It all started 3.5 years ago with a question on BioStar: how can one import RDF into R and because lack of an answer, I hacked up rrdf. Previously, I showed two examples and a vignette. Apparently, it was a niche, and I received good feedback. And it is starting to get cited in literature, e.g. by Vissoci et al. Furthermore, I used it in the ropenphacts package so when I write that up, I like to have something to refer people to for detail about the used rrdf package.

Thus, during the x-mas holidays I wrote up what I had in my mind, resulting in this preprint on the PeerJ PrePrints server, for you to comment on.


Yes, please go ahead, read it, try the package ("install.packages(pkgs=c("rrdf"))"), ask questions, and comment on the preprint. I anticipate to submit it to a peer-reviewed journal by the end of this month.

Along with the preprint, I updated the rrdf package (now at 2.0.2). These are the changes:

  • added methods to read/write RDF from strings
  • updated to Apache Jena 2.11 (yeah, I am hardly doing things from scratch)
  • remote SPARQLing now skips Jena by default (add jena=TRUE to use it again)
  • better conversion of SPARQL results to a matrix
    • proper removal of language and types
    • better handling of anonymous nodes
    • also output variables (columns) if they have no data (thank to Alan Ruttenberg)
  • fixed the output of supported formats in documentation and error messages
Have fun!

Vissoci, J. R. N. et al. A framework for reproducible, interactive research: Application to health and social sciences (2013). URL http://arxiv.org/abs/1304.5688.
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Hi all, as posted about a year ago, I moved this blog to a different domain and different platform. Noting that I still have many followers on this domain (and not on my new domain, including over 300 on Feedly.com along).

This is my last post on blogger.com. At least, that is the plan. It has been a great 18 years. I like to thank the owners of blogger.com and Google later for providing this service. I am continuing the chem-bla-ics on a new domain: https://chem-bla-ics.linkedchemistry.info/

I, like so many others, struggle with choosing open infrastructure versus the freebie model. Of course, we know these things come and go. Google Reader, FriendFeed, Twitter/X (see doi:10.1038/d41586-023-02554-0).

Some days ago, I started added boiling points to Wikidata, referenced from Basic Laboratory and Industrial Chemicals (wikidata:Q22236188), David R. Lide's 'a CRC quick reference handbook' from 1993 (well, the edition I have). But Wikidata wants pressure (wikidata:P2077) info at which the boiling point (wikidata:P2102) was measured. Rightfully so. But I had not added those yet, because it slows me and can be automated with QuickStatements.

Just a quick note: I just love the level of detail Wikidata allows us to use. One of the marvels is the practices of 'named as', which can be used in statements for subject and objects. The notion and importance here is that things are referred to in different ways, and these properties allows us to link the interpretation with the source.

I am still an avid user of RSS/Atom feeds. I use Feedly daily, partly because of their easy to use app. My blog is part of Planet RDF, a blog planet. Blog planets aggregate blogs from many people around a certain topic. It's like a forum, but open, free, community driven. It's exactly what the web should be.

This blog is almost 18 years old now. I have long wanted to migrate it to a version control system and at the same time have more control over things. Markdown would be awesome. In the past year, I learned a lot about the power of Jekyll and needed to get more experienced with it to use it for more databases, like we now do for WikiPathways.

So, time to migrate this blog :) This is probably a multiyear project, so feel free to continue reading it hear.
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The role of a university is manifold. Being a place where people can find knowledge and the track record how that knowledge was reached is often seen as part of that. Over the past decades universities outsources this role, for example to publishers. This is seeing a lot of discussion and I am happy to see that the Dutch Universities are taking back control fast now.

I am pleased to learn that the Dutch Universities start looking at rankings of a more scientific way. It is long overdue that we take scientific peer review of the indicators used in those rankings seriously, instead of hiding beyond fud around the decline of quality of research.

So, what defines the quality of a journal? Or better, of any scholarly dissemination channel? After all, some databases do better peer review than some journals.

A bit over a year ago I got introduced to Qeios when I was asked to review an article by Michie, West, and Hasting: "Creating ontological definitions for use in science" (doi:10.32388/YGIF9B.2). I wrote up my thoughts after reading the paper, and the review was posted openly online and got a DOI. Not the first platform to do this (think F1000), but it is always nice to see some publishers taking publishing seriously. Since then, I reviewed two more papers.
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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!
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