![\"\"](\"https://storage.ghost.io/c/c5/33/c533c955-b5f3-4ff1-ae2d-6b52a212e602/content/images/2025/08/Bildschirmfoto-2025-08-04-um-11.24.58.png\")
Cancer is caused by genetic changes. Oncogenes harbor activating mutations that cause or promote cancer, whereas tumor suppressor genes protect from cancer. In this model, genetic changes in one copy of an oncogene, but both copies of a tumor suppressor gene are required to initiate cancer. This simple model is complicated by the fact that more than one genetic change is usually required to initiate cancer, and that other so called epigenetic changes (such as promoter hypermethylation) are also important.
Myelodysplastic syndromes are malignant disorders of the bone marrow that show insufficient production of blood cells and harbor the risk of progressing to acute myeloid leukemia. The 5q syndrome is a distinct subtype that is characterized by loss of genetic material at chromosome 5q31, a characteristic morphology of the bone marrow, and a fairly benign clinical course. We would expect to find a tumor suppressor gene in the deleted region on chromosome 5, but no genetic changes on the other allele of chromosome 5 could be detected. The traditional strategies to identify the genetic changes responsible for the 5q syndrome therefore didn't work.
Research by Benjamin Ebert et al. presented at the American Society of Hematology meeting in December and now published in Nature claims to have finally identified the genetic change responsible for 5q syndrome. They used RNA interference to in turn knock out each of the 40 genes in the common deleted region on chromosome 5q31. They observed the phenotype of human hematopoetic progenitor cells transfected with short hairpin RNAs. The shRNA targeting the gene RPS14 recapitulated the phenotype of patients with 5q syndrome.
To confirm the role of RPS14 in 5q syndrome, RPS14 was overexpressed in hematopoetic cells from patients with 5q syndrome and indeed reverted the erythroid differentiation effect. Reduced expression or inactivating mutations of the one remaining RPS14 gene in 5q syndrome patients was ruled out by sequencing and gene expression profiling.
Further evidence for the importance of RPS14 in 5q syndrome comes from studies of related genes. Expression of RPS14 is required for proper function of the 40s ribosomal subunit. Germline mutations of two other ribosomal proteins, RPS19 and RPS24, have been identified in the congenital disorder Diamond-Blackfan anemia, and the disease in these children has similar features.
As a medical student, I was fortunate enough to listen to Alfred Knudson give a talk about is two-hit hypothesis of tumor suppressor genes, and I was fascinated by cancer genetics ever since. Genetics continues to be a driving force in our understanding of cancer. The next big step in the 5q syndrome story will be a better understanding of why the drug lenalidomide works so well in this disease, and how this relates to RPS14 function. More information about the Ebert paper can be found in this Nature News and Views article.
The Hirsch number tries to quantify the (scientific) productivity of a scientist. The Hirsch number was first described by the physicist J.E. Hirsch in a 2005 PNAS paper: An index to quantify an individual's scientific research output. Hirsch says:
I propose the index h, defined as the number of papers with citation number h, as a useful index to characterize the scientific output of a researcher.
Thus, in contrast to the widely used impact factor, the Hirsch number measures the productivity of an individual scientist and not the journal he publishes in. The Hirsch number tries to factor in both the number of papers and the number of citations of these papers.
Your personal Hirsch number should be equal or greater the number of years you have already spent in science. Again in contrast to the impact factor, you can calculate your Hirsch number with freely available tools. You can look up your papers in Google Scholar and write down the citations for each paper. Or, use online tools such as scHolar index to do the work for you.
Using a simple number to measure the productivity of scientist is a dangerous undertaking. But if numbers are needed (e.g. grant or job applications), the Hirsch number is a good tool. Widespread use of the Hirsch number could have broad implications, as authors would more carefully consider which journals would give them the highest number of citations.
We refactored the R-universe CI workflows to make it possible to run the exact same workflow from your own GitHub repository. This allows you to test or debug the build and check process on your R package, exactly as it will happen on R-universe, but without actually deploying to https://r-universe.dev.
