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Sunday, February 19, 2017

Talk: "Making open science a reality, from a researcher perspective"

Slide from the presentations with
a screenshot of the
Woordenboek Organische Chemie.
Last week I was in Paris (wonderful, but like London, a city that makes you understand Ankh-morpork) for the AgreenSkills+ annual meeting. AgreenSkills+ is a program for postdoc funding in France and the postdocs presented their works. Wednesday (#agreenskills) was a day to learn about Open Science, with other talks from Nancy Potinka and Ivo Grigorov from Foster Open Science, Martin Donnelly from the Edinburgh Digital Curation Centre about data management and the DMPonline tool, and Michael Witt of Purdue University about digital repositories and DataCite (which I should really make time to blog aobut too).

I was asked to talk about my experiences from a researcher perspective (which started with the Woordenboek Organische Chemie). Here are my slides:


Saturday, February 18, 2017

Open Science is already a thing in The Netherlands

It has been hard to miss it: the Dutch National Plan Open Science (doi:10.4233/uuid:9e9fa82e-06c1-4d0d-9e20-5620259a6c65). It sets out an important step forward: it goes beyond Open Access publishing, which has become a tainted topic. After all, green Open Access does not provide enough rights. For example, teachers can still not share green Open Access publications with their students easily.

I am happy I have been able to give feedback on a draft version, and hope it helped. During the weeks before the release I also looked how the Open Science working group of the Open Knowledge International foundation(?) is doing, and happy that at least the Dutch mailing list is still in action. Things are a bit in a flux, as the OKI is undergoing a migration to a new platform. Maybe more about that later.

But one of my main comments was that there already is a lot of Open Science ongoing in The Netherlands. And then I am not talking about all those scientists that already publish part of their work as (gold) Open Access, but the many researchers that already share Open Data, Open Source, or other Open research outputs. In fact, I started a public (CCZero) spreadsheet with GitHub repositories of Dutch research groups, which now also covers many educational groups, at our universities and "hogescholen". This now includes some fourty(!) git repositories, mostly on GitHub but also on GitLab. Wageningen even have their own public git website!


Mind you, I had to educate myself a bit in the exact history of the term Open Science. It actually seems to go back to the USA Open Source community (see these references and particularly this article). And that's actually where I also knew it from, in particular from Dan Gezelter, founding author of the well-known Jmol viewer for small molecules and protein structures, and host of the www.openscience.org domain.

Tuesday, January 03, 2017

Wikidata-powered citation lists with citation.js

I don't get enough time with the kids as I would like, but if your son is doing interesting coding projects it makes that a lot easier. One project he is working on is citation.js, a JavaScript library to edit bibliographies. It has become really powerful and totally awesome! We all hate formatting bibliographies and that every journal has its own format. LaTeX and Citation Style Language have done wonders here, but all should even be simpler. As an author I want to be able to just give a DOI and that should be enough.

Or a Wikidata entity identifier.

And citation.js makes that last thing possible, and I spent some time with Lars to implement this for my homepage:


This is more or less what I had before too, but then everything hard coded. The citation.js way allow me to give just a list of two entity IDs (Q27062312 and Q27062639) and citation.js outputs the above. I just have this snippet in the HTML:

      <ul class="cite" id="cite1" />
      <script class="code" type="text/javascript">
        var wikidata = new Cite()
        wikidata.set( [ "Q27062312", "Q27062639" ] )
        htmlOutput = wikidata.get( opt )
        $('#cite1').html(
          htmlOutput.replace( /&(lt|#60);/g, '<' )
                    .replace( /&(gt|#62);/g, '>' )
        )
      </script>

The formatting is actually mostly done with a CSL template (though it needs a hack to get it to output HTML), though adapted to also output the DOI hyperlink and Altmetric icon (you can find the customized CSL in the HTML source code as CC-BY-SA 3.0). The citation.js library fetches the data from Wikidata and actually has to deal with the structure there, which includes a mixture of 'author' and 'author name string' fields for author information. Well done!

If you like this, make sure to check out Wikicite, OpenCitations, and Scholia, projects that enabled and triggered some of the ideas behind the above citation.js use!

"10 everyday things on the web the EU Commission wants to make illegal" #04

Fourth example is harder then the third and I hope I got the translation of Julia Reda's example in good way. The starting point is simple enough, bookmarking things where an image is used. However, I am less sure to what extend we use this in online science.

