For some time I have been stealing an hour here and there for the rrdf package for R. This package is based on Apache Jena and allows reading and writing of RDF triples, as well as doing local and remote SPARQL querying. BTW, rrdf is not only R package to provide SPARQL functionality, and another package will be demoed at SWAT4LS.

It took me some time to get around to it, but I finally set up a vignette with Sweave for this package, but here it is, explaining some basic functionality of the package, just in time for #swat4ls:



So, with a week or so, I used <iframe> in the blog a few times now. The above one is being served by Google Drive.
Posted by
Labels: Google Drive R RDF SPARQL sweave vignette
2

View comments

Please change your RSS URL of this blog
Please change your RSS URL of this blog
Last post here / the Freebie model online
Last post here / the Freebie model online
Boiling points in Wikidata
Boiling points in Wikidata
History, provenance, detail
Blog planets: blogging about Debian, GNOME, Wikimedia, FSFE, and many more
Archiving and updating my blog
4
Universities and open infrastructures
Universities and open infrastructures
Journal Rankings
Journal Rankings
Qeios, an open dissemination platform for research output
Community activity #2: FAIRsharing
Information Retrieval versus ChatGPT
Information Retrieval versus ChatGPT
Paper: "The FAIR Cookbook - the essential resource for and by FAIR doers"
Paper: "The FAIR Cookbook - the essential resource for and by FAIR doers"
Paper: "Extending inherited metabolic disorder diagnostics with biomarker interaction visualizations"
Community activity #1: Bioschemas annotation
Community activity #1: Bioschemas annotation
CiTO updates #4: annotations in datasets
BridgeDb NWO grant update #7: wrapping up the project
Paper: "PSnpBind-ML: predicting the effect of binding site mutations on protein-ligand binding affinity"
Why I free up time to give lectures (and about ChatGPT)
Why I free up time to give lectures (and about ChatGPT)
BridgeDb NWO grant update #6: second hackathon
Citation Typing: progress but we need more uptake
Scholia timeline
Doing the "Open Science Challenge"
Paper: "Guiding the choice of informatics software and tools for lipidomics research applications"
BridgeDb NWO grant update #5: BioHackathon, Webservice, Bioregistry
Paper: "Unifying the identification of biomedical entities with the Bioregistry"
Paper: "The NORMAN Suspect List Exchange (NORMAN-SLE): facilitating European and worldwide collaboration on suspect screening in high resolution mass spectrometry"
1
Paper: "Wikipedia on the CompTox Chemicals Dashboard: Connecting Resources to Enrich Public Chemical Data"
Finding Mastodon accounts with Wikidata (a few SPARQL queries)
Wikidata script for SMILES, SMARTS, and CXSMILES depiction
Is your research cited by a Nobel prize winner?
Tracking citations, to all research output
How to mark something CCZero/CC0 on Zenodo
How to mark something CCZero/CC0 on Zenodo
Nanomaterial identifiers: the ERM identifier paper and NanoJava gets NanoInChI support
Wikidata now escapes SMILES and CXSMILES!
3
Biology, ACPs, lipids, cheminformatics, and Dagstuhl
Extracting triples from HTML+RDFa pages
April 2022: #cdk20y
BridgeDb NWO grant update #4: Bioregistry.io and a BioSB workshop
new: "FAIR assessment tools: evaluating use and performance"
"But look at how few citations she got" - The problematic nature of citations
4
new: "The LOTUS initiative for open knowledge management in natural products research"
new: "CAS Common Chemistry in 2021: Expanding Access to Trusted Chemical Information for the Scientific Community"
1
new: "Understanding signaling and metabolic paths using semantified and harmonized information about biological interactions"
DECIMER: a new chemical OCR kid on the block
new: "PSnpBind: a database of mutated binding site protein-ligand complexes constructed using a multithreaded virtual screening workflow"
new: "Providing Adverse Outcome Pathways from the AOP-Wiki in a Semantic Web Format to Increase Usability and Accessibility of the Content"
BridgeDb NWO grant update #3: Pandora's box
