Thursday, August 17, 2017

Text mining literature that mention JRC representative nanomaterials

The week before a short holiday in France (nature, cycling, hiking, touristic CERN visit; thanks to Philippe for the ViaRhone tip!), I did some further work on contentmining literature that mention the JRC representative nanomaterials. One important reason was that I could play with the tools developed by Lars in his fellowship with The ContentMine.

I had about one day, as there always is work left over to finish in your first week of holiday, and had several OS upgrades to do too (happily running the latest 64bit Debian!). But, as a good practice, I kept an Open Notebook Science practice, and the initial run of the workflow turned out quite satisfactory:

What we see here is content mined from literature searched with "titanium dioxide" with the getpapers tool. AMI then extracted the nanomaterials and species information. Tools developed by Lars aggregated all information into a single JSON, which I converted into input for cytoscape.js with a simple Groovy script. Yeah, click on the image, and you get the live network.

So, if I find a bit of time before I get back to work, I'll convert this output also to eNanoMapper RDF for loading into Of course, then I will run this on other EuropePMC searches too, for other nanomaterials.

Sunday, July 30, 2017

Wikidata visualizes SMILES strings with John Mayfield's CDK Depict

SVG depiction of D-ribulose.
Wikidata is building up a curated collection of information about chemicals. A lot of data originates from Wikipedia, but active users are augmenting this information. Of particular interest, in this respect, is Sebastian's PubChem ID curation work (he can use a few helping hands!). Followers of my blog know that I am using Wikidata as source of compound ID mapping data for BridgeDb.

Each chemical can have one or two associated SMILES strings. A canonical SMILES, that excludes any chirality, and a isomeric SMILES that does include chirality. Because statement values can be linked to a formatter URL, Wikidata often has values associated with a link. For example, for the EPA CompTox Dashboard identifiers it links to that database. Kopiersperre used this approach to link to John Mayfield's CDK Depict.

Until two weeks ago, the formatter URL for both the canonical and isomeric SMILES was he same. I changed that, so that when a isomeric SMILES is depicted, it shows the perceived R,S (CIP) annotation as well. That should help further curation of Wikidata and Wikipedia content.

Wednesday, July 05, 2017

new paper: "A transcriptomics data-driven gene space accurately predicts liver cytopathology and drug-induced liver injury"

Figure from the article. CC-BY.
One of the projects I worked on at Karolinska Institutet with Prof. Grafström was the idea of combining transcriptomics data with dose-response data. Because we wanted to know if there was a relation between the structures of chemicals (drugs, toxicants, etc) and how biological systems react to that. Basically, testing the whole idea behind quantitative-structure activity relationship (QSAR) modeling.

Using data from the Connectivity Map (Cmap, doi:10.1126/science.1132939) and NCI60, we set out to do just that. My role in this work was to explore the actual structure-activity relationship. The Chemistry Development Kit (doi:10.1186/s13321-017-0220-4) was used to calculate molecular descriptor, and we used various machine learning approaches to explore possible regression models. Bottom line was, it is not possible to correlate the chemical structures with the biological activities. We explored the reason and ascribe this to the high diversity of the chemical structures in the Cmap data set. In fact, they selected the chemicals in that study based on chemical diversity. All the details can be found in this new paper.

It's important to note that these findings does not validate the QSAR concept, but just that they very unfortunately selected their compounds, making exploration of this idea impossible, by design.

However, using the transcriptomics data and a method developed by Juuso Parkkinen it is able to find multivariate patterns. In fact, what we saw is more than is presented in this paper, as we have not been able to support further findings with supporting evidence yet. This paper, however, presents experimental confirmation that predictions based on this component model, coined the Predictive Toxicogenocics Gene Space, actually makes sense. Biological interpretation is presented using a variety of bioinformatics analyses. But a full mechanistic description of the components is yet to be developed. My expectation is that we will be able to link these components to key events in biological responses to exposure to toxicants.

 Kohonen, P., Parkkinen, J. A., Willighagen, E. L., Ceder, R., Wennerberg, K., Kaski, S., Grafström, R. C., Jul. 2017. A transcriptomics data-driven gene space accurately predicts liver cytopathology and drug-induced liver injury. Nature Communications 8.

Saturday, June 24, 2017

The Elsevier-SciHub story

I blogged earlier today why I try to publish all my work gold Open Access. My ImpactStory profile shows I score 93% and note that with that 10% of the scientists in general score in that range. But then again, some publisher do make it hard for us to publish gold Open Access. And then if STM industries spreads FUD for their and only their good ("Sci-Hub does not add any value to the scholarly community.", doi:10.1038/nature.2017.22196), I get annoyed. Particularly, as the system makes young scientists believe that transferring copyright to a publisher (for free, in most cases) is a normal thing to do.

As said, I have no doubt that under current copyright law it was to be expected that Sci-Hub was going to be judged to violate that law. I also blogged previously that I believe copyright is not doing our society a favor (mind you, all my literature is copyrighted, and much of it I license to readers allowing them to read my work, copy it (e.g. share it with colleagues and students), and even modify it, e.g. allowing journals to change their website layout without having to ask me). About copyright, I still highly recommend Free Culture by Prof. Lessig (who unfortunately did not run for presidency).

To get a better understand of Sci-Hub and its popularity (I believe gold Open Access is the real solution), I looked at what literature was in Wikidata, using Scholia (wonderful work by Finn Nielsen, see arXiv). I added a few papers and annotated papers with their main subject's. I guess there must be more literature about Sci-Hub, but this is the "co-occuring topics graph" provided by Scholia at the time of writing:

It's a growing story.

As a PhD student, I was often confronted with Closed Access.

It sounds like a problem not so common in western Europe, but it was when I was a fresh student (around 1994). The Radboud's University Library certainly did not have all journals and for one journal I had to go to a research department and sit in their coffee room. Not a problem at all. Big Package deals improved access, but created a vendor lock-in. And we're paying Big Time for these deals now, with insane year-over-year inflation of the prices.

But even then, I was repeatedly confronted with not having access to literature I wanted to read. Not just me, btw, for PhD students this was very common too. In fact, they regularly visited other universities, just to make some copies there. An article basically costed a PhD a train travel and a euro or two copying cost (besides the package deal cost for the visited university, of course). Nothing much has changed, despite the fact that in this electronic age the cost should have gone down significantly, instead of up.

That Elsevier sues Sci-Hub (about Sci-Hub, see this and this), I can understand. It's good to have a court decide what is more important: Elsevier's profit or the human right of access to literature (doi:10.1038/nature.2017.22196). This is extremely important: how does our society want to continue: do we want a fact-based society, where dissemination of knowledge is essential; or, do we want a society where power and money decides who benefits from knowledge.

But the STM industry claiming that Sci-Hub does not contribute to the scholarly community is plain outright FUD. In fact, it's outright lies. The fact that Nature does not call out those lies in their write up is very disappointing, indeed.

I do not know if it is the ultimate solution, but I strongly believe in a knowledge dissemination system where knowledge can be freely read, modified, and redistributed. Whether Open Science, or gold Open Access.

Therefore, I am proud to be one of the 10 Open Access proponents at Maastricht University. And a huge thank you to our library to keep pushing Open Access in Maastricht.