From linkedchemistry.info
CiTO updates #4: annotations in datasets
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Okay, the Pilot is over ending with 17 papers, 16 of which have CiTO annotations (and so far 4 J.Cheminform. papers after the pilot), but my interest in the Citation Typing Ontology continues and we just need more adoption.
on Sep 6
From linkedchemistry.info
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Chemblaics (pronounced chem-bla-ics) is the science that uses open science and computers to solve problems in chemistry, biochemistry and related fields.
#cito #fair #publishing #nanopublications
on Aug 14
From linkedchemistry.info
CiTO updates: Wakefield and WikiPathways
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This summer I am trying to finish up some smaller projects that I did not have time for to finish, with mixed successes. I am combing this with a nice Dutch staycation, and I already cycled in Overijssel and in south-west Friesland and learning about their histories. But this post is about an...
on Aug 7
From linkedchemistry.info
Open Science Retreat #2: CiTO Nanopublications
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During the Open Science Retreat I organized a short session where we looking into typing citation intentions using a new nanopublication template. First, let’s describe nanopublications (originally used in doi:10.3233/ISU-2010-0613) a bit. Scholia gives a nice overview of (macro?)publications on...
#cito #fair #publishing #nanopublications
on Apr 6
From linkedchemistry.info
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The x-odus continues and there is a wave of researchers moving from X to another walled-garden called Bluesky. This is good and bad. First, it is good that people are leaving X (imho) and it is good that they move to a platform that supports open standards, the AT Protocol. But I am less sure,...
on Sun, 11AM
From linkedchemistry.info
On Open Access in The Netherlands
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Yesterday, I received a letter from the Association of Universities The Netherlands (VSNU, @deVSNU) about Open Access. The Netherlands is for research a very interesting country: it’s small, meaning we have few resources to establish and maintain high profile centers, we also believe strong...
on Sun, 9AM
From linkedchemistry.info
Tag: Programming in the Life Science (PRA3006)
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Chemblaics (pronounced chem-bla-ics) is the science that uses open science and computers to solve problems in chemistry, biochemistry and related fields.
on Nov 3
From linkedchemistry.info
Additional files, data, datasets, databases, and published data
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Open Science doesn’t make publishing easier. That that’s all for the better: our research efforts are complex, so why should the publishing be. Sure, I am not talking about references formatting or moving the Methods section to the right location, or some silly statement that all authors agree...
on Nov 2
From linkedchemistry.info
New paper: The Virtual Human Platform for Safety Assessment (VHP4Safety)
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I have not posted a lot about our Virtual Human Platform for Safety Assessment (VHP4Safety) project yet. Actually, more generally I do not post frequently about the funded projects. This is likely that few of them are Open Science by contract and often they have some formal process in place to...
on Oct 25
From linkedchemistry.info
NASA Transform to Open Science (TOPS) Open Science 101
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It was on my radar for some time already, but did not get around to finishing it. But I completed all five modules of the NASA Transform to Open Science (TOPS) Open Science 101 (doi:10.5281/zenodo.10161527). This Open Science 101 consists of several modules, starting with The Ethos of Open...
on Oct 22
From linkedchemistry.info
Is that Jmol in that D-Wave demo?
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Slashdot reported on D-Wave’s recent demo of their 16-qubit quantum computing system. Video’s of the demo can be watched on Google Video. The second video demonstrates the use of the machine in similarity searching:
on Oct 18
From linkedchemistry.info
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If you read my blog, it should not surprise you that I have long experimented with technologies to improve knowledge dissemination, for example in HTML. And I have blogged about publishing from an author and researcher, and editor perspective, for many years (see this longer list on my old...
on Sep 16
From linkedchemistry.info
Adding citations between existing articles in Wikidata
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Scholarly articles provide context to the factualness of statements in Wikidata, similar to the [citation needed] in Wikipedia. And just like the cited references in each scholarly article itself. The citation network is general seen as an essential part of (doing) science, even without citation...
on Sep 8
From linkedchemistry.info
Join me in encouraging the ACS to join the Initiative for Open Citations
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My research is into abstract representation of chemical information, important for other research to be performed. Indeed, my work is generally reused, but knowing which research fields my work is used in, or which societal problems it is helping solve, is not easily retrieved or determined....
on Sep 7
From linkedchemistry.info
When is open source chemoinformatics successful?
