The meeting consisted of four keynotes, each one was quite interesting. Cornet gave a nice historic perspective of the venue and of the semantic web field, which is a great way to welcome the participants to your institute. The talk also touches on the main theme of the meeting: clinical data. It is a long standing (and important) research field, but progress is slow. Cornet comments along the lines that we have been talking about reasoning over patient data for more than twenty years, but we still have not solve it.

The problem is really not only privacy, but simple also lack of a common language. As Sabine Österle explains about sharing health/patient data in Switzerland, across 26 kantons and legislations and 4 national languages. Another issue is more technical, running SPARQL across hospitals involves more than just aligning ontologies, but also requires (too much) fiddling with SPARQL queries.

There was plenty of other content too, however. For example, I was pleasantly surprised by the RDF4RiskAssessment work, the RO-Crates for BioImaging, and FDPcrawleR. All these projects have direct links to research ongoing in our TGX team.

Hanna Bast gave the second keynote of the first day, about QLever (doi:10.1145/3132847.3132921). She talked about some of the recent improvements, something we really needed for Scholia. She showed a technical approach to make federated queries faster, tho it currently only works between endpoints that both run QLever. One thing I am looking forward to, is playing with the notion of materialized views, but the biohackathon was too short to get around to that during the Thursday.

The second day kicked off with a keynote by Janna Hastings, whose work I greatly admire. I was not disappointed today, and she showed the Behaviour Change Intervention Ontology and Chebifier (doi:10.1039/D3DD00238A).

The last talk I want to mention in the blog is by two researcher working with Michel Dumontier. They presented a study about deduplication in/of knowledge graphs. This is something I want to read in more detail.

Now, about the fediverse…

Mastodon (service by SURF)

Mastodon is one of the more well-known corners of the fediverse, and I blogged about it before. It is intrinsically open, while it has extensive options to make things more private. It is like Twitter but then without the central control. It is unlike Slack, Zulip, and LinkedIn which has clear walls around communities. It also is unlike past efforts like Google Wave and FriendFeed which created much more structured discourse.

But I enjoy Mastodon. It has all the good science, the friendly, helpful people, and I have many options to block people, fediverse servers, and even individual keywords (you can remove anything “PFAS”, for example, something hard in the real world). But you also have linear timeline, with just content of the people you follow.

And, with the SURF social.edu.nl server, every researcher from a SURF-linked research insitute can get an account there via SURFconext (the Mastodon solution may need to be activited by your institute first; if so, ask your institute ICT to enable it). The list of accounts on this SURF Mastodon server shows a veried list of people and organisations, but you can also check this list of 80 Ways to follow Research, Science and Education on Mastodon. Or this list of Wikidata queries.

I think every organization that communicates their research should have at least one open world communication channel, and if they then like to keep their wall-garden LinkedIn account too, that is fine. But societal impact for just a select group of people feels a bit awkward to me.

PeerTube (service by SURF)

But SURF operates a second fediverse server, one using the PeerTube software, also extended with the SURFconext interoperability. PeerTube is a platform to share videos, like YouTube. Just before the winter holiday, I got the opportunity to create two project accounts on SURF’s video.edu.nl, one for the VHP4Safety project and one for the FAIR4ChemNL project.

The cool thing actually is that SURFconext has group accounts via SURFconext Invite (it was earlier called SURFconext Teams), so these two PeerTube channels are operated by two or more people from the project, and the two videos that are now available, have not actually been uploaded by me.

But I am very excited we now have channels to share our video communication, here for VHP4Safety:

And here for FAIR4ChemNL:

Almost half a year ago I read this post by Bastian about, well, integrating comments via the Fediverse. He explains a solution worked out in 2021 by Robert W. Gehl. I liked this idea and had the blog post bookmarked for some time. But I did not get around working it out until Monday. I had to do some CSS fixing after that, but I can now have fediverse-powered comments in my blog by adding a bit of YAML, like this:

comments:
  host: social.edu.nl
  username: egonw
  id: 115009169485329450

I have annotated a few posts now, and will have some curation to do. But when I have made such a link, the this is what it will look like by default:

After clicking the button (I want to style that a bit better), it shows the fediverse reactions:

There are some things that I like to improve. For example, clicking the reply, boost, or like buttons doesn’t do anything yet. But there is code around that will show a popup box to redirect you to your home fediserver. Let’s see how this evolves.

