Issue 2014 Index
nmrshiftdb-rdf: RDF interface to the NMRShiftDB data.
nmsa: Personalized abstract suggestions for the New Tools and Applications for Nanomaterial Safety Assessment
norma: Convert XML/SVG/PDF into normalised, sectioned, scholarly HTML
odk: Orbital Development Kit
ojdcheck: OpenJavaDocCheck
ons: My Open NoteBook
ontologies: ontologies
openapi-examples: Example openapi definitions by OpenRiskNet partners.
openchemlib: Open source Java-based chemistry library
OpenPaleo: Resources to investigate the 'openness' of Paleontological research
OpenSMILES: The OpenSMILES specification
ops4j: Java client API for Open PHACTS.
ops.js: null
OPS_LinkedDataApi: A repository to host API configuration files, and code extensions
orcid-affiliations: Extract affiliations from ORCID public data
orcid-js: A general purpose ORCID javascript client and reference list generator, supporting CSL, citeproc-JSON and bibtex
org.openscience.cdk: Repository with Eclipse bundle exports of the CDK modules and matching required third party libraries.
orn-ontology: Risk Assessment Ontology
orn-ontotest: null
OSDB: The Open Spectral Database - Its all about the data
OSM_To_Do_List: null
oss-desc: null
pathvisio: PathVisio
pathvisio-1: PathVisio - pathway editor, visualization and analysis software
PathVisioRPC: PathVisioRPC is an XML-RPC implementation of PathVisio that allows users to create and edit biological pathways, visualize data on pathways, perform pathway statistics and exports results in various image formats. Since most major programming languages have a library/module providing XML-RPC functionality, this application enables users to access PathVisio functionality from their favourite analytical environment.
pathway_interaction_models: null
pils: Programming In the Life Sciences
pimp: The Polyomics Integrated Metabolomics Pipeline
pubchem-cdk: PubChem from a CDK perspective.
PyChEBI: "Chemical Entities of Biological Interest (ChEBI) is a freely available dictionary of molecular entities focused on ?small? chemical compounds."
RDMMP: Drug Markov Mean Properties in R
reactome2gpml-converter: Converts Reactome pathways to GPML format
rednael: IRC bot that propagates Git commit messages.
RobotDF: Google Wave robot for RDF functionality
ron: Tools for rdf.openmolecule.net
ropenphacts: R client for Open PHACTS.
rrdf: R package for handling RDF data.
rrdf-paper: Paper around rrdf.
RRegrs: Searching the best regression model using R (correlation filter, data scaling, best regression model, etc.)
rwikipathways: R client package for the WikiPathways API.
rWikiPathways-1: R package for WikiPathways API
scholia: Wikidata scholarly profile
Science-3.0: Online collaborative science community.
semanticchemistry: Automatically exported from code.google.com/p/semanticchemistry
smilesDrawer: A small, highly performant JavaScript component for parsing and drawing SMILES strings. Released under the MIT license.
SNORQL: a ajaxy front-end for exploring triple stores
sparql_to_pandas: Example for accessing SPARQL endpoints in Python with Pandas
spectra-hash: The splash, this is the reference documentation
styles: Official repository for Citation Style Language (CSL) citation styles.
suppInfoFullerenol: Computational supplementary information for the fullerenol paper.
svg: ContentMine Fork of the WWMM svg Package
swagger2BioTools: Tool to convert Swagger configuration files to Bio.Tools input XML.
swagger-js: Javascript library to connect to swagger-enabled APIs via browser or nodejs
swat4ls2016-art40: Poster contribution to SWAT4LS 2016.
thesis-proposal: null
Total-Impact: Uncovering the invisible impacts of your research.
toxbank-api-beans: null
toxbank-api-client: The Java ToxBank API client software
toxbank-api-server: ToxBank Protocol service
toxbank-ontology: null
tweet-conf: Some simple R scripts to collect and visualize twitter happenings around a conference hashtag
vecmath: Public Domain implemenation of the Java Vecmath libraries.
virtuoso-opensource: Virtuoso is a scalable cross-platform server that combines Relational, Graph, and Document Data Management with Web Application Server and Web Services Platform functionality.
webchem: Chemical Information from the Web
wikidata2pubchem: Repository to coordinate getting Wikidata compounds into PubChem
wikidataBots: Copy of the wikidataBots repository on BitBucket.
Wikidata-Toolkit: null
wikipathways-api-client-java: Java library for WikiPathways webservice
wikipathways-chromosomes: Mapping WikiPathways to chromosomes
WikiPathwaysDataSummaries: Summaries of WikiPathways data using the SPARQL end point and d3.js and derived libraries.
wikipathways.org: The main web site for the WikiPathways project.
WikiPathwaysRDFConversion: null
WikiPathwaysSDF: Code to create WikiPathways SD files.
WinterSolsticeChallenge2017: Winter Solstice Challenge 2017
wordpress-github-sync: A WordPress plugin to sync content with a GitHub repository (or Jekyll site)
wp2lod: Java source for conversion of WikiPathways GPML to triples
wprdfLoadScripts: Scripts for loading the WP inferred interaction triples into Virtuoso.
xmetdb-server: xmetdb web application
xproc-ebook-conv: XProc E-Book Processor
xws-taverna: XWS Plugin for Taverna
zikaVirus: Bioclipse scripts to add information about potential Zika virus leads to Wikidata

Commits To

Repository	Most Recent Commit	# Commits
edamontology/edamontology	2015-12-01 17:17:20.0	4
fnielsen/scholia	2018-03-18 16:13:26.0	63

This work is supported by the National Institutes of Health's National Center for Advancing Translational Sciences, Grant Number U24TR002306. This work is solely the responsibility of the creators and does not necessarily represent the official views of the National Institutes of Health.