Monday, November 30, 2020

CiTO updates #3: third paper in the collection and updated Scholia patch

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.

Saturday, November 28, 2020

new paper: "WikiPathways: connecting communities"

The number of revisions and contributors
for all pathways in the human pathway
analysis collection.
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. There is also a lot happening in the background, to make our tools better (much needed), our curation support better (in the future available in multiple ways), our data model better, and our dissemination even better (e.g. with Scholia/Toolforge and nanopublications). A huge thanks to Marvin and Tina to get everything together. Finally, if you haven't recently checked the WikiPathways SPARQL endpoint, read the paper :)

Sunday, November 01, 2020

CiTO updates #2: annotation migration to Wikidata and first Scholia patch

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:

Screenshot of CiTO annotation of references in Wikidata:

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). At this moment the citation intention "uses method in cited work" is currently the most common. And 20 journals now have one or more articles with CiTO annotation, with the Journal of Cheminformatics the most (no surprise).


Next up is to enrich Scholia. This may be a bit tricky at this moment, with the annotation not being very abundant at this moment. However, I have started a patch (WIP, work in progress) to show CiTO information. The first step is an extension to the venue aspect, here in action (locally) for the Journal of Cheminformatics:

Scholia page being developed that shows what CiTO types are being used in J.Cheminform. at this moment, with 'updates the cited work' as most annotation of articles citing J.Cheminform. articles.

What we learn from this bubble graph is that at this moment that 'updates the cited work' is the most common annotation of articles citing J.Cheminform. articles. Similar pages will have to be developed for works, authors, etc.

This Scholia work, btw, was funded by a Alfred P. Sloan under grant number G-2019-11458

CiTO updates #1: first research paper in the Journal of Cheminformatics with CiTO annotation published

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. published a few weeks ago the first research article with CiTO annotation of references ("Predicting target profiles with confidence as a service using docking scores")!

Title, author list, and part of the abstract of the article by Ahmed et al.

Title, author list, and part of the abstract of the article by Ahmed et al.

Of course, I also have to show a screenshot of what the annotation actually looks like, so here goes:

References 21-23 from the article, showing the CiTO annotation.

Thanks for the authors for adding these annotations!