This week, the Journal of Chemical Information and Modeling introduced new editorial guidelines around data and source code sharing. They basically do not change much around their open science policies: they continue want to support closed science. Well, there has to be a journal for that too, perhaps. So, what changed? 

The editorial is aimed at the needs of the reviewer. With that, it puts additional stress on that the review process as sole gatekeeper of the publication process. The two or three reviewers will now have new responsibility to assess the potentially temporarily access to the data and source code. As a reader, you have to trust that those reviewers actually reviewed the data and code sufficiently.

One of the things around Open Science is how some think they can use the term. To me, when I was introduced to the term, back in 1999, it was from a USA-centric view that originated from and based on the ideas of open source software: You can find this back in literature. There is even earlier literature that uses the term in a more economic context tho.

I have been fan of code coverage. When combined with (unit) testing, it indicates which code of your software has been run and therefore tested. Some 15 years ago, when I worked on making the Chemistry Development Kit code base more stable, I worked on various things: modularization, documentation, (unit) testing. I explored the option in Java. I even extended PMD with CDK-specific unit tests.

I do not like questions as titles of articles: you either found an answer or not. In this case, the answer is likely a maybe. The paper milestones a discussion that started some years ago with the aim to create a standardized identifier for nanomaterials. Quite ambitious. I am happy to have been invited to contribute to this discussions and paper, but can hardly take much credit. The team dit an awesome job in capturing the complexities of representation of the chemistry of nanomaterials.

Open Standards, or Open Specifications as I personally prefer, remove another hurdle in locked-in science. They allow others to understand your language, the nuances of your message. They mean independence, freedom. One important international standard is the Open Document Format (ODF). It is supported by all major editors (yes, MS Word too). Indeed, scholars have been quite persistent and insisting on using closed source and semi-closed solutions like .docx files.

Last week the third paper got published in the Citation Typing Ontology Collection and this weekend I finished adding the citation annotations to Wikidata.

While the number of papers in the Journal of Cheminformatics is only slowly growing, the number of journals receiving annotated citations is growing faster. And there are 70 now:

The Scholia patch needed for this updated table is not online yet.

The last WikiPathways was already 3 years ago, an often used frequency for Nucleic Acids Research updates. So, time for an update, and what an updates we had: WikiPathways: connecting communities (doi:10.1093/nar/gkaa1024). This update focuses on the open, collaborative nature of WikiPathway and on the growing role of the portals, like the lipids portal, the AOP portal, the nanomaterials portal, and the inborn errors of metabolism (IEM) portal.

During the time of the editorial about the Journal of Cheminformatics Citation Typing Ontology (CiTO) Pilot I already worked out a model to add CiTO annotation in Wikidata. It looks like this for the first research article with annotation:

At the time I also write some SPARQL queries against Wikidata to summaries the current use. There are, for example, at this moment 128 CiTO annotations in Wikidata (with the above model).

After a time of exploration of technical needs, idea, plans, the Journal of Cheminformatics launched its Citation Typing Ontology (CiTO) Pilot this summer (doi:10.1186/s13321-020-00448-1). I am very excited about this, because the CiTO tells us why we are citing literature. We are a very long way away from publishing industry adoption, but we have to start somewhere. Laeeq Ahmed et al.

Voices are getting stronger over how important Open Science is. Insiders have known the advantages for decades. We also know the issues in the transition, but the transition has been steady. Contributing to Open Science is simple: there are plenty of project where you can contribute without jeopardizing your own research (funding or prestige). Myself, my small contributions have been done without funding too. But I needed to do something.
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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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