Sunday, August 30, 2015

Linking papers to database to papers: PubMed Commons and

I argued earlier this year (doi:10.5281/zenodo.17892) in the Journal of Brief Ideas that measuring reuse of data and/or results in databases is a good measure of impact of that research. Who knows, it may even beat the citation count, which does not measure quality or correctness of data (e.g. you may cite a paper because you disagree with the content; I have long and still am advocating the Citation Typing Ontology).

But making the link between databases and papers is not only benefiting measuring reuse, it is also just critical for doing research. Without clear links, finding answers is hard. I experience that myself frequently, and so do others, like Christopher Southan, and it puzzles me that so few people worry about this. Of course, databases do a good part of linking, but only if they expose an API (still rare, but upcoming), it is hard to use these links. PubMed Commons can be used to link to (machine readable) version of data in a paper. See, for example, these four comments by me.

Better is when the database provides an API. And that is used by Ferret. I have no idea where this project is going to; it does not seem Open Source, I am not entirely sure how the implemented the history, but the idea is interesting. Not novel, as UtopiaDocs does a similar thing. Difference is, Ferret is not a PDF reader, but works directly in your Chrome browser. That makes it more powerful, but also more scary, which is why it is critical they send a clear message about any involvement of Ferret servers, or if everything is done locally (otherwise they can forget about (pharma) company uptake, and they'd have a hard time restoring trust). That said, there privacy policy document is already quite informative!

Last week, I asked them about their tool and if it was hard to add databases, as that is one thing Ferret does: if you open it up for a paper, it will show the databases that cite that paper (and thus likely have information or data from that paper, e.g. supplementary information). Here's an example:

This screenshots shows the results for a nanotoxicity paper and we see it picked up "titanium oxide" (accurately picking up actual nanomaterials or nanoparticles is an unsolved text mining issue). We get some impact statistics, but if you read my blog and my brief idea about capturing reuse, I think they got "impact" wrong. Anyway, they do have a knowledge graph section, which has the paper-database links, and Ferret found this paper cited in UniProt.

Thus, when I asked them if it would be hard to add new databases to that section, and I mentioned Open PHACTS and WikiPathways, they replied. In fact, within hours they told me they found the WikiPathways SPARQL end point that Andra started, which they find easier to use than the WikiPathways webservices :)  They asked me for a webpage to point users too, and while I was thinking about that, they found another WikiPathways trick I did not know about, you can browse for WP2371 OR WP2059. Tina then replied that, given a PubMed ID, there was even a nicer way, just browse for all pathways with a particular PubMed ID.

Well, a bit later, they release Ferret 0.4.2 with WikiPathways support. The below screenshot shows the output for a paper (doi:10.2174/1389200214666131118234138) by Rianne (who did internships in our group, and now does here PhD in toxicology):

The Ferret infobar shows seventeen WikiPathways that are linked to this paper, which happens to be the collection that Rianne made during her internship leading to this paper, and uploaded to WikiPathways some months ago. Earlier this year we sat down with her, Freddie, and Linda to make them more machine readable. This is what this list looks like in the browse functionality:

Ferret version 0.4.2 did not work for me, but they fixed the issue within a day, and the above screenshot was made with version 0.4.3. So, besides like a bunch of good hackers, they also seem to listen to their customers. So, what databases do you feel they should add? Leave a comment here, or tweet them at @getferret (pls cc me).

Willighagen, E., Capturing reuse in altmetrics. J. Brief Ideas. May 2015. URL
Fijten, R. R. R., Jennen, D. G. J., Delft, Dec. 2013. Pathways for ligand activated nuclear receptors to unravel the genomic responses induced by hepatotoxicants. Current Drug Metabolism, 1022-1028.