Ten simple rules for scholarly blogging

The fragmentation of social media and the rise of Generative Artificial intelligence (AI) have renewed the importance of scholarly blogs. Similar to preprints, blogs enable researchers to communicate ...

doi.org

Rogue Scholar is becoming a German Non-Profit Organization

The science blog archive Rogue Scholar started the process of becoming a German non-profit organization in 2026. This blog post summarizes the reasoning and the main steps needed to achieve this. Two weeks ago, I published a self-assessment of how Rogue Scholar adheres to the Principles of Open Scholarly Infrastructure (POSI). Major gaps were identified in the areas of _governance_ and _sustainability_. To address these gaps, a major step forward would be to start a non-profit membership organization. The need to take this step at some point was obvious to me since I launched Rogue Scholar in April 2023. With the basic service operating and on a good path forward with 50,000 science blog posts archived by the end of the year, the time has arrived to make this step. Starting a non-profit membership organization in Germany means starting a _Verein_ , or registered association. The steps involved to formally register the association are clearly laid out and mainly involve the following: * at least seven founding members, * drafting statutes (_Satzung_), * founding general assembly with members approving statutes and electing a founding board, * registration at a local court, * registration for charitable status with the tax authorities. It helps that I have worked for non-profit organizations most of my professional life. Not only public universities, but also a non-profit publisher (PLOS), and two membership organizations (ORCID and DataCite), with the latter also being a German Verein. Interestingly, Research Organization Registry (ROR), an initiative that I helped launch in early 2019, is not a membership organization. Running a non-profit organization in Germany requires more paperwork compared to, for example, Belgium or the Netherlands, mainly to obtain and keep charitable status. This means a good amount of work for the founding board, especially the president and treasurer. One important question is the rights and responsibilities of members. As individuals or groups of people, rather than formal organizations, run many science blogs, membership has to be open to all legal entities, individuals and organizations. Membership fees should differentiate between individuals and organizations, and include at least two tiers for small and large organizations, for example: * individual 25 EUR/year * small organization 250 EUR/year * supporting organization 2500 EUR/year Rogue Scholar is a Diamond Open Access infrastructure with no fees to readers or authors. This means that membership can't be a requirement for a science blog to be archived in Rogue Scholar, but rather that membership comes with other benefits. Members not only help support a unique open scholarly infrastructure but also have a say in the governance of the organization via the general assembly, participation in the board, and potentially working groups going forward. For Rogue Scholar to achieve sustainability, membership fees are an important element. Two other aspects are also important: * **Volunteer labor** , particularly in the areas of outreach, support, and software development, becomes easier once Rogue Scholar has formal members * **Grant funding** , which becomes easier once Rogue Scholar obtains charitable status Please use Slack, email, Mastodon, or Bluesky if you have any questions or comments regarding Rogue Scholar becoming a non-profit membership organization. Rogue Scholar is a scholarly infrastructure that is free for all authors and readers. You can support Rogue Scholar with a one-time or recurring donation, by becoming a sponsor, or soon by becoming a member. ## References 1. Fenner, M. (2025, October 20). Rogue Scholar follows the Principles of Open Scholarly Infrastructure (POSI). _Front Matter_. https://doi.org/10.53731/m65a8-6sm21 2. POSI Adopters. (2025). _The Principles of Open Scholarly Infrastructure v2.0_. https://doi.org/10.14454/G8WV-VM65 3. Fenner, M. (2023, April 4). The Rogue Scholar is now open for business. _Front Matter_. https://doi.org/10.53731/z9v2s-bh329 4. California Digital Library, DataCite, Crossref, & Digital Science (United Kingdom). (2018). _The ROR of the crowd: Get involved!_. https://doi.org/10.71938/SNA1-ZC49

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Supporting blog contributions beyond authorship