The instructions on r-universe-org/workflows explain how it works: simply create a file /.github/workflows/r-universe-test.yml in your R package git repo with the following config:
name: Test R-universeon: push: pull_request:jobs: build: name: R-universe testing uses: r-universe-org/workflows/.github/workflows/build.yml@v3 with: universe: ${{ github.repository_owner }}That is everything. The workflow will use the fully automated R-universe setup to build and check the package on a range of R versions on Linux, Windows, and MacOS configurations very similar to CRAN.
It is possible to use this workflow in your R package for pushes and/or pull requests alongside those from r-lib/actions. Both will check your R package, but note that the purpose is very different: workflows from r-lib/actions are highly configurable and can test R packages using countless options and environments. The R-universe workflow on the other hand is, just like CRAN, not customizable at all: it uses the exact setup and process as it happens on R-universe, nothing else.
The ability to test-run the build workflow has been recurring feature request, and I hope that it will indeed help package maintainers with debugging problems. I also hope the refactoring might make it a little bit easier to understand the R-universe build process, and enable the community to hack on the workflows and actions to contribute improvements.
","doi":"https://doi.org/10.53731/9r3yj-zwy78","guid":"https://doi.org/","language":"en","license":"https://creativecommons.org/licenses/by/4.0/legalcode","published_at":1767398400,"rid":"vy50z-6dv41","summary":"We refactored the R-universe CI workflows to make it possible to run the exact same workflow from your own GitHub repository. This allows you to test or debug the build and check process on your R package, exactly as it will happen on R-universe, but without actually deploying to https://r-universe.dev.","tags":["R-universe","Infrastructure"],"title":"Testing the R-universe build workflow from your own GitHub repository","updated_at":1787975323,"url":"https://ropensci.org/blog/2026/01/03/r-universe-workflows/","version":"v1"}},{"document":{"authors":[{"affiliation":[{"name":"Front Matter"}],"contributor_roles":[],"family":"Fenner","given":"Martin","url":"https://orcid.org/0000-0003-1419-2405"}],"blog":{"authors":[{"name":"Martin Fenner","url":"https://orcid.org/0000-0003-1419-2405"}],"community_id":"15a362ea-8138-42b8-917f-1840a92addf8","created":1672531200,"current_feed_url":null,"description":"The Front Matter Blog covers the intersection of science and technology since 2007.","doi":"https://doi.org/10.53731/front_matter","favicon":"https://rogue-scholar.org/api/communities/15a362ea-8138-42b8-917f-1840a92addf8/logo","feed_format":"application/atom+xml","feed_url":"https://blog.front-matter.de/atom","filter":null,"generator":"Ghost","home_page_url":"https://blog.front-matter.de/","issn":"2749-9952","language":"eng","license":"https://creativecommons.org/licenses/by/4.0/legalcode","prefix":"10.53731","relative_url":null,"secure":true,"slug":"front_matter","status":"active","subfield":"1710","title":"Front Matter","updated":1787944127,"use_api":true},"blog_name":"Front Matter","blog_slug":"front_matter","content_html":"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:
![\"\"](\"https://storage.ghost.io/c/c5/33/c533c955-b5f3-4ff1-ae2d-6b52a212e602/content/images/2025/08/Bildschirmfoto-2025-08-04-um-11.22.34.png\")
![\"\"](\"https://storage.ghost.io/c/c5/33/c533c955-b5f3-4ff1-ae2d-6b52a212e602/content/images/2025/08/Bildschirmfoto-2025-08-04-um-11.19.25.png\")
![\"\"](\"https://storage.ghost.io/c/c5/33/c533c955-b5f3-4ff1-ae2d-6b52a212e602/content/images/2025/08/Bildschirmfoto-2025-08-04-um-11.15.58.png\")
The Altmetrics manifesto stated in 2010 that
Altmetrics are fast, using public APIs to gather data in days or weeks. They're open \u2013 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 \u2013 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:
Please use Slack, email, Mastodon, or Bluesky if you have any questions or comments regarding the Rogue Scholar citation tracking service.
