Found my way back to my room a few kilometers from the San Francisco city center, after a third day at the WikiPathways 2018 Summit at the Gladstone Institutes in Mission Bay, celebrating 10 years of the project, which I only joined some six and a half years ago. The Summit was awesome and the whole trip was awesome. The flight was long, with a stop in Seattle.
Slice of the spreadsheet in the supplementary info.
There was a lot of Open Science news this week.
Bar chart showing the number of compounds with a particular chemical identifier. I think Wikidata is a groundbreaking project, which will have a major impact on science. One of the reasons is the open license (CCZero), the very basic approach (Wikibase), and the superb community around it. For example, setting up your own Wikibase including a cool SPARQL endpoint, is easily done with Docker.
The U.S.A and European nanosafety communities have a longstanding history of collaboration. On both sides there are working groups, NanoWG and WG-F (previously called WG4) of the NanoSafety Cluster. I have been chair of WG4 for about three years and still active in the group, though in the past half year, without dedicated funding, less active. That is already changing again with the imminent start of the NanoCommons project.
Hi all, welcome to this winter solstice challenge! Umm, to not give our southern hemisphere colleagues not a disadvantage, as their winter solstice has already passes, you’re up for a summer solstice challenge!
It takes effort to move scholarly publishing forward. And the traditional publishers have not all shown to be good at that: we’re still basically stuck with machine-broken channels like PDFs and ReadCubes. They seem to all love text mining, but only if they can do it themselves.
SWAT4LS was once again a great meeting.
Doing searches in RDF stores is commonly done with SPARQL queries. I have been using this with the semantic web translation of WikiPathways by Andra to find common content issues, though sometimes combined with some additional Java code. For example, find PubMed identifiers that are not numbers.
Andra Waagmeester published a paper on his work on a semantic web version of the WikiPathways (doi:10.1371/journal.pcbi.1004989). The paper outlines the design decisions, shows the SPARQL endpoint, and several examples SPARQL queries. These include federates queries, like a mashup with DisGeNET (doi:10.1093/database/bav028) and EMBL-EBI’s Expression Atlas.
In 2010 Samuel Lampa and I started a pet project: collecting pKa data: he was working on RDF extension of MediaWiki and I like consuming RDF data. We started DrugMet. When you read this post, this MediaWiki installation may already be down, which is why I am migrating the data to Wikidata. Why?