This week the Rogue Scholar science blog archive has launched a new feature: contributor roles. Blog posts can now have contributor roles attached to each author, and this information is shown in the Rogue Scholar and Crossref metadata. We have discussed contributor roles for blog posts for several months, in particular with the ropensci team. And when the ropensci blog launched support for contributor roles two weeks ago, Rogue Scholar finally had blog post metadata with contributor roles. ropensci implemented the following roles, and they are now all picked up by Rogue Scholar: * Editor (who edited the blog post), e.g. https://doi.org/10.59350/510pg-zzf58 * Translator (who translated the blog post), e.g. https://doi.org/10.59350/b73e6-3wm19 * Interviewee (who was interviewed for a blog post), e.g. https://doi.org/10.59350/s8m95-ap410 The last blog post looks like this in the Rogue Scholar frontend: In the backend InvenioRDM makes a distinction between authors/creators and contributors, similar to the DataCite data model it is based on. Therefore Rogue Scholar first lists the authors (who can't have a role in DataCite), followed by the contributors (who must have a role, aka _contributorType_). Crossref metadata support the roles _editor_ and _translator_ , so this information is passed on during DOI registration, as Rogue Scholar uses Crossref DOIs. Whether these roles are shown in a formatted citation depends on the citation style, and currently this is probably the exception. At this time neither InvenioRDM (the repository platform powering Rogue Scholar) nor Crossref support multiple contributor roles. Crossref plans to add support for CrediT contributor roles in 2026, and at this point might add support for multiple roles, which are common in CrediT. Rogue Scholar and Crossref support other contributor roles currently not used by the ropensci blog, e.g. _reviewer_. And Rogue Scholar will support _CrediT_ contributor roles as soon as they are implemented by Crossref. ### Contributor roles in blog feeds The rOpenSci blogs (in English, Spanish, and French) use JSON Feed as syndication format, and that is how Rogue Scholar automatically receives content and metadata. JSON Feed supports custom extensions that start with an underscore, e.g. "authors": [ { "name": "Maëlle Salmon", "url": "https://orcid.org/0000-0002-2815-0399", "avatar": "https://ropensci.org/img/team/maelle_salmon.jpg", "_roles": ["author"] }, { "name": "Steffi LaZerte", "url": "https://orcid.org/0000-0002-7690-8360", "avatar": "https://github.com/steffilazerte.png", "_roles": ["editor"] }, { "name": "Yanina Bellini Saibene", "url": "https://orcid.org/0000-0002-4522-7466", "avatar": "https://github.com/yabellini.png", "_roles": ["author"] } ], For blogs using Atom feeds, the specification allows mixing in other namespaces that define custom XML elements. For contributor roles we can use the relators vocabulary from the Library of Congress that defines the above three roles (edt editor, trl translator, ive interviewee, but also rev reviewer), e.g. <feed xmlns="http://www.w3.org/2005/Atom" xmlns:mrel="http://id.loc.gov/vocabulary/relators/"> ... <author> <name>Maëlle Salmon</name> <uri>https://orcid.org/0000-0002-2815-0399</uri> </author> <author> <name>Steffi LaZerte</name> <uri>https://orcid.org/0000-0002-7690-8360</uri> <mrel:roleTerm valueURI="http://id.loc.gov/vocabulary/relators/edt">edt</mrel:roleTerm> </author> <author> <name>Yanina Bellini Saibene</name> <uri>https://orcid.org/0000-0002-4522-7466</uri> </author> ... </feed> Blogs that provide a JSON API and are database-driven (e.g. WordPress, Blogger, Ghost, or Substack) can be extended if they are open source, e.g. via a WordPress plugin. ### Other uses of contributor roles Rogue Scholar is a science blog archive, so contributor roles for other types of scholarly content, e.g. datasets or software, are out of scope. The DataCite data model currently doesn't support roles for creators, making it difficult to implement CrediT, or contributor roles adapted to non-textual content types. As a science blog archive, Rogue Scholar is not really concerned with research evaluation, and whether contributor roles might help with this work. Please use Slack, email, Mastodon, or Bluesky if you have any questions or comments regarding Rogue Scholar contributor roles. Rogue Scholar is a scholarly infrastructure that is free for all authors and readers. You can support Rogue Scholar with a one-time or recurring donation or by becoming a sponsor. ## References 1. Salmon, M., Bellini Saibene, Y., & LaZerte, S. (2025, October 14). Recognition Beyond Blog Post Authors. _rOpenSci - Open Tools for Open Science_. https://doi.org/10.59350/510pg-zzf58 2. Salmon, M., LaZerte, S., & Bellini Saibene, Y. (2025, October 22). ¡Prepárense para el lanzamiento! Paquetes enviados al R-multiverse. _Ropensci - herramientas abiertas para una ciencia abierta_. https://doi.org/10.59350/b73e6-3wm19 3. Bellini, A., Casalla, L., Bellini Saibene, Y., & LaZerte, S. (2023, June 6). Meeting the Stars of the R-Universe: PEcAn, an Open Source Project to Take Care of the Planet. _rOpenSci - Open Tools for Open Science_. https://doi.org/10.59350/s8m95-ap410 4. Brand, A., Allen, L., Altman, M., Hlava, M., & Scott, J. (2015). Beyond authorship: Attribution, contribution, collaboration, and credit. _Learned Publishing_ , _28_(2), 151–155. https://doi.org/10.1087/20150211

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25 years of the Chemistry Development Kit

Twenty five years ago the Chemistry Development Kit (CDK) was founded. The Chemistry and Internet (ChemInt2000) had just ended (it ran from 23 to 26 September) and my friend and I had taken the Amtrak night train from Washington to South Bend. At that time there were two leading Java applets for chemistry, JChemPaint and Jmol. I had hacked Chemical Markup Language support into both of them, and Dan Gezelter (Jmol and openscience.org), Christoph Steinbeck (JChemPaint), and me took the opportunity of being in North America to discuss if we could use a common code base. Chris’ _compchem_ had done something similar. Peter Murray-Rust, who had also attended ChemInt2000 like me and Chris did not attend. I do not remember exactly, but I guess we must have met on the 28th and 29th? Maybe already on Wednesday. During this meeting we discussed a common data model (yes, Jmol used the CDK data model at some point) and somewhere during the meeting we wrote down a name for the project. There was the Java Development Kit, so this could be the Chemistry Development Kit. The name stuck. A quick post like this cannot do credit to the history of the CDK, nor of everyone involved in the past or still is. You can browse some of the history of the CDK in my blog and in Chris’ blog. It has been an amazing journey and with a small grant just behind us (with Alyanne de Haan, René van der Ploeg, and Marc Teunis from Hogeschool Utrecht), and all the awesome things ongoing (new JChemPaint, various extensions, upgraded downstream tools), the CDK is alive and kicking. A huge congrats and thanks to everyone (and every company and organization) who contributed code to the CDK with this huge milestone. There are a few people that I want to particularly thank (see the AUTHORS file for all names): Chris, who in the late nineties made a difference with open source in chemistry, Dan, for Jmol and hosting this memorable meeting at Notre Dame University, Rajarshi Guha, who operated _CDK Nightly_ for many years, well before Travis and Google Actions, Stefan, Miguel, Gilleain, and Christian, for many years of contributions to the CDK, and John Mayfield, the current CDK release manager.