The International Conference on Chemical Structures scientific program is online!
BridgeDb NWO grant update #2: building up momentum
Book chapter: "WikiPathways: Integrating Pathway Knowledge with Clinical Data"
Bacting, pyBacting, and Google Colab
JATS updates
Contributions to two new papers: skin lipids and AOPs
BridgeDb NWO grant update #1: first steps
Wikidata, Open Infrastructures, Recognition&Rewards
log4j
log4j
BioHackathon Europe 2021 #1: CiTO annotations in BioHackrXiv
1
preprint: "ELIXIR and Toxicology: a community in development"
Translating science
1
contributed bits to: "Complex Portal 2022: new curation frontiers"
The COVID19 Disease Map, a computational knowledge repository of virus–host interaction mechanisms
Chemical names: IUPAC names and Nonsensical nomenclature
The Ethics of not releasing Data #1: the context
new: "Investigating the Molecular Processes behind the Cell-Specific Toxicity Response to Titanium Dioxide Nanobelts"
Open infrastructures with open citations
2
Nice RDF editor doubling as visualizer: sketch.zazuko.com
Scholarly journals should use "Archived on" instead of "Accessed on"
WC11 session S67 on "Using the Sematic Web for Rapid Integration of Publicly Available Biological Information"
new: "Ten simple rules for creating reusable pathway models for computational analysis and visualization"
Installing Groovy 3 on Debian Bullseye
From a Journal of Cheminformatics knowledge base to automated downloading of JATS
In which I use my API account to download and redistribute Springer Nature articles
Thank you. Let's be the future.
Conflict of Interest. Or why I am stepping down as Editor-in-Chief of the Journal of Cheminformatics.
new: "A strategy towards the generation of testable adverse outcome pathways for nanomaterials"
EU Trials Tracker about Maastricht University
coalibry.org 0.0.5 peer reviewed
Maastricht University elections: the university council, and The Party of the Academic Staff
Maastricht University elections: the university council, and LEAD
Maastricht University elections: open science in the faculty council
Maastricht University elections: positions about Open Science
new: "A resource to explore the discovery of rare diseases and their causative genes"
CDK, OPSIN, BridgeDb in Python 3.7 with scyjava and Bacting
No access to a 95 year old Nature paper? Normal at Maastricht University.
1
Markdown template for the Journal of Cheminformatics with CiTO support
Half a million CAS registry numbers are now Open Science
Upcoming meeting: "NIH Virtual Workshop on InChI, March 22-24, 2021"
Upcoming meeting: "NIH Virtual Workshop on InChI, March 22-24, 2021"
Downloading all currently released BridgeDb identifier mapping databases
Atom resolution
Cheminformatics and Open Peer Review
1
new: "A protocol for adding knowledge to Wikidata: aligning resources on human coronaviruses"
new: "A catalogue of 863 Rett-syndrome-causing MECP2 mutations and lessons learned from data integration"
Journal of Chemical Information and Modeling introduces new editorial guidelines around Open Science
21 Tips on how to sound #openscience
Bacting: Code coverage, JaCoCo, codecov.io, and API coverage
new: "Can an InChI for Nano Address the Need for a Simplified Representation of Complex Nanomaterials across Experimental and Nanoinformatics Studies?"
Open Standards mean independence, freedom
CiTO updates #3: third paper in the collection and updated Scholia patch
Text
Text
This blog deals with chemblaics in the broader sense. Chemblaics (pronounced chem-bla-ics) is the science that uses computers to solve problems in chemistry, biochemistry and related fields. The big difference between chemblaics and areas such as chem(o)?informatics, chemometrics, computational chemistry, etc, is that chemblaics only uses open source software, open data, and open standards, making experimental results reproducible and validatable. And this is a big difference!
About Me
About Me
Popular Posts
Popular Posts
Pageviews past week
Pageviews past week
1911
Blog Archive
Blog Archive
Labels
Labels
Loading
Dynamic Views theme. Powered by Blogger. Report Abuse.