chem-bla-ics: 2021

BioHackathon Europe 2021 #1: CiTO annotations in BioHackrXiv

Serendipity. I did not plan this hack at the BioHackathon Europe 2021 but it happened anyway. Based on earlier work in the Journal of Cheminformatics, extending on the work by Krewinkel et al. I looked into the idea of using the Lua filter for BioHackrXiv, a preprint server for BioHackathons. Actually, I started by looking at the Citation Styling Language file used by the BioHackrXiv tools. But that was just wrong.

Long story short: it worked! Thanks to the encouragements from Pjotr and Tazro and suggestions from Lars and some code on how to dump a Lua data structure to stdout.

In the Markdown/BibTeX combination you would normally write [@bibtexkey] to add the reference to the article with the given key in the .bib file.

Nov

preprint: "ELIXIR and Toxicology: a community in development"

The Whitepaper

For some time now this whitepaper for an ELIXIR Toxicology community has been in preparation and I am pleased it is now online. There will be another layer of review, but a proper peer review process by F1000Research. So, the paper is both finished and a preprint.

How to join?

A website site is under development, as is a logo. But you can already join the mailing list. I am looking forward to seeing you there.

Nov

Translating science

Many moons ago I was involved in LinuxFocus (Wikipedia entry), and Open Access magazine around the Linux operating system. Over a few years I translated articles and wrote a few articles that themselves got translated into other languages, including the main supported languages English, Chinese, Arabic, Dutch, French, German, Italian, Korean, Portugues, Polish, Russian, Spanish, and Turkish. Some scientific journals do this kind of translation too, like Angewandte Chemie.

Nov

contributed bits to: "Complex Portal 2022: new curation frontiers"

One thing the pandemic brought me was a strong interest in understanding the SARS-CoV-2 virus better. I am not a virologist, but I do know how to read the literature. Sadly, I stopped reading SARS-CoV-2 literature a year ago. It was getting too serious, too exhausting. I'm trying to find the energy to pick it up again. You will find me repeatedly mention learnability, an undervalued aspect of usability. One of the strengths of linked data is its support for learnability.

Oct

The COVID19 Disease Map, a computational knowledge repository of virus–host interaction mechanisms

Just read the paper (doi:10.15252/msb.202110387).

Abstract

We need to effectively combine the knowledge from surging literature with complex datasets to propose mechanistic models of SARS-CoV-2 infection, improving data interpretation and predicting key targets of intervention. Here, we describe a large-scale community effort to build an open access, interoperable and computable repository of COVID-19 molecular mechanisms.

Oct

Chemical names: IUPAC names and Nonsensical nomenclature

Kat Day wrote this summer about nonsensical nomenclature: "The name wasn’t in my dictionary, nor the index of the few expensive textbooks I’d scraped together the funds to buy". Day is talking here about capric acid (GHVNFZFCNZKVNT-UHFFFAOYSA-N).

That sounds so familiar: both looking up facts, and collecting some second hand books. I found myself in the same situation in 1993-1994 when I started my chemistry degree.

Oct

The Ethics of not releasing Data #1: the context

I have been funded to answer biological questions around the safety of nanomaterials. In particular, to what extend can we understand and therefore predict the safety of new materials, often referred to as safe-by-design. We started with eNanoMapper and continued with NanoCommons, NanoSolveIT, RiskGONE, and SbD4Nano, and supervising a PhD student working on the EU-ToxRisk and OpenRiskNet projects.

Oct

new: "Investigating the Molecular Processes behind the Cell-Specific Toxicity Response to Titanium Dioxide Nanobelts"

Omics analysis gives results for many entities at the same time. Pathways databases describe the interactions of those entities. Combining this gives a lot of statements about that state of the biological system, but without filtering looks like a hairbal, all in an attempt to see the forest for the trees. But the forest is dense, large, and full of ever moving ents. Over the years many approaches have been invented to help us see the paths through the hairball.

Sep

Open infrastructures with open citations

Research output comes in many ways. Journal articles, books, and book chapters took benefit from the Matthew effect: most abundant format, reinforcing itself. So much, in fact, that some scholars will have no trouble that research quality depends on these forms. Particularly journals articles. With impact factors. Evidence is missing, claims baseless, or just contradicting evidence people did collect.

Sep

Nice RDF editor doubling as visualizer: sketch.zazuko.com

Today a tweet alerted me of a nice new tool httpsketch.zazuko.com so I gave it a spin for some RDF:

Have fun!