github.com

Rogue Scholar now registers DOIs with InvenioRDM

This week, the Rogue Scholar science blog archive started registering DOIs and metadata with Crossref using the InvenioRDM repository platform rather than relying on external tooling. InvenioRDM has of course supported DOI registration with DataCite for a long time, so this adds another option for repositories hosting reports, preprints, dissertations, or other textual documents. Rogue Scholar has registered content with Crossref since its launch two years ago (more than 45,000 blog posts to date), and migrated to the InvenioRDM repository platform 12 months ago, but it always relied on external tooling for Crossref integration. This new Crossref integration into InvenioRDM simplifies the DOI registration workflow. The main difference for Rogue Scholar blog authors and readers is that automatic DOI registration has become faster, happening within a few minutes after a blog post on a participating blog is published or updated. Rogue Scholar checks the RSS feeds of participating blogs for new or updated content every 10 minutes. When new or updated content is found, uploading the post to InvenioRDM and registering/updating a DOI and metadata with Crossref now happens in 1-2 minutes (depending on how many posts have to be updated at the same time). Further improvements in the time it takes to register blog posts with InvenioRDM and Crossref will depend on improving the monitoring of RSS feeds, e.g. by adding a _push_ mechanism (triggered by the blog when content is updated) instead of the current _pull_ mechanism. ### Versioning The InvenioRDM platform supports versioning of content, which is particularly important for datasets and software, but also relevant for text documents such as blog posts. Examples include major new versions of content, possibly after having received feedback via peer review using the Publish, Review, Curate workflow. Other use cases are corrections and retractions. Crossref added version information to its metadata schema with the 5.4.0 release in March, and I am currently testing this functionality in the Rogue Scholar Staging server: One challenge is that the InvenioRDM Crossref integration supports multiple DOI prefixes, so this is a bit more work compared to the DataCite integration only supporting one DOI prefix. In addition, versioning adds complexity to DOI suffix generation. Luckily, the built-in InvenioRDM tooling uses the same DOI naming scheme that Rogue Scholar has used since its launch, but going forward, Rogue Scholar will no longer support custom DOI suffixes that I introduced for WordPress and Substack blogs. Several blogs participating in Rogue Scholar do their own DOI registrations, and those DOIs (what InvenioRDM calls externally managed DOIs) will not be versioned. ### InvenioRDM Crossref DOI registration uses the `commonmeta-py` Python package to generate Crossref XML metadata and a fork of the `invenio-rdm-records` package to integrate with InvenioRDM. After completing versioning support and more testing, the functionality will be merged into the InvenioRDM core functionality, and the discussion with the other InvenioRDM maintainers has started. Soon, every InvenioRDM instance will be able to use Crossref DOI registration with a simple configuration setting (and Crossref member credentials), very similar to how DataCite DOI registration works. ## References 1. Fenner, M. (2024, September 2). Rogue Scholar migrates to InvenioRDM. _Front Matter_. https://doi.org/10.53731/sdazp-kzn55 2. Feeney, P. (2025, March 19). Version 5.4.0 metadata schema update now available. _Crossref Blog_. https://doi.org/10.13003/325070 3. Fenner, M. (2025, January 16). Persistent identifiers, random strings, and checksums. _Front Matter_. https://doi.org/10.53731/6kfyy-nq280 4. Marcum, C. S. (2025, April 8). Drinking from the firehose? Write more and Publish Less (Version 2). _Upstream_. https://doi.org/10.54900/vr8ax-nz653 5. Marcum, C. S. (2025, April 8). Peer-Review for a Blog Post? My Experience with MetaROR. _Upstream_. https://doi.org/10.54900/bymaz-4fw37 6. Hendricks, G., Lammey, R., & Rittman, M. (2022). _Towards a connected and dynamic scholarly record of updates, corrections, and retractions_. MetaArXiv. https://doi.org/10.31222/osf.io/6z7s3

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NIH explores capping APCs: Let’s look at the evidence

by Stefanie Haustein, Eric Schares, Juan Pablo Alperin, Flavia Camargo, Lisa Matthias, Lucía Céspedes, Constance Poitras & Dorothea Strecker On April 30 2025, the US National Institutes of Heal…

doi.org

Rogue Scholar citation tracking launches to production

The Rogue Scholar science blog archive uses DOIs to uniquely identify blog posts with meaningful metadata. This enables tracking citations of scholar blog posts in the scholarly literature using traditional citation tracking methods rather than altmetrics. Initially launched as a Rogue Scholar service six months ago, citation tracking has launched to production this week. The following features are now available: * Automatically fetch citations of Rogue Scholar posts from the Crossref Cited-by service once a week, * Automatically add these citations to Rogue Scholar posts as custom metadata (in the same format as references), * Make these citation metadata available via the Rogue Scholar API, * Added a Citations search facet to filter Rogue Scholar posts, * Show the number of citations in the Rogue Scholar dashboard. Citations in the Rogue Scholar APICitations shown in a Rogue Scholar recordCitations Search FacetCitations in the Rogue Scholar Dashboard The Altmetrics manifesto stated in 2010 that > Altmetrics are fast, using public APIs to gather data in days or weeks. They’re open – not just the data, but the scripts and algorithms that collect and interpret it. In the past 15 years we have seen that the tools and services around altmetrics have taken a different path: altmetrics data from sources like Twitter, Facebook or Mendeley never really became open, and neither did the services aggregating and showing them, or the algorithms aggregating and interpreting them. Efforts like PLOS Article-Level Metrics (where I was the technical lead from 2012 to 2015) or Crossref and DataCite Event Data tried hard but ultimately failed because the data sources were not open, and social media feeds were increasingly driven by algorithms. This social media platform decay was coined _enshittification_ by Cory Doctorow in November 2022. Rogue Scholar is trying a different approach. Instead of altmetrics as a filter to make sense of the scholarly literature, it helps scholarly blogs to become part of the scholarly literature. Rogue Scholar applies the concepts of persistent identifiers (DOI, ORCID, ROR), standardized metadata (Crossref, DataCite), Open Data and Open Access (CC-BY licenses for all content, OSI-approved licenses for all software), and even experiments with peer review. And it now adds citation tracking. Blog posts are rarely cited in the scholarly literature, but that is more about current citation practices than the ability to do so. Crossref is smart enough to figure out that links to blog post URLs in reference lists are conceptually the same as citing a DOI, and that is why Rogue Scholar can find citations to Rogue Scholar blog posts published long before these blogs joined Rogue Scholar. Open Access News was published 2003-2010 and joined Rogue Scholar in 2025, and Crossref finds 22 citations in the scholarly literature to its blog posts. Blog posts are typically published much faster than scholarly articles or even preprints. That is why the post on the Crossref blog announcing that the blog started assigning DOIs to all its posts published in June already has two citations two weeks later, both from Rogue Scholar blogs. Citation tracking of course has limitations. I am not talking using citation counts as a proxy for scientific impact, but rather about technical limitations of automated citation tracking. The main challenge is that only citations that show up in reference lists with an identifier (DOI or URL) and where the reference list is openly made available to Crossref (I4OC) are found. Another challenge is that automated workflows make mistakes – for this reason, Rogue Scholar can exclude falsely linked citations, and has occasionally done so. Please reach out if you find a citation in Rogue Scholar that is not found in the reference list of the citing scholarly work. Rogue Scholar registers Crossref DOIs for blog posts but also includes blogs that register their DOIs using DataCite. Less than 10 blogs of the currently 168 Rogue Scholar blogs do so, and I currently have no easy way to collect citations for these blog posts. DataCite has a similar service to Crossref Cited-by, but the citing scholarly literature is currently mostly in Crossref. Third-party services such as OpenAlex also show the citations of the Crossref blog post mentioned above, but OpenAlex currently has only limited support for scholarly blog posts registered by DataCite. I hope that the new citation tracking service encourages Rogue Scholar bloggers to publish more blog posts with references (currently only 4.98 % of posts), as references and citations are closely connected (how to include references in blog posts is documented here). And I hope that readers of Rogue Scholar blog posts discover interesting scholarly works through the citation tracking service. 460 of the 1370 Rogue Scholar citations are also blog posts, but the most popular citing content type is journal article: * journal article 648 * blog post 460 * preprint 117 * book chapter 117 * proceedings article 12 * book 7 * other 9 Please use Slack, email, Mastodon, or Bluesky if you have any questions or comments regarding the Rogue Scholar citation tracking service. ## References 1. Priem, J., Taraborelli, D., Groth, P., & Neylon, C. (2010). _Altmetrics: A manifesto_. https://doi.org/10.5281/zenodo.12684249 2. Fenner, M. (2025, February 3). Rogue Scholar now shows citations of science blog posts. _Front Matter_. https://doi.org/10.53731/4bvt3-hmd07 3. Fenner, M. (2013). What Can Article-Level Metrics Do for You? _PLoS Biology_ , _11_(10), e1001687. https://doi.org/10.1371/journal.pbio.1001687 4. Doctorow, C. (2022, November 17). Social Quitting. _Medium_. https://doctorow.medium.com/social-quitting-1ce85b67b456 5. Marcum, C. S. (2025, April 8). Peer-Review for a Blog Post? My Experience with MetaROR. _Upstream_. https://doi.org/10.54900/bymaz-4fw37 6. Stoll, L., Vale, P., & Clark, R. M. (2025, June 24). Scholarly blogs and their place in the research nexus. _Crossref Blog_. https://doi.org/10.64000/552ec-b8g03 7. Shotton, D. M. (2017, April 6). The Initiative for Open Citations. _OpenCitations Blog_. https://doi.org/10.59350/jdwj8-at997

