chem-bla-ics: December 2017

Adding SMILES, InChI, etc to Wikidata alkane pages

While working on the 'chemical class' aspect for Scholia yesterday I noted that the page for alkanes was quite large, with a list of more than 50 long chain alkanes with pages in the Japanese Wikipedia with no SMILES, InChI, InChIKey, etc.

So, I dug up my Bioclipse scripts to add chemicals to Wikidata starting with a SMILES (btw, the script has significantly evolved since) and extended the query of that Scholia aspect to list just the Wikidata Q-code and name. This script starts with one or more SMILES strings and generated QuickStatements (a must-learner).

Because the Wikidata entries also had the English IUPAC name, I can use that to autogenerate SMILES.

Dec

Using Scholia as Open Notebook Science tool to support literature searching

I have blogged about Scholia and the underlying Wikidata before. Following the example of this WikiProject Zika Corpus I am using Scholia (doi:10.1007/978-3-319-70407-4_36, or in Scholia, of course :) as a tool to support a literature study, to collect articles about a certain topic. Previously I used it to track the publication trail around the Elsevier-SciHub interactions.

Dec

Two Papers about Adverse Outcome Pathways

Over the past year our group got involved in two projects where Adverse Outcome Pathways (AOPs) are used. These AOPs are risk assessment tools, but when linked to biological pathways they get a lot more interesting. the key events (KEs) in the AOPs can be linked to bioassays and thus biological processes. Earlier this year Marvin Martens (follow him on Twitter) started as PhD candidate to work on EU-ToxRisk and OpenRiskNet on exactly this integration.

Dec

Winter solstice challenge #2: first submission

Bianca Kramer (of 101 Innovations fame) is the first to submit results for the Winter solstice challenge and it's impressive! She has an overall score based on her own publications and the first level citations of 54%!

So, the current rankings in the challenge are as follows.

Highest Score

Bianca Kramer

Best Tool

Bianca Kramer

I'm sure she is more than happy if you use her tool to calculate your score. If you're patient, you may even wish to take it one level deeper.

Dec

The National Plan Open Science Estafette: my own first Open Science steps

Noot: als je liever Nederlands leest, lees dan het origineel.

Earlier this year Delft hosted a meeting for Dutch scholars aimed at hearing and learning about, and to give feedback on the National Plan Open Science (doi:10.2777/061652). I'm very happy I have been able to contribute to this effort, because more and better access to knowledge is very dear to me. During lunch time everyone could demonstrate their own Open Science. From this the idea evolved to have a relay race ("estafette").

Dec

Suggestions for ScholarlyHub

ScholarlyHub is a open scholar profile project. I have yet no idea where this platform is going, but they planned open source nature makes me want to explore it nevertheless. The project is currently running a crowdfunding campaign and developing their plans.

Dec

New paper: "Integration among databases and data sets to support productive nanotechnology: Challenges and recommendations"

The U.S.A and European nanosafety communities have a longstanding history of collaboration. On both sides there are working groups, NanoWG and WG-F (previously called WG4) of the NanoSafety Cluster. I have been chair of WG4 for about three years and still active in the group, though in the past half year, without dedicated funding, less active. That is already changing again with the imminent start of the NanoCommons project.

Dec

inventaire.io: every house a library

Two weeks ago someone made me aware of inventaire.io. This new social profile page allows you to digitize a list of your books. That in itself is already very useful. In the past I have made some efforts to create overviews of the books I own. If only to get some count, with respect to insurance, etc.

Dec

De Nationaal Plan Open Science Estafette: mijn eerste Open Science stappen

Note: For my English-only followers, I translated this to English.

Eerder dit jaar werd er in Delft een meeting voor Nederlandse onderzoekers georganiseerd om te horen over en feedback te geven op het Nationaal Plan Open Science (doi:10.2777/061652). Ik prijs me rijk dat ik hieraan heb kunnen en mogen meedenken, want meer toegankelijkheid tot wetenschappelijke kennis ligt me aan het hart. Tijdens de lunch konden mensen hun Open Science laten zien.