04. Pinning a photo to an online shopping list

Well, you can see how much trouble I had with finding a good equivalent here. So, what is a science shopping list? The above example shows a Google+ post by Björn Brembs. Now, G+ is not really a shopping list, but then again, literature is what researchers buy. Literally. We pay millions and millions for it. Second, we do have dedicated shopping lists for these products, but they not always support images. Of course, these shopping lists are our CiteULike, Mendeley, ResearchGate, etc accounts.

Second limitation of this example is that we would not consider most of our literature of journalistic nature. Therefore the above example. Blogs are typically a mixture of science writing and a kind of journalism. It's a grey area. Now, under the new laws, Björn would have to ask my permission, and worse, G+ needs to install a monitoring system to see if Björn got a proper license as to not break my copyright.

So, back to the likes of ResearchGate and ScienceOpen. With the current proposal, any system of this kind with some commercial model in mind (both are set up by SMEs), they will have to install this monitoring system (after all, we also happily bookmark Nature News articles). The cost of that investment will have to come from somewhere, so this has an enormous impact on their sustainability.

Even worse, the wordings in the proposal I have seen so far, and to the extend I understand Julia's worries, there are no limitations set on this; few or no words on allowed behavior. So, what about dissemination systems in general? I think later examples (we still have six to go!), will shed more light on that.

(And make sure to read the original article by Julia Read!)

Monday, January 02, 2017

EPA CompTox Dashboard IDs in Wikidata

After Antony Williams left the ChemSpider team, he moved on to the EPA. Since then, he has set up the EPA CompTox Dashboard (see also doi:10.1007/s00216-016-0139-z [€]). And in August he was kind enough to upload mappings between InChIKeys (doi:10.1186/s13321-015-0068-4) and their identifiers on Figshare (doi:10.6084/m9.figshare.3578313.v1) as a tab-separated values (TSV) file. Because this database is of interest to our pathway and systems biology work, I realized I wanted ID-ID mappings in our BridgeDb identifier mappings files (doi:10.1186/1471-2105-11-5). As I wrote earlier, I have adopted Wikidata (doi:10.3897/rio.1.e7573) as data source. So, entering these new identifiers in Wikidata is helpful.

Somewhere in the past few months I proposed the needed Wikidata property, P3117 ("DSSTOX substance identifier"), which was approved some time later. For entering the mappings, I have opted to write a Bioclipse script (doi:10.1186/1471-2105-10-397) that uses the Wikidata SPARQL endpoint to get about 150 thousand Wikidata item identifiers (Q-codes) and their InChIKeys. I then parses over the lines in the TSV file from Figshare and creates input for Wikidata for each match, based on exact InChIKey string equivalence.

This output is formatted QuickStatements instructions, a great tool set up by Magnus Manske. Each line looks like (here for N6-methyl-deoxy-adenosine-5'-monophosphate, aka Q27456455):

Q27456455 P3117 "DTXSID30678817" S248 Q28061352

The P248 ("stated in") property is used to link the source (hence: S248) information as reference, with points to the Q28061352 item which is for the Figshare entry for Tony's mapping data. The result in this Wikidata item looks like:


I entered about 36 thousand of such statements to Wikidata. Thus, the yield is about 5%, calculating from the CompTox Dashboard as starting point with about 720 thousand identifiers. From a Wikidata perspective, the yield is higher. There are about 150 thousand items with an InChIKey, so that 24% could be mapped.

Based on properties of the property, it does some automatic validation. For example, it is specified that any Wikidata item can only have one DSSTOX substance identifier, because it can only have one InChIKey too. Similarly, there can not be two Wikidata items with the same DSSTOX identifier. Normally, because because of how Wikidata works, there can be isolated examples. With less then 25 constraint violations, the quality of the process turned out pretty high (>99.9%).


Some of the issues have been manually inspected. Causes vary. One issue was that the Wikidata item in fact had more than one InChIKey. A possible reason for that is that it does not distinguish between various forms of a compound. Two Wikidata items have been split up accordingly. Other problems are due to features of the CompTox Dashboard, and some issues have been tweeted to the Dashboard team.

This mashup of these two resources, as anticipated in our H2020 proposal (doi:10.3897/rio.1.e7573), makes it possible to easily make slices of data. For example, we can query for experimental data for compounds in the EPA CompTox Dashboard with a SPARQL query like for the dipole moment:


Importantly, this query shows the source where this data comes from, one of the advantages of Wikidata.