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Rogue Scholar Updates: full-text search as default and basic blog self-management

This week the Rogue Scholar science blog archive as received to important updates: full-text search becomes the default search configuration, and blog authors can now self-manage basic settings of their Rogue Scholar blog community. ### Full-text search as default Rogue Scholar has long supported full-text search of all its content. With this update, users no longer have to specify that they want to search in the full-text content using the `content:` prefix. All queries now automatically search the full-text, e.g. this query for the term xanadu: https://rogue-scholar.org/search?q=xanadu. You still can specify `content:` if you want to search only in the full-text, similar to how you can specify other fields to search in. And you can search either all of Rogue Scholar or a specific community. See the Rogue Scholar search guide for details. ### Basic blog self-management With the latest update the basic settings of Rogue Scholar blog communities can be managed by blog authors. They need a Rogue Scholar account and have to accept an invitation (send an email) as _manager_ of the blog community. The basic blog settings (name, short description, website, and profile picture) are automatically extracted from the blog RSS feed. Still, they can be overridden in the blog community form, for example to add a profile picture if that is not included in the feed. Registration of new blogs still requires filling out a separate form (found here), and the automatic blog post extraction can't be configured in the community form. Blog community managers also can't update their posts in Rogue Scholar, but they can submit their blog posts to one or more topic communities (such as R or Book Review) using the Communities sidebar settings. Please use Slack, email, Mastodon, or Bluesky if you have any questions or comments regarding these updates.

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Original post on fediscience.org

fediscience.org

InvenioRDM v13.0 released — inveniosoftware.org

inveniosoftware.org

Rogue Scholar Newsletter June 2026

This is the June issue of the monthly newsletter from the Rogue Scholar science blog archive. The newsletter reports on new blogs that have joined the platform, important technical updates in Rogue Scholar infrastructure, community updates, and other news relevant to Rogue Scholar users. ## Blogs added to Rogue Scholar Two blogs were added in June. Welcome everybody! This brings the number of participating blogs to 150, a big milestone for Rogue Scholar. ### carrier-bag.net _Arts, English._ https://carrier-bag.net/ ### ACM SIGCSE Journal Club Better teaching and learning, one paper at a time... _Computer and information sciences, English_ https://sigcse.cs.manchester.ac.uk/[ ](https://rogue-scholar.org/communities/sigcse) ### ## Technical Updates Starting June 2nd, Rogue Scholar experienced major issues with its search index that were finally resolved on June 18. The underlying cause was a failed update of the InvenioRDM software, as reported here. No data were lost, but some Rogue Scholar functionality, e.g. listing all posts by a given blog, was temporarily unavailable. One consequence was to set up additional Rogue Scholar infrastructure for more extensive testing of major new software versions. The new Rogue Scholar staging server is available at staging.rogue-scholar.org, and the underlying technology (the Kamal tool) is described here. Kamal makes deploying Rogue Scholar simpler and cheaper, and will be used for the migration to the next major InvenioRDM release (v13 v13.0.0rc3 was published today) over the coming weeks. ### Community Update In collaboration with the Infra Wiss Blogs project, Rogue Scholar started a webinar series on best practices for science blogs. The first webinar (in German) on June 11 focused on WordPress, with participation by the DINI and CSTOnline blogs. The webinar is summarized here, and the presentation slides have also been made available. On June 24 the Crossref Blog published a blog post about the roles Crossref sees for blogs in the scholarly ecosystem, and the work that Crossref has done with Rogue Scholar to assign DOIs to posts in the Crossref blog, and to archive the content with Rogue Scholar and the Internet Archive. Please use Slack, email, Mastodon, or Bluesky if you have any questions or comments regarding this monthly newsletter. Rogue Scholar is a scholarly infrastructure that is free for all authors and readers. You can support Rogue Scholar with a one-time or recurring donation or by becoming a sponsor. ## References Fenner, M. (2025, June 6). Rogue Scholar upgrade pains. _Front Matter_. https://doi.org/10.53731/9nam9-w9k29 Fenner, M. (2025, June 27). Kamal deploys InvenioRDM Starter to production. _Front Matter_. https://doi.org/10.53731/m7gng-jmm19 Höfting, J., Ochsner, C., & Pampel, H. (2025, May 17). Zusammenfassung: Infra Wiss Blogs Webinar zu Rogue Scholar. _Infra Wiss Blogs_. https://doi.org/10.59350/h7rh7-jb575 Stoll, L., Vale, P., & Clark, R. M. (2025, June 24). Scholarly blogs and their place in the research nexus. _Crossref Blog_. https://doi.org/10.64000/552ec-b8g03

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Scholarly blogs and their place in the research nexus - Crossref