The Rogue Scholar science blog archive has introduced authentication with passkeys and will disable local accounts on September 15. Reading Rogue Scholar content has always been free and never required user accounts or cookie permissions. This is true both for web and API usage.
Science blogs participating in Rogue Scholar also don't require user accounts, but only a contact email, and the initial registration of the blog is via a web form. The import of new or updated blog posts into Rogue Scholar happens automatically via RSS feed or JSON API integration, and there is no ability to update blog posts archived in Rogue Scholar outside of that workflow.
Rogue Scholar offers user accounts that everyone can sign up for. They are currently only intended for blog authors, and two weeks ago their functionality was expanded. Rogue Scholar blog posts are organized around communities, and there are three community types:
The blog community includes basic information about the blog, such as name, description and logo. This information is automatically extracted from the blog feed, but in some cases manual curation is desired, e.g. to include a description or logo that the feed does not provide. Blog authors with a Rogue Scholar account, and after they have received an invitation as community manager, can now manage this information themselves:
![\"\"](\"https://storage.ghost.io/c/c5/33/c533c955-b5f3-4ff1-ae2d-6b52a212e602/content/images/2025/08/Bildschirmfoto-2025-07-30-um-17.18.48.png\")
Going forward Rogue Scholar will also allow blog authors to provide more information, such as the blog default OECD Field of Science (currently provided in the blog registration form) and International Standard Serial Number (ISSN), currently provided via email.
Topic communities aggregate blog posts from multiple blogs around a common topic, typically referred to as a tag or category in blogs. These tags/categories have naturally evolved as folksonomy rather than a centrally defined taxonomy, and fully automatic classification of blog posts into topics is neither desired nor easily achievable. For these reasons, manual curation of topics is needed, and currently this requires user accounts. Blog authors who are community managers of their blog can submit blog posts to topic communities, or manage the communities the blog post is included.
![\"\"](\"https://storage.ghost.io/c/c5/33/c533c955-b5f3-4ff1-ae2d-6b52a212e602/content/images/2025/08/Bildschirmfoto-2025-08-12-um-08.52.06.png\")
The creation of topic communities currently requires an admin account, but if people are interested in becoming Rogue Scholar community managers, creating new topic communities, or adding blog posts to topic communities where they are not the author, please reach out to me.
Subject communities are automatically added to blog posts based on the blog subject area, and user accounts are not relevant here. Going forward, I want to enable automatic classification based on blog post content, and inclusion in more than one subject community. We can take advantage of the new collections feature introduced in InvenioRDM v13 earlier this month.
Now that I have explained that user accounts are not required to use Rogue Scholar, but there are important use cases where they are needed, we can talk about how user accounts are managed in Rogue Scholar. Users can register for a user account with Rogue Scholar in one of two ways:
![\"\"](\"https://storage.ghost.io/c/c5/33/c533c955-b5f3-4ff1-ae2d-6b52a212e602/content/images/2025/08/Bildschirmfoto-2025-08-12-um-07.55.29.png\")
Authentication via ORCID is a widely used authentication workflow in the scholarly community that is free (no ORCID organizational membership required) and built into the InvenioRDM platform.
Depending on a single external authentication service is not desirable, as not all users will have an ORCID (e.g. group or admin accounts), and this would make it impossible to sign in to Rogue Scholar if the ORCID service is temporarily down. ORCID is primarily a service to provide unique identifiers to scholars, and not an identity provider (IdP) that provides single sign-on services.
One option is to provide authentication via local accounts with username/password, but that is both potentially insecure without additional measures such as multi-factor authentication (MFA) and inconvenient without a password manager. The InvenioRDM platform that Rogue Scholar uses has built-in local account management, but not built-in multi-factor authentication or other more advanced functionalities. Many InvenioRDM instances use an external authentication service that integrates with InvenioRDM.
