## Saturday, June 22, 2019

### Bacting: Bioclipse from the command line

 Source. Wikiepdia. Public Domain.
Because more and more cheminformatics I do is with Bioclipse scripts (see doi:10.1186/1471-2105-10-397) and that Bioclipse is currently unmaintained and has become hard to install, I decided to take the plunge and rewrite some stuff so that I could run the scripts from the command line. I wrote up the first release back in April.

Today, I release Bacting 0.0.5 (doi:10.5281/zenodo.3252486) which is the first release you can download from one of the main Maven repositories. I'm still far from a Maven or Grapes expert, but at least you can use Bacting now like this without actually having to download and compile the source code locally first:

@GrabResolver(
name='ossrh',
root='https://oss.sonatype.org/content/groups/public'
)
@Grab(
group='io.github.egonw.bacting',
module='managers-cdk',
version='0.0.5'
)

workspaceRoot = "."
cdk = new net.bioclipse.managers.CDKManager(workspaceRoot);

println cdk.fromSMILES("CCO")

If you have been using Bacting before, then please note the change in groupId. If you want to check out all functionality, have a look at the changelogs of the releases.

If you want to cite Bacting, please cite the Bioclipse 2 paper and for the version release, follow the instructions on Zenodo. Pending an article. The Journal of Open Source Software? Sounds like a good idea!

## Sunday, June 16, 2019

### National scholarly societies. Why?

Plan S has caused quite some discussion about what knowledge dissemination is. When it was announced, I was hesitant. But very quickly the opposition of Plan S convinced me that apparently something like Plan S is needed. I think Plan S focuses way too much on journal-channeled publishing, whereas I had rather seen it focus on Open Science (it partly does). We argued that much with cOAlition S recently (doi:10.5281/zenodo.2560200):

The risks brought forward by Plan S opponent are real. I don't always agree on the arguments, or simply just don't understand them. With some I agree, but disagree on the alternative. This has been a difficult position to follow, as some discussions taught me. For example, some claimed that I am in favor of article processing costs. Only in a toxic, black-white world, not being against them equals being in favor of them.

Journals articles have shown to be an expensive exercise of knowledge dissemination. It was the right solution, certainly 200 years ago. The cost has to be paid by someone. Via subscription (the "old" model), via package deals with nationals, universities, etc (upcoming), via a friendly funder (some wealthy foundation), or via the authors. Not accepting that the publishing costs money is utopian, if you ask me.

However, what is essential, and what too few people talk about, is that the open license of the research output. If you cannot share research output without paying again and again (instead of once), we inhibit innovation. If I cannot share literature with students, I cannot properly train them for their job.

So, it feels kinda awkward that I am considered doing something wrong, if I ensure my work is available under an CC-BY license. Check my fail rate at ImpactStory (e.g. a series of poster abstracts in Tox Sci).

Anyway, about two topics I want to clarify. First, APC should be as low as possible. That means the infrastructure should be efficient, reducing the amount of work. Open infrastructures likely have an important role here. Why do we not have open source articles submission platforms? Why don't we have open standard XML formats with matching editors so that we can submit articles in that format, rather than LaTeX or Word? Etc.

Every cent I spend on APC, I cannot spend on other research tasks. One obvious answer then, IMHO, is to return to publishing less in journals, and sharing more via other, better channels, such as open databases. I find it hard to reconcile complainers about the cost of publishing, but insisting on expensive business models.

So, I wondered what the APCs are of CC-BY publishing of the journals I published in. And I started adding this data to Wikidata (#opennotebookscience), with a zero APC:

I did not always pay this. There are reductions, sometimes a co-author pays, etc. But I have no problem paying for services rendered. And when I paid, it was always part of my job, and my employer (or project) pays. Now, there are rumors that scholars sometimes have to pay on their own account, as if it is representation cost. I'm appalled by this. I think the employers are bullying their scholars in an unacceptable way. There was a lot of discussion about academic freedom, but your employer forcing you this way into publishing in certain journals sounds like an example of that. We can discuss who is responsible for this: the funder or the employer. I know my answer.

Scholarly societies
Two other aspects in the discussions are "what about poor countries" and "what about scholarly societies". I like to combine these. I welcome scholarly societies to pick up knowledge dissemination, in an open science way. I wish all scholarly societies would do that. But I am not sure why that necessarily has to be coupled at sponsoring society activities. That particularly feels awkward in the notion that we tend to have national societies. Why?

Why should an African scholar have to fund educational activities held in the United States or Europe via publishing in their journals? What is wrong with me paying a scholarly society APC so that everyone in the world can read my literature? What is wrong with wanting them to have access to all literature?

What is wrong with me wanting to be able to read all literature? Despite The Netherlands not being a poor country, Maastricht University is far from a rich university, and I regularly run into paywalls myself.

Yes, asking the Global South, or anyone (like a small SME) to pay 5000 euro is a lot (hell, for me it is; I'm happy that that is rare). Most publishers are not doing that. There is price differentiation and the Global South doesn't pay the European prices (tho publishers must do better in being transparent about this), which in response, some see as patronizing or even colonial (dividing the world in economic zones is quite common; is it unethical? well, there are more aspects of our economic systems I am not happy about).