If you are reading this blog on our website, you may have noticed that alongside each post we now list a Crossref DOI link, which was not the case a few months ago (though we have retroactively added ...

crossref.org

annualreviews.org

Kamal deploys InvenioRDM Starter to production

InvenioRDM is the open source turn-key research data management platform, with detailed documentation available here. InvenioRDM Starter facilitates deployment and configuration of InvenioRDM, allowing you to run InvenioRDM on your local computer within 15 min. This is achieved by providing a) a prebuilt Invenio-App-RDM Docker image, and b) a Docker Compose configuration file with sensible defaults. Starting this week, InvenioRDM starter can also be used to deploy InvenioRDM to production, using the Kamal tool. Kamal is similar to Docker Compose, but adds important functionality, including automatic remote builds, zero-downtime deployments, and deployments to multiple servers. Kamal is a command-line utility with a YAML configuration file, and much simpler to use than Kubernetes or commercial Docker container orchestration services such as Amazon Elastic Container Service (Amazon ECS). Kamal can deploy InvenioRDM to your hardware or to a virtual machine provided by your organization or a cloud provider. Whereas Kubernetes is a good option for large InvenioRDM installations, smaller InvenioRDM instances benefit from simpler deployment tools both in terms of cost and required maintenance. The science blog archive Rogue Scholar managed by Front Matter is a good example of an InvenioRDM repository that can benefit from simpler deployment options. As the next major release of InvenioRDM (v13.0) will happen in the next few weeks, Rogue Scholar needs to prepare for the upgrade, and I have this week launched a Rogue Scholar staging instance at https://staging.rogue-scholar.org using Kamal and a virtual machine provisioned by Hetzner and located in Germany. The setup was mostly straightforward, except for the integration with the Kamal proxy server, which turned out to be very painful. In the end I had to set the InvenioRDM`APP_ALLOWED_HOSTS` ENV variable to `None` and patch the REST API cross site request forgery (CRSF) check to not check the request host. This needs more discussion but appears safe, as all requests must go through the Kamal proxy, where the host header is already checked. More work is needed on the staging server, including regular automatic backups of the database, and setting up monitoring (logs and metrics). The instance is running the latest stable release (v12.1.0), but I will soon be able to install the latest v13 release candidate – v13.0.0rc2 was released three days ago. Kamal was released in 2023 by 37signals, the company behind the Basecamp and Hey services, and one of the major contributors to the Rails platform. Kamal is installed as a Ruby gem, but is not specific to Rails or Ruby. Kamal can be seen as the successor to the Capistrano deployment tool, also originally written by 37signals, but Kamal is working with Docker containers. When I was the technical lead of the Article Level Metrics project at the publisher PLOS 2012-2015 (at the time Docker was not yet adopted for production deployments), I made heavy use of Capistrano. InvenioRDM Starter now includes a Kamal configuration option, and I deployed an InvenioRDM instance to https://demo.front-matter.io using Kamal. Feel free to play around, but only admin accounts can create records – use the official InvenioRDM demo instance (also linked in the footer) if you want to create and/or update records. I will spend the next few weeks refining the Kamal setup and documentation, so that InvenioRDM Starter is ready for Kamal deployments when InvenioRDM v13.0 is officially released. ## References Fenner, M. (2024, June 17). Announcing InvenioRDM Starter Beta. _Front Matter_. https://doi.org/10.53731/jxecm-0me48 Fenner, M. (2015, July 29). Thank you PLOS. _Front Matter_. https://doi.org/10.53731/r294649-6f79289-8cvzn

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Rogue Scholar upgrade pains

This week the Rogue Scholar science blog archive experienced major upgrade pains, and Rogue Scholar search became unavailable from Tuesday until Thursday. I tried to upgrade to a pre-release version (13.0.0b4.dev0) of the InvenioRDM repository software, and ran into multiple issues. Going back to the previously installed v12.1.0 took longer than anticipated, mainly because of issues with the Opensearch index. This morning Rogue Scholar is almost working normally again, except for the blog communities, which will take until Monday to be fixed. The primary reason for upgrading the InvenioRDM software was so that I could integrate Crossref DOI registration, based on work I completed last week. The experience with installing a pre-release version of InvenioRDM told me a few things: * install InvenioRDM to production only after extensive testing (as I did last September/October), * service stability is more important than new features, and I am adjusting my deployment strategy and tooling, * observability is critical when running infrastructure, and this can be improved for Rogue Scholar. ### Postpone upgrading to InvenioRDM v13.0 Integrating Crossref DOI registration into InvenioRDM requires a current development version of InvenioRDM, which is currently v13.x, ahead of the last released version v12.1​. As InvenioRDM v13.0 will be released in a few weeks, I will wait with that work until v13.0 is released and Rogue Scholar is updated to that version. There is additional DOI registration work needed, as Rogue Scholar not only registers DOIs with Crossref, but uses multiple DOI prefixes (not yet supported in InvenioRDM) and also accepts blog posts with DOIs registered externally with DataCite. ### Upgrade Rogue Scholar Infrastructure After growing to more than 40,000 blog posts in recent months, the Rogue Scholar infrastructure, particularly the Opensearch search index, needs a hardware upgrade. I will take this opportunity to also change my deployment strategy and tooling, and will start to use Kamal to deploy the InvenioRDM software to a dedicated server (provided by Hetzner). ### Improve Observability Rogue Scholar uses metrics and logging provided by Prometheus/Grafana and error reporting provided by Sentry. More work is needed to improve this observability to better handle incidents such as this week's upgrade issues. ## References Fenner, M. (2025, May 27). Major update on Commonmeta Crossref DOI registration. _Front Matter_. https://doi.org/10.53731/69k7z-w7030

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Rogue Scholar Newsletter May 2025