ORCID authentication is implemented via the OpenID Connect (OIDC) authentication protocol, and OIDC can be used with many other third-party logins, including GitHub, which is built into InvenioRDM. For Rogue Scholar I wanted to implement a local OIDC provider that I can configure and control. The most popular authentication service for InvenioRDM for this use case is probably Keycloak. Keycloak is a powerful and well-tested open-source solution for identity management, but it is almost too complex for smaller instances such as Rogue Scholar. For these reasons, Rogue Scholar went with Pocket ID,
A simple and easy-to-use OIDC provider that allows users to authenticate with their passkeys to your services.
Pocket ID depends on passkeys, a secure and user-friendly authentication method that is (slowly) becoming a new authentication standard.
![\"\"](\"https://storage.ghost.io/c/c5/33/c533c955-b5f3-4ff1-ae2d-6b52a212e602/content/images/2025/08/Bildschirmfoto-2025-07-23-um-17.33.10.png\")
Pocket ID authentication for Rogue Scholar was launched three weeks ago, and the service is hosted at https://auth.rogue-scholar.org. The setup was straightforward, and Pocket ID supports some advanced features currently not needed by Rogue Scholar, e.g. restricting user groups, LDAP integration, or a REST API.
With the launch of Pocket ID authentication, registration for new local accounts has been disabled, and login via username/password will be disabled on September 15. Users with existing local accounts can link their accounts to ORCID and/or passkeys until that date.
Please use Slack, email, Mastodon, or Bluesky if you have any questions or comments regarding Rogue Scholar authentication.
The Rogue Scholar science blog archive has supported ORCID and DOI identifiers for linking to authors and blog posts since its launch. Starting this week, these two identifiers can also be used to navigate within the Rogue Scholar archive.
![\"\"](\"https://storage.ghost.io/c/c5/33/c533c955-b5f3-4ff1-ae2d-6b52a212e602/content/images/2025/08/Bildschirmfoto-2025-08-17-um-10.12.21.png\")
ORCID, which stands for Open Researcher and Contributor ID, is a free, unique, persistent identifier (PID) for individuals to use as they engage in research, scholarship, and innovation activities.
ORCID for Researchers
One third (32.71%) of science blog posts in Rogue Scholar are linked to the ORCID of at least one of their authors. Searching Rogue Scholar by ORCID returns a list of all blog posts authored by that person, e.g. using my ORCID:
![\"\"](\"https://storage.ghost.io/c/c5/33/c533c955-b5f3-4ff1-ae2d-6b52a212e602/content/images/2025/08/Bildschirmfoto-2025-08-17-um-10.19.12.png\")
Starting this week, clicking on an author name with an ORCID icon in Rogue Scholar will return all records (co-)authored by that author:
![\"\"](\"https://storage.ghost.io/c/c5/33/c533c955-b5f3-4ff1-ae2d-6b52a212e602/content/images/2025/08/Bildschirmfoto-2025-08-17-um-10.29.41.png\")
This feature works in both search results and single record views. For authors without an ORCID (e.g. organizational authors), Rogue Scholar continues to return a search result by name, which is the built-in behavior of the InvenioRDM repository platform. Clicking on the ORCID icon continues to link to the ORCID profile page for that author.
All blog posts in Rogue Scholar have a Digital Object Identifier (DOI) assigned to them to uniquely identify the blog post and include relevant metadata. These metadata can optionally include references (currently 5.04% of Rogue Scholar posts) that again can use DOIs. Citations of Rogue Scholar posts (currently 1387 citations of 763 blog posts) using their DOI are also shown in the Rogue Scholar record.
Starting this week, clicking on the title of a DOI reference or citation in the Rogue Scholar record returns all records using that DOI as identifier, reference, or citation, with the Rogue Scholar record on top of the list.