I think the bigger problem is why Western scholars (the Global North?) is not publishing in journals published in/by the Global South. Why is that?

If we want a scholarly community to be internationally inclusive, why do we still have national scholarly societies? Maybe we can stop with that, please? What if I was not member of the Dutch chemical society, KNCV, but I was member of the Chemical Society, an scholarly society independent from continent or country?

Now, I am happy to see others are thinking in this direction too. For example, the Metabolomics Society takes this approach and a growing group of universities is rebooting the idea of a university publisher, but not limited to one university of even country (e.g. University Journals, HT Jeroen and Erik).

Because if we keep insisting on publishing in Global North (or western-led) journals (e.g. journals of Global North societies), I think we have a bigger problem than APCs, with respect to the North/South divide (and there certainly is a problem!).

I'm looking forward to reading your thoughts on how we can really reform open science knowledge dissemination.

## Monday, June 10, 2019

### Preprint servers. Why?

 Recent preprints from researchersin the BiGCaT group.
Henry Rzepa asked us the following recently: ChemRxiv. Why? I strongly recommend reading his pondering. I agree with a number of them, particularly the point about the following. To follow the narrative of the joke: "how many article versions does it take for knowledge to disseminate?", the answer sometimes seems to be: "at least three, to make enough money of the system".

Now, I tend to believe preprints are a good thing (see also my interview in Preprintservers, doen of niet?, C2W, 2016. PDF): release soon, release often has served open science well. In that sense, a preprint can be like that: an form of open notebook science.

However, just as we suffer from data dumps for open source software, we see exactly the same with (open access) publishing now. Is the paper ready to be submitted for peer review, oh, let's quickly put it on a preprint server. A very much agree with Henry that the last thing we are waiting for is a third version of a published article. This is what worries me a great deal in the "green Open Access" discussion.

But it can be different. For example, people in our BiGCaT group actually are building up a routine of posting papers just before conferences. Then the oral presentation gives a laymens outline of the work, and if people want to really understand what the work is about, they can read the full paper. Of course, with the note that a manuscript may actually not be sufficient for that, so the preprint should support open science.

But importantly, a preprint is not a replacement for an proper CC-BY-licensed version of record (VoR). If the consensus that that is what preprints are about, then I'm no longer a fan.

## Tuesday, May 21, 2019

### Scholia: an open source platform around open data

Some 2.5 years ago Finn Nielsen started Scholia. I have been blogging about it a few times, and thanks to Finn, Lane Rasberry, and Daniel Mietchen, we were awarded a grant by the Alfred P. Sloan Foundation to continue working on it (grant: G-2019-11458). I'll tweet more about how it fits the infrastructure to support our core research lines, but for now just want to mention that we published the full proposal in RIO Journal.

Oh, just as a teaser and clickbait, here's one of the use cases. dissemination of knowledge of metabolites and chemicals in general (full poster):

## Saturday, May 18, 2019

### LIPID MAPS: mass spectra and species annotation from Wikidata

 Part of the LIPID MAPS classificationscheme in Wikidata (try it).
A bit over a week I attended LIPID MAPS Working Group meeting in Cambridge, as I have become member of the Working Group 2: Tools and Technical Committee in autumn. That followed a fruitful effort by Eoin Fahy to make several LIPID MAPS pathways available in WikiPathways (see this Lipids Portal), e.g. the Omega-3/Omega-6 FA synthesis pathway. It was a great pleasure to attend the meeting, meet everyone, and I learned a lot about the internals of the LIPID MAPS project.

I showed them how we contribute to WikiPathways, particularly in the area of lipids. Denise Slenter and I have been working on having more identifier mappings in Wikidata, among which the lipids. Some results of that work was part of this presentation. One of the nice things about Wikidata is that you can make live Venn diagrams, e.g. compounds in LIPID MAPS for which Wikidata also has a statement about which species it is found in (try it):

SELECT ?lipid ?lipidLabel ?lmid ?species ?speciesLabel
?source ?sourceLabel ?doi
WHERE {
?lipid wdt:P2063 ?lmid ;
p:P703 ?speciesStatement .
OPTIONAL {
?speciesStatement prov:wasDerivedFrom/pr:P248 ?source ;
ps:P703 ?species .
OPTIONAL { ?source wdt:P356 ?doi }
}
SERVICE wikibase:label {
bd:serviceParam wikibase:language "[AUTO_LANGUAGE],en".
}
}


A second query searches lipids for which also mass spectra are found in MassBank (try it):

SELECT
?lipid ?lipidLabel ?lmid
(GROUP_CONCAT(DISTINCT ?massbanks) as ?massbank)
WHERE {
?lipid wdt:P2063 ?lmid ;
wdt:P6689 ?massbanks .
SERVICE wikibase:label {
bd:serviceParam wikibase:language "[AUTO_LANGUAGE],en".
}
} GROUP BY ?lipid ?lipidLabel ?lmid


Enjoy!