This is the May issue of the monthly newsletter from the Rogue Scholar science blog archive. The newsletter reports on new blogs that have joined the platform, important technical updates in Rogue Scholar infrastructure, community updates, and other news relevant to Rogue Scholar users. ## Blogs added to Rogue Scholar No new blogs were added in May, but the processing of two blog submissions is being worked on. ## Technical Updates On May 6, the Rogue Scholar registration workflow received a major update in how personal names are handled to better accommodate edge cases such as multiple family names. Starting on May 15, new DOI registrations for all WordPress blogs use a new scheme for the DOI suffix, using the Rogue Scholar _blog identifier_ and WordPress _post_id_ , e.g. https://doi.org/10.59350/rzepa.28773 for the latest post on Henry Rzepa's Blog. This allows WordPress blog authors to know the DOI for their blog posts before publication. On May 27, Rogue Scholar switched the DOI registration workflow to the commonmeta-py Python library. This was an important step towards integrating Crossref DOI registration directly into the InvenioRDM repository platform. Since that switch, several smaller issues have been fixed, and in June, the work on Crossref DOI registration in InvenioRDM can begin. ### Community Update On May 15, I published the Rogue Scholar authorship guidelines to clarify the rights and responsibilities of Rogue Scholar blog post authors, following the same basic guidelines that apply to other scholarly outputs. One particular focus was on the limitations and transparency in reporting when using the help of Artificial Intelligence in writing scholarly blog posts. Please use Slack, email, Mastodon, or Bluesky if you have any questions or comments regarding this monthly newsletter. Rogue Scholar is a scholarly infrastructure that is free for all authors and readers. You can support Rogue Scholar with a one-time or recurring donation or by becoming a sponsor. ## References 1. Fenner, M. (2025, May 6). Personal names in science blogs. _Front Matter_. https://doi.org/10.53731/r5fw0-tdd11 2. Fenner, M. (2025, May 27). Major update on Commonmeta Crossref DOI registration. _Front Matter_. https://doi.org/10.53731/69k7z-w7030 3. Fenner, M. (2025). _Commonmeta-py_ (Version 0.113) Computer software]. Zenodo. [https://doi.org/10.5281/ZENODO.15524711 4. Fenner, M. (2025, May 15). Rogue Scholar Authorship Guidelines. _Front Matter_. https://doi.org/10.53731/fnv8b-qfy78 5. McNutt, M. K., Bradford, M., Drazen, J. M., Hanson, B., Howard, B., Jamieson, K. H., Kiermer, V., Marcus, E., Pope, B. K., Schekman, R., Swaminathan, S., Stang, P. J., & Verma, I. M. (2018). Transparency in authors’ contributions and responsibilities to promote integrity in scientific publication. _Proceedings of the National Academy of Sciences_ , _115_(11), 2557–2560. https://doi.org/10.1073/pnas.1715374115

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Major update on Commonmeta Crossref DOI registration

Today I released a new version of the commonmeta-py Python library with major improvements in Crossref DOI registration, including refactoring to use the Python marshmallow library, XML schema validation, and API calls to Crossref and InvenioRDM instances via the commonmeta-py command-line interface. ### Using the marshmallow library Marshmallow is a popular Python library for converting complex objects to and from simple Python datatypes. The InvenioRDM repository software heavily uses marshmallow to convert metadata from and to JSON. Marshmallow is not specific to JSON, and writing Crossref metadata in XML requires an additional serialization step. commonmeta-py uses xmltodict to convert XML to Python data structures, and now also uses xmltodict for writing XML. This replaces lxml and the ElementTree API for XML writing. This worked well but didn't integrate with the rest of commonmeta-py, as the Crossref XML writer is the only place where commonmeta-py currently writes XML. More importantly, this change will make integrating commonmeta-py into InvenioRDM easier for Crossref DOI registration. ### XML schema validation Crossref metadata are fairly complex and have different requirements depending on content type, e.g. International Standard Serial Numbers (ISSN) are only supported for some content types, or the order of metadata elements might be different. For this reason, XML schema validation before submission is critical, and commonmeta-py now supports this, using the recently released schema 5.4.0. A large part of the work for this update was generating and validating XML for the various Crossref content types. I could not cover all use cases, so feedback is appreciated, e.g., by sending me DOIs registered with Crossref but not validating in commonmeta-py. Commonmeta (both the Python and Go versions) relies heavily on JSON schema validation, which I greatly prefer over XML Schema Definition (XSD) validation. But until Crossref allows content registration via JSON metadata (similarly to the change DataCite made a few years ago), XML schema validation remains important. The commonmeta Go library does not yet use XML schema validation. ### API calls via the CLI The Rogue Scholar science blogging archive switched to the InvenioRDM repository platform in October 2024 and uses the commonmeta Go library and GitHub Actions for Crossref DOI registration. GitHub Actions are wonderful, but for more complex workflows it is easier to have the logic built into the application running in the GitHub Action. Since May 2024 that was the commonmeta Go library, and commonmeta-py now has similar functionality, including calling the Crossref and InvenioRDM APIs directly. Starting today, the GitHub Actions for Rogue Scholar DOI registrations and updates use commonmeta-py instead of the commonmeta Go library. The next two weeks I will carefully monitor them for any issues that might have escaped testing. The next major milestone is integrating Crossref DOI registration directly into InvenioRDM. This will not only simplify the workflows for Rogue Scholar, but makes InvenioRDM a more interesting option for repositories with original textual content, e.g. preprints, reports or dissertations. ## References Fenner, M. (2025). _Commonmeta-py_ (Version 0.113) Computer software]. Zenodo. [https://doi.org/10.5281/ZENODO.15524711 Feeney, P. (2025, March 19). Version 5.4.0 metadata schema update now available. _Crossref Blog_. https://doi.org/10.13003/325070

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Commonmeta understands OpenAlex

Last week I released updated Python, and Go versions of the commonmeta library that can now read metadata from OpenAlex. OpenAlex is an open index of over 250 million scholarly works from 250k sources. OpenAlex uses its own identifier for works, people, organizations, sources, and concepts, but also understands common identifiers for works (e.g. DOI or PMID), people (e.g. ORCID), or organizations, including funders (e.g. ROR). Commonmeta can now fetch metadata from the OpenAlex API and convert them into the commonmeta or any other supported format. An example command-line call would look like this: commonmeta convert https://pubmed.ncbi.nlm.nih.gov/17160063 --from openalex Or you could fetch a random sample of 100 preprints: commonmeta list --sample --type preprint -n 100 --from openalex OpenAlex is an impressive service for the scholarly community, launched three years ago when the Microsoft Academic Graph database stopped being updated. I particularly like the following features: * coverage of a large number of text publications, including content registered via Crossref and DataCite, * links to legal copies of full-text versions of publications, * enrichment of metadata with persistent identifiers, e.g. affiliation information, * rich automated subject area classification into 4500 topics. When working on integrating OpenAlex into commonmeta, I noticed some areas where the service (still only three years old) could be improved upon: * personal names are not treated as a combination of given and family names. This can cause problems in cases of unusual names and formatted citations, which typically split personal names into given and family names, * Metadata enrichment should not be done with personal names, as this is very difficult and may have privacy implications. My OpenAlex profile – which covers publications over 30 years in different research areas (mainly basic and clinical cancer research and scholarly infrastructure) – contains most of my publications but also publications not written by me, including several papers published before I finished high school in 1983, * license information uses a simple schema that aligns with Creative Commons licenses, but for example doesn't consider different versions (e.g. CC-BY 3.0 vs. CC-BY 4.0). Commonmeta supports the SPDX license list that includes all Creative Commons license versions but also many software licenses. The initial OpenAlex support in commonmeta is the result of a wonderful pull request for the Python version. I mainly added test coverage and added the same functionality to the Go version. Please provide feedback via email, Slack, or GitHub if you discover bugs or missing functionality of the OpenAlex support in commonmeta. ## References Fenner, M. (2025). _Commonmeta-py_ (Version 0.107) Computer software]. Zenodo. [https://doi.org/10.5281/ZENODO.15465786 Martin Fenner. (2025). _front-matter/commonmeta: V0.25.0_ (Version v0.25.0) Computer software]. Zenodo. [https://doi.org/10.5281/ZENODO.15461402