But while you can follow me Mastodon accounts with RSS (or just by checking the two webpages, this is a read-only access. That is, you cannot reply. For that, you still need an Mastodon (or Fediverse) account too.

But then there is Bridgy Fed. It “is a decentralized social network bridge. It connects the fediverse, the web, and Bluesky”. I learned about this recently, and it seems to do what it promises. Using the AT Protocol, it allows me to follow and reply to BlueSky users (if they have enabled the bridge), and BlueSky users can interact with me.

So, if you have BlueSky and want to follow one or both of my Mastodon accounts, check out:

• @egonw.social.edu.nl.ap.brid.gy (focused on my research)
• @egonw.mastodon.social.ap.brid.gy (more general open science)

But only if they enabled the bridge too, I can follow them back.

This effort is calling for more universities to go into the direction of open infrastructures. I am looking forward to seeing all Dutch Universities post news on Mastodon, post videos on PeerTube, etc.

Would it not be awesome if the Fediverse would become the new multidimensional knowledge dissemination and peer review system we have all been waiting for?

Update: universities with a Mastodon listed in Wikidata on the world map: https://w.wiki/6zR3

For example, this is what happens when you go to twitter.com/wikipathways:

Fortunately, WikiPathways does have a Mastodon account, that anyone can see without having a Mastodon account. You can even follow WikiPathways’s account with its RSS feed. Dissemination should not be paywalled.

Maybe Musk has been talking to Elsevier and Springer Nature.

Tip: Finding Mastodon accounts with Wikidata (a few SPARQL queries)

Update: Musk said this was a temporary measure. The problem was scraping of content, you know, the content we openly share on Twitter. Maybe they could have done this with APIs. Oh wait, they closed those behind a very expensive paywall.

Update 2: Another rumor is that the forgot to make a deal with a cloud provider and suddenly were left with a fraction of the computing power.

Update 3: The access has been restored, so you can start scraping/archiving all interesting tweets again.

So, here are some Wikidata SPARQL queries to see the uptake:

• Universities with Mastodon
• All Mastodon accounts in Wikidata (or subset with also a Twitter account)
• Nobel Prize winners with Mastodon
• Academic journals with Mastodon
• People with Mastodon that published in a PLOS journal (you can pick another publisher)
• Find your co-authors with your ORCID (just replace my ORCID with yours)

If you find yourself missing, back in April I tweeted (sorry) how you can find yourself and others in Wikidata and how to add your or their Mastodon account.

It’s a fascinating platform: federated, community driven, and open source. Oh, and it uses an open standard: ActivityPub. I have still a lot to learn, but there are some reasons why Mastodon is better and some reasons why it is worse than Twitter.

First, how can you follow me:

• main scholarly account: https://social.edu.nl/@egonw
• politics, foss, hobby account: https://mastodon.social/@egonw

Better

Well, this is personal, of course, but the following points makes Mastodon for me a better platform:

• distributed, open standard
  • e.g. no more tweeting of new Zotero entries (soon I hope), just follow my Zotero account
• community standards
  • you can pick; if you don’t like the terms of your current server (read: service provider), just move to another server
  • images must have alternate descriptions on many servers
• edit button with version control
• content warnings
• ability to hide anything with #caturday (or any other word)
• detailed annotation of privacy (public, unlisted, etc; no encryption, tho)

Worse

Maybe this category can better be called opportunities. After all, it’s the community that defines how it will evolve, just like Twitter did (which did not originally have hashtags, retweets). One big elephant in the scientific social media world wright now is the uncertainty about searching and indexing: will it be useful as (post-publication) platform? will we be able to use if for conference tweeting?

Another aspect is that in some countries mobile internet is deeply coupled with big companies. Think coupling of access with free whatsapp.

Finally: growing pains. The platform is growing fast, and right now it can be hard to find a server that accepts new accounts.

Tips?

Sure. Start with https://fedi.tips/. Have fun! And I love to hear what your tips are :)

Image from WikiCommons.