![\"\"](\"https://storage.ghost.io/c/c5/33/c533c955-b5f3-4ff1-ae2d-6b52a212e602/content/images/2025/08/Bildschirmfoto-2025-08-17-um-10.47.20.png\")
Clicking on the title of the citation returns a search result with the cited Rogue Scholar post and also the citing post. Clicking on the DOI link continues to link to the scholarly work with that DOI.
![\"\"](\"https://storage.ghost.io/c/c5/33/c533c955-b5f3-4ff1-ae2d-6b52a212e602/content/images/2025/08/Bildschirmfoto-2025-08-17-um-10.50.56-1.png\")
This also works in the case of references or citations that are not Rogue Scholar posts (most of them):
![\"\"](\"https://storage.ghost.io/c/c5/33/c533c955-b5f3-4ff1-ae2d-6b52a212e602/content/images/2025/08/Bildschirmfoto-2025-08-17-um-11.03.58.png\")
Clicking on the title of reference #6 returns a search result with all Rogue Scholar records referencing or citing that DOI:
![\"\"](\"https://storage.ghost.io/c/c5/33/c533c955-b5f3-4ff1-ae2d-6b52a212e602/content/images/2025/08/Bildschirmfoto-2025-08-17-um-11.08.55-1.png\")
The first search result is the record where I clicked the link. The second search result is another Rogue Scholar blog post referencing the same Scientometrics paper.
Implementing DOI linking within Rogue Scholar poses an interesting user interface challenge. I decided to always return search results instead of directly linking to the Rogue Scholar record. By including references and citations in the search results, Rogue Scholar will always return at least one result, but may show more Rogue Scholar records referencing the same blog post or other scholarly work.
This additional functionality around Rogue Scholar references hopefully encourages more Rogue Scholar bloggers to include formal references with their posts. My goal for 2026 is to have 10% Rogue Scholar posts include references (currently 5.04%). Including formal references in blog posts is straightforward, but so far has not been a best practice. Some Rogue Scholar blogs already have high percentages of posts with references, including Research Group Information Management @ Humboldt-Universit\u00e4t zu Berlin (40 posts, 75%), Henry Rzepa's Blog (518 posts, 61%), or chem-bla-ics (499 posts, 39%), and this blog (590 posts, 33%).
Please use Slack, email, Mastodon, or Bluesky if you have any questions or comments regarding Rogue Scholar ORCID or DOI linking.
Fenner, M. (2025, August 4). Rogue Scholar citation tracking launches to production. Front Matter. https://doi.org/10.53731/zyg15-qv911
","doi":"https://doi.org/10.53731/yjq4w-5yr32","guid":"https://doi.org/10.53731/yjq4w-5yr32","image":"https://images.unsplash.com/photo-1694596747902-626600534e80?crop=entropy&cs=tinysrgb&fit=max&fm=jpg&ixid=M3wxMTc3M3wwfDF8c2VhcmNofDU0fHxsaW5raW5nfGVufDB8fHx8MTc1NTQxNzYxNnww&ixlib=rb-4.1.0&q=80&w=2000","language":"en","license":"https://creativecommons.org/licenses/by/4.0/legalcode","published_at":1755475200,"reference":[{"id":"https://doi.org/10.53731/zyg15-qv911","unstructured":"Fenner, M. (2025, August 4). Rogue Scholar citation tracking launches to production. Front Matter."}],"rid":"4sfxs-drd44","summary":"The Rogue Scholar science blog archive has supported ORCID and DOI identifiers for linking to authors and blog posts since its launch. Starting this week, these two identifiers can also be used to navigate within the Rogue Scholar archive.ORCID One third (32.71%) of science blog posts in Rogue Scholar are linked to the ORCID of at least one of their authors.","tags":["Rogue Scholar","Metadata"],"title":"Rogue Scholar links records via ORCID and DOI","updated_at":1787973900,"url":"https://blog.front-matter.de/posts/rogue-scholar-links-records-via-orcid-and-doi/","version":"v1"}},{"document":{"authors":[{"affiliation":[{"name":"Front Matter"}],"contributor_roles":[],"family":"Fenner","given":"Martin","url":"https://orcid.org/0000-0003-1419-2405"}],"blog":{"authors":[{"name":"Martin Fenner","url":"https://orcid.org/0000-0003-1419-2405"}],"community_id":"15a362ea-8138-42b8-917f-1840a92addf8","created":1672531200,"current_feed_url":null,"description":"The Front Matter Blog covers the intersection of science and technology since 