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Rogue Scholar Authorship Guidelines

Rogue Scholar archives the content of currently more than 150 science blogs with more than 40,000 blog posts. In this blog post, I want to clarify the guidelines that Rogue Scholar tries to follow regarding authorship. Rogue Scholar blog posts are scholarly content and thus follow the same basic guidelines as other scholarly outputs, such as journal articles, preprints, or book chapters. ### Authorship All authors are expected to have made substantial contributions to the submitted work and to be accountable for the work both before and after publication. Those who contributed to the work but do not meet the criteria for authorship can be mentioned in the Acknowledgments. ### Artificial Intelligence (AI) AI tools cannot meet the requirements for authorship, as explained by the Committee on Publication Ethics (COPE): > AI tools cannot meet the requirements for authorship as they cannot take responsibility for the submitted work. As non-legal entities, they cannot assert the presence or absence of conflicts of interest nor manage copyright and license agreements. And COPE recommends that: > Authors who use AI tools in the writing of a manuscript, production of images or graphical elements of the paper, or in the collection and analysis of data, must be transparent in disclosing in the Materials and Methods (or similar section) of the paper how the AI tool was used and which tool was used. Rogue Scholar blogger Mark Dingemanse recently made a strong case for why synthetic text is incompatible with science blogging. ### Contributor Roles For blog posts with multiple authors, Rogue Scholar plans to add support for the Contributor Role Taxonomy (CRediT). And for blog posts handled by an editor or undergoing peer review, Rogue Scholar also wants to add those roles. ### Possible Actions Rogue Scholar is an archive of science blog posts, the content is originally published elsewhere, and the decision for publication was taken by the blog authors. In rare cases, blog authors might retract a blog post or post a correction, and that information should also be communicated by Rogue Scholar and via the DOI metadata. When blog posts don't follow the above guidelines, e.g. when inappropriately using AI Tools, Rogue Scholar staff, after consultation with the Rogue Scholar Advisory Board, will decide on appropriate actions, including retraction. ## References 1. McNutt, M. K., Bradford, M., Drazen, J. M., Hanson, B., Howard, B., Jamieson, K. H., Kiermer, V., Marcus, E., Pope, B. K., Schekman, R., Swaminathan, S., Stang, P. J., & Verma, I. M. (2018). Transparency in authors’ contributions and responsibilities to promote integrity in scientific publication. _Proceedings of the National Academy of Sciences_ , _115_(11), 2557–2560. https://doi.org/10.1073/pnas.1715374115 2. _Authorship and AI tools_. (2024). Committee on Publication Ethics. https://doi.org/10.24318/cCVRZBms 3. Holcombe, A. O. (2019). Contributorship, Not Authorship: Use CRediT to Indicate Who Did What. _Publications_ , _7_(3), 48. https://doi.org/10.3390/publications7030048 4. Marcum, C. S. (2025, April 8). Peer-Review for a Blog Post? My Experience with MetaROR. _Front Matter_. https://doi.org/10.54900/bymaz-4fw37 5. Dingemanse, M. (2025, May 2). Why synthetic text is incompatible with science blogging. _Front Matter_. https://doi.org/10.59350/63b1y-1js90

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Germany's Plan for an Open and Independent PubMed Safety Net - Absolutely Maybe

A few months ago, I wrote about reasons to be concerned about the reliability of PubMed under the new regime at the…

absolutelymaybe.plos.org

The resilience of open science in times of crisis

The increasingly hostile attitude of the new U.S. government towards science and academia leaves many of us deeply concerned— if not outright alarmed. In an effort to better understand the unfolding s...

doi.org

Sciety secures funding from NLNet Foundation to help build discourse around preprints

At Sciety we're pioneering a new layer of open scholarly communication, one that captures informal conversations around preprints and makes them discoverable and reusable. Sciety has secured new…

blog.sciety.org

Science in survival mode

In this post I diagnose the symptoms of scientific malpractice as similar to those of trauma and emotional abuse.