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Open source chemoinformatics has become a common phenomenon, though many projects are small in nature: source code is developed by only few developers, or even in a closed manner and released when considered done. Within open source software there is room for distinguishing a subset of open...
on Aug 16
From linkedchemistry.info
Kasabi archive at the Internet Archive
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Kasabi was an innovative RDF publishing platform from around 2011. Shortlived, and maybe just too early. I published two open datasets there. One was ChEMBL-RDF (see these posts). The second was a small data sets called ChemPedia, a open science effort to crowdsource chemical names. This is...
on Aug 15
From linkedchemistry.info
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Chemblaics (pronounced chem-bla-ics) is the science that uses open science and computers to solve problems in chemistry, biochemistry and related fields.
on Aug 1
From linkedchemistry.info
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Kasabi is a new, RDF hosting service by Talis. It’s still in beta, and I have been testing their beta service with the RDF version I created of ChemPedia Substances (the now no longer existing cool web service from MetaMolecular to draw and name organic molecules).
on Aug 1
From linkedchemistry.info
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I am still catching up with a lot of work, and found out I actually had forgotten to blog about this cool article by Denise Slenter: “Discovering life’s directed metabolic (sub)paths to interpret human biochemical markers using the DSMN tool” (doi:10.1039/D3DD00069A). This paper explains how...
on Jul 31
From linkedchemistry.info
GoatCounter, Rogue Scholar and more new things
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About a year ago I started migrating my blogger.com blog to a git-version-controlled, Markdown-based blogging platform. I have to say, it has been a happy year. It actually is awesome to port old blog posts (follow that here) and to see what I have been working on some 17, 18 years ago.
on Jul 21
From linkedchemistry.info
cdk2024 #3: an unexpected downstream project
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In the CDK2024 grant we wrote about updating various software projects using the Chemistry Development Kit. We even wrote that “[r]equired API changes will be publicly shared and disseminated with the Groovy Cheminformatics with the Chemistry Development Kit book (egonw.github.io/cdkbook/)”. The...
on Jun 25
From linkedchemistry.info
0 0
Chemblaics (pronounced chem-bla-ics) is the science that uses open science and computers to solve problems in chemistry, biochemistry and related fields.
on Jun 25
From linkedchemistry.info
cdk2024 #1: NWO Open Science grant for the Chemistry Development Kit
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We recently got awarded our second NWO Open Science grant (OSF23.2.097), this time for the Chemistry Development Kit (CDK). “We” here is me and Alyanne de Haan, René van der Ploeg, and Marc Teunis from Hogeschool Utrecht. The proposal has been submitted for public dissemination in RIO Journal,...
on Jun 25
From linkedchemistry.info
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Chemblaics (pronounced chem-bla-ics) is the science that uses open science and computers to solve problems in chemistry, biochemistry and related fields.
on Jun 25
From linkedchemistry.info
My Google Scholar Citations profile arrived
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Web of Science is my de facto standard for citation statistics (I need these for VR grant applications), and defines the lower limit of citations (it is pretty clean, but I do have to ping them now and then to fix something). The public front-end of it is Researcher ID. There is an Microsoft...
on Jun 2
From linkedchemistry.info
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I was about to call this blog post From spreadsheets to RDF, after the post last week. But then I decided to just use the pattern I typically use. Why I wanted to use that shorter term in the first place was that one of the thing I like about the AMBIT software (of OpenTox and eNanoMapper fame)...
on May 27
From linkedchemistry.info
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Making something FAIR is hard, particularly when you do more than making something findable. We’ve seen before that making something usefully findable requires deep indexing, and already that continues to be difficult, because we are not seeing it enough. So, when I thought convert a paper led...
on May 21
From linkedchemistry.info
cdk2024 #2: publishing grant proposals
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Publishing grant proposal is still not very common. The proposal published in Research Ideas and Outcomes) (doi:10.3897/rio.10.e124884) for the NWO Open Science grant for the CDK is, however, not the first and hopefully not the last. Interestingly, it is already cited in (the German) Wikipedia....
on May 21
From linkedchemistry.info
0 0
Chemblaics (pronounced chem-bla-ics) is the science that uses open science and computers to solve problems in chemistry, biochemistry and related fields.
on May 18
From linkedchemistry.info
Finding Mastodon accounts with Wikidata (a few SPARQL queries)
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There are multiple initiatives to support the migration from Twitter to Mastodon (see also this blog post ). But Wikidata should not be forgotten here which has been tracking Mastodon accounts of things in their database:
on May 17
From linkedchemistry.info
Open Science Retreat #1: impressions
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Last week I attended the Open Science Retreat (#osr24nl) in a quite and relaxing region in North-Holland. The meeting was how I like all meetings to be (and I count myself lucky many of my meetings are like this): open, welcoming, constructive, diverse, and intellectually challenging. Not all...
on Apr 1
From linkedchemistry.info
Open Data: the Panton Principles
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The announcement of the Panton Principles is the big news today, though Peter already spoke about them in May last year (see coverage on FriendFeed and Twitter). The four principles list in their short versions:
on Mar 23
From linkedchemistry.info
The Cologne University BioInformatics Center (CUBIC)
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As of April 3, I will be working as postdoc in the group of Christoph Steinbeck at the Cologne University BioInformatics Center , or simply CUBIC, for a year. Though no exact plans have been decided upon, the work will include CDK, CML, ontologies, Bioclipse, semantic web technologies, Jmol, and...
on Feb 8