chem-bla-ics: May 2022

new: "The LOTUS initiative for open knowledge management in natural products research"

There is a ton of knowledge still not disclosed in a FAIR way. I am proud to have contributed to this new paper about the new LOTUS initiative for open knowledge management in natural products research (doi:10.7554/eLife.70780). The eLife editor wrote:

The strength of this initiative lies in the effort the authors had put in creating a database that is both reproducible and usable. The result is thus a complete and user-friendly product that will respond to people's needs.

The intrinsic feature of depositing in Wikidata is one of the (many) interesting aspect of LOTUS: wide dissemination is essential and Wikidata fulfills the technical requirements (see also this, this, and this).

May

new: "CAS Common Chemistry in 2021: Expanding Access to Trusted Chemical Information for the Scientific Community"

Open Science is happening. The merits are no longer theoretical or idealistic but tangible. Research is faster than ever, more vetted than ever (think PubPeer), more cited than ever. Fairly, not just because of Open Science, but open access causes readership causes impact causes citations. When new people and organizations start adopting Open Science this warms my hearth.

May

new: "Understanding signaling and metabolic paths using semantified and harmonized information about biological interactions"

I joined the BiGCaT research team because of their open science work on WikiPathways (Scholia summary). To me, WikiPathways is an essential tool to move forward. It's different from Reactome and KEGG and I think for good reasons (read the articles to get some idea). I also believe collaboration with both databases is very useful. I have seen how open science cheminformatics boosted the field in general, and do not see how that would not work here too.

May

DECIMER: a new chemical OCR kid on the block

When I started blogging this was in the first place to reduce the amount of time it took me to inform people about cool new open science. That became really hard: my group grew and the amount of open science nowadays is enormous. We were right in the late nineties that open science was the way forward Anyway, I am trying to blog more about noteworthy things again. I am about 2 months behind and have not even blogged about the CDK meeting in April.

Today I want to highlight DECIMER.

May

new: "PSnpBind: a database of mutated binding site protein-ligand complexes constructed using a multithreaded virtual screening workflow"

Two years ago one of the students from our university's Systems Biology Master (sign up info here) came up to me with an idea he had. And he wanted to study that question under my supervision. His name was Ammar, and he wanted to know how the genetic human variation translates to ligand-target-binding variation.

After all, missense SNPs change the protein structure. There are a lot of derived questions here.

May

new: "Providing Adverse Outcome Pathways from the AOP-Wiki in a Semantic Web Format to Increase Usability and Accessibility of the Content"

I am a bit behind with tweeting about new published papers, but let that not reflect that these papers are not very exciting. The first paper is by Marvin an almost-finished PhD candidate in our group and now working as postdoc on the VHP4Safety project. He has been working on linking adverse outcome pathways (AOPs) with molecular pathways, such as in WikiPathways.

May

BridgeDb NWO grant update #3: Pandora's box

We (Denise, Martina, Tooba (funded by the FAIRplus project), Helena, and me) really picked up momentum with the NWO Open Science grant for BridgeDb. On the right you can see the activity in the BridgeDb Organisation on GitHub: at least nine repositories have seen activity in the past 2 weeks. Some updates:Tooba released new gene/protein ID mapping databases, e.g.