crowdid.hypotheses.org

Working with the Research Organization Registry (ROR) Data Dump

The commonmeta Go library has seen a major update this week that dramatically simplifies working with the Research Organization Registry (ROR) data dump, including conversion to other serialization formats (e.g. JSON Lines) and metadata formats (InvenioRDM), and integrated affiliation matching. ### File Download ROR metadata are updated regularly (typically about once a month) and made available as a file download via the Zenodo repository under a Creative Commons Zero waiver. The single file is a compressed zip archive with the metadata in JSON and CSV formats, each for v1 and v2 of the ROR schema. There are two challenges with the ROR data dump file download: while there is a stable DOI for the latest version of the data, that DOI resolves to the dataset landing page, and there is no easy way to automatically get to the file download URL for automatic downloads of new versions. The other challenge is that the compressed zip archive contains four archived files that can't be downloaded individually. The complete archive is 58.6 MB, whereas the zipped v2 JSON would be 17.7 MB (the uncompressed file is 256.9 MB). In the commonmeta library, the download URL of the most recent ROR data dump and the file names in that zip archive are hard-coded. commonmeta can automatically fetch the full zip archive and selectively extract the v2 JSON. When using commands that require ROR metadata, commonmeta looks for a data dump in zipped Avro format (more on Avro below) in the folder where the command is run. If that file isn't found, commonmeta looks for a v2 JSON file from the data dump, and if that file isn't found either, fetches the data dump from Zenodo, extracts the v2 JSON file, and generates the compressed Avro file. For example a local lookup of an organization via its ROR identifier: commonmeta convert https://ror.org/04jvcky17 Running this command transparently downloads, extracts, and converts the latest ROR data dump and looks up the metadata for https://ror.org/04jvcky17 (Newport Festivals Foundation). This takes only a few seconds (depending on your network connection), and going forward uses ROR data stored locally. ### File Formats Commonmeta can automatically convert the JSON data of all 115K ROR records into other serialization formats, currently JSON Lines, YAML, CSV, and Avro. And optionally compress them as zip archive, for example: commonmeta list --from ror --file mydata.csv.zip This command in a few seconds generates a compressed CSV file (almost) identical to the CSV provided in the ROR data dump. Whereas JSON, JSON Lines, and YAML are straightforward to work with, the CSV format has limitations and shows only a (large) subset of the metadata. Avro is another special format; it is focused on efficient storage and transmission over network connections, but is not human-readable. Avro uses a schema in JSON format, which has advantages over the schema-less JSON, YAML, and CSV, including data validation and smaller file sizes. These are the file sizes for the ROR data dump (the JSON file is slightly smaller than the original file because null values were omitted). Format | Size (MB) | Size ZIP (MB) ---|---|--- JSON | 182.3 | 17.0 JSON Lines | 108.1 | 14.5 YAML | 125.5 | 15.3 CSV | 33.5 | 10.3 Avro | 41.6 | 13.2 Other criteria besides file size are the speed of reading and writing files in this format, readability by humans, and supported data types. CSV is very readable, but is only useful as output format, as data types other than text and numbers are not supported. Avro generates the smallest files, but is more complicated to work with as it requires a schema. YAML is very human-readable, whereas JSON Lines works well over network connections as it is easier to stream than JSON. commonmeta allows working with all these formats for ROR data (CSV only as output as it doesn''t include all metadata), so you can for example give a JSON Lines file to a colleague and she can use it as commonmeta input: commonmeta list mydata.jsonl --from ror --file mydata2.csv ### Metadata formats and filtering The ROR schema describes the metadata needed for the affiliation use case in scholarly works. A related metadata schema is used by the InvenioRDM repository platform that the Rogue Scholar blogging platform also uses. Here metadata vocabularies are typically described in YAML and use a subset of the ROR metadata, both for author affiliations and for funders. One small twist is that one metadata field is different: affiliations support acronyms for names, whereas funders support the country code. commonmeta can handle this and also generate a subset of organizations that are of type `funder` : commonmeta list --from ror --to inveniordm --file funders.yaml One challenge in the current version of the InvenioRDM platform (v12.0) is that importing large vocabularies (e.g. all ROR data) is slow and error-prone. In a previous blog post I suggested to only import the affiliations needed, but that workflow is slow and complicated. The upcoming version v13.0 of InvenioRDM has better handling of large vocabulary imports, in the meantime commonmeta supports the generation of smaller vocabularies that can be imported in batches, e.g. commonmeta list --from ror --to inveniordm --file affilations_ror.yaml -n 10000 --page 1 This command generates a YAML file in a format InvenioRDM understands and containing only 10,000 organizations. By installing commonmeta on the InvenioRDM server and running this command repeatedly and importing the YAML in batches we can overcome the limitations of the v12.0 vocabulary import. commonmeta currently supports two filters to generate subsets of the ROR data: by organization type (e.g. funder or university) and/or by country. Please reach out if you are interested in other metadata formats for organizations and/or filters. ### Queries commonmeta supports simple queries of the local ROR data by ROR ID or external ID (Crossref Funder ID, GRID, ISNI, Wikidata): commonmeta convert Q7713086 More complex queries are currently not possible with local data, but commonmeta integrates with the ROR API to support affiliation matching. commonmeta match --from ror "The Alfred Hospital" This will return a single ROR record if a match with a score of 0.9 or higher is found by the ROR API. The affiliation matching can be combined with looking up metadata from Crossref, DataCite, or InvenioRDM, a core functionality of commonmeta. If affiliation names but no ROR ids are provided, commonmeta can automatically merge the information found by affiliation matching. To indicate that the metadata was found by ROR and not the publisher, commonmeta adds an `assertedBy` field with the value `ror` to the response. Affiliation identifiers provided by the publisher will have a `publisher` value in the response. The following query returns a random sample of 50 publications from Crossref member 31795 (Front Matter) with affiliation matching applied and the results stored in commonmeta schema format. commonmeta list --from crossref --member 31795 --sample=true -n 50 --match=true --file matching.json ### Conclusions The work on using Go to read, format, and integrate ROR metadata was inspired by a session at the recent InvenioRDM Partner meeting in Hamburg. InvenioRDM is written in Python and Javascript/React, but Go is a great alternative for simple installations (commonmeta is a single 5 MB binary) and performance-critical functions (e.g. converting the ROR data dump into the InvenioRDM YAML format). Rust is another language that people use in these situations, and more work is needed to compare the relative strengths and weaknesses. More work is also needed to decide on the best file format for storing scholarly metadata at scale. Avro looks promising, but needs to be compared with JSON in more detail. Another interesting newer format is Parquet. It is a column-oriented file format in contrast to the formats described here, which are row-based. This makes some things harder but other things much easier, and this becomes more critical as the number of metadata records grows from 100K (ROR) to the millions (DataCite, Crossref). Finally, this work demonstrates that a good proportion of metadata work can be done locally, working with data dumps rather than high frequencies of API calls. ## References Research Organization Registry. (2025). _ROR Data_ (Version v1.63) Dataset]. Zenodo. [https://doi.org/10.5281/ZENODO.6347574 Martin Fenner. (2025). _front-matter/commonmeta: V0.19.4_ (Version v0.19.4) Computer software]. Zenodo. [https://doi.org/10.5281/ZENODO.15256488 Fenner, M. (2025, April 7). Where I simplified ROR affiliation metadata handling. _Front Matter_. https://doi.org/10.53731/ymbv8-7jm78 Fenner, M. (2025, March 19). Rogue Scholar meets the InvenioRDM community. _Front Matter_. https://doi.org/10.53731/1aw0b-pr243

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