2007.","doi":"https://doi.org/10.53731/front_matter","favicon":"https://rogue-scholar.org/api/communities/15a362ea-8138-42b8-917f-1840a92addf8/logo","feed_format":"application/atom+xml","feed_url":"https://blog.front-matter.de/atom","filter":null,"generator":"Ghost","home_page_url":"https://blog.front-matter.de/","issn":"2749-9952","language":"eng","license":"https://creativecommons.org/licenses/by/4.0/legalcode","prefix":"10.53731","relative_url":null,"secure":true,"slug":"front_matter","status":"active","subfield":"1710","title":"Front Matter","updated":1787944127,"use_api":true},"blog_name":"Front Matter","blog_slug":"front_matter","content_html":"References are an important element of scholarly metadata, and that is also true for science blog posts. Currently 5.06% of all Rogue Scholar posts include at least one reference, which are then registered with Crossref metadata.
Citations are the counterpart of references. When other scholarly works are cited in the references of a scholarly work, this citation information can be communicated to the cited work.
Citations are the links that knit together our scientific and cultural knowledge. They are primary data that provide both provenance and an explanation for how we know facts. They allow us to attribute and credit scientific contributions, and they enable the evaluation of research and its impacts. In sum, citations are the most important vehicle for the discovery, dissemination, and evaluation of all scholarly knowledge.
Initiative for Open Citations (I4OC)
The first step is making the references metadata openly available in Crossref metadata, and thanks to the Initiative for Open Citations (I4OC) and the work of many publishers, nearly 100% of all references are now open by default.
The next step is aggregating all these references by the cited work. Crossref members receive this information via the Crossref Cited-By service, other aggregators are OpenCitations and OpenAlex, and of course a number of commercial services.
Rogue Scholar is collecting citations to its blog posts via the Crossref Cited-By service every week and makes that information available with each record, and with a search filter. As of today, there are 1,392 citations of 766 Rogue Scholar posts (1.65%). You can get basically the same information from OpenAlex or other aggregators.
DataCite references and citations add several challenges to this. A small number of Rogue Scholar blogs register their own DOI metadata and use DataCite for this. DataCite metadata use related_identifiers with a number of relation_types instead of references, which adds ambiguity, e.g. what relation_types should be treated as references (probably Cites and References, but maybe also IsSupplementedBy). There are also relation_types for the inverse relation (IsCitedBy, IsReferencedBy) with the challenge that a repository has to update these metadata after publication as citations happen. And aggregators face the same problems. In addition, services such as OpenAlex are still building up workflows to index DataCite metadata at scale.
For science blogs where Rogue Scholar registers the DOI metadata, the above is not relevant. The challenge is to provide reference metadata in a format Rogue Scholar can understand. Besides experimental support for a JSON Feed extension (as RSS, Atom.,or blogging platform JSON APIs don't support references), this means extracting the references from the full-text content.
Luckily references in scholarly documents follow an established format: a section called references (or similar) at the end of the document, followed by one or more references. The recommendation by Rogue Scholar is to format these references as an ordered or unordered HTML list (<ol> or <ul> tag), as this is easier to parse than a list of <div> or <p>. The citation style (there are thousands) doesn't matter, but the reference should include a link to the DOI or URL of the cited resource.
Reference metadata can be generated by copy/paste from your favorite reference manager, or can be automatically generated. From the popular blogging platforms only Quarto can generate references (what they call citations, a common confusion). With Wordpress, the most popular blogging platform in Rogue Scholar, you can use a plugin to automate reference generation. Either Zotpress, which tightly integrates with the reference manager Zotero, or kcite.
Kcite works by collecting reference metadata for DOIs, PubMed, or random web resources via the Greycite service. Greycite was discontinued years ago, and the plugin was last updated 12 years ago, so that the plugin is no longer working with current PHP and Wordpress versions.
The plugin makes it very easy to cite DOI resources, just use a Wordpress shortcode in a blog post:
[cite]10.59350/xqerh-wam97[/cite]The Rogue Scholar blogger (and Advisory Board member) Henry Rzepa has made heavy use of the plugin for many years, and ultimately convinced me to update the plugin. Last week, I did that and released a fixed kcite version. You can download the latest version (1.7.97) here as zip file, that you can upload to your Wordpress instance:
![\"\"](\"https://storage.ghost.io/c/c5/33/c533c955-b5f3-4ff1-ae2d-6b52a212e602/content/images/2025/08/Bildschirmfoto-2025-08-25-um-13.36.23.png\")
A more streamlined installation via the plugin installer requires this fork to become the official kcite plugin, something I am working on.
The focus on the initial work was compatibility with recent versions of PHP (8.4) and Wordpres (6.8.2). The included citeproc.js Javascript file was updated to the latest version (1.4.61), and the citation styles and locales used are the latest versions.
The plugin by default works in server mode, where references are formatted with a generic template. In client mode, the built-in citeproc.js processor is used to generate references with richer metadata. I included a fix to properly show the name of Rogue Scholar blogs. An example reference list in client mode generated by the plugin is shown below:
![\"\"](\"https://storage.ghost.io/c/c5/33/c533c955-b5f3-4ff1-ae2d-6b52a212e602/content/images/2025/08/Bildschirmfoto-2025-08-25-um-13.45.42.png\")
A lot more work is needed with testing the plugin, and potentially adding more functionality, especially the following:
Please use Slack, email, Mastodon, or Bluesky if you have any questions or comments regarding references, citations, or the kcite plugin.
","doi":"https://doi.org/10.53731/326tr-95k32","guid":"https://doi.org/10.53731/326tr-95k32","image":"https://images.unsplash.com/photo-1584266049120-f8c39aaaccb1?crop=entropy&cs=tinysrgb&fit=max&fm=jpg&ixid=M3wxMTc3M3wwfDF8c2VhcmNofDQzfHxyZWZlcmVuY2VzfGVufDB8fHx8MTc1NjExNjMzMHww&ixlib=rb-4.1.0&q=80&w=2000","language":"en","license":"https://creativecommons.org/licenses/by/4.0/legalcode","published_at":1756080000,"reference":[{"id":"https://doi.org/10.59350/xqerh-wam97","unstructured":"Rzepa, H. (2024, March 21). Internet Archeology: reviving a 2001 article published in the Internet Journal of Chemistry. Henry Rzepa's Blog."}],"rid":"9rtkj-36y78","summary":"References are an important element of scholarly metadata, and that is also true for science blog posts. Currently 5.06% of all Rogue Scholar posts include at least one reference, which are then registered with Crossref metadata. Citations are the counterpart of references. When other scholarly works are cited in the references of a scholarly work, this citation information can be communicated to the cited work.","tags":["Rogue Scholar","Metadata"],"title":"Adding references to Wordpress posts: updated kcite plugin","updated_at":1787973896,"url":"https://blog.front-matter.de/posts/adding-references-to-wordpress-posts-updated-kcite-plugin/","version":"v1"}},{"document":{"authors":[{"affiliation":[{"name":"Front Matter"}],"contributor_roles":[],"family":"Fenner","given":"Martin","url":"https://orcid.org/0000-0003-1419-2405"}],"blog":{"authors":[{"name":"Martin Fenner","url":"https://orcid.org/0000-0003-1419-2405"}],"community_id":"15a362ea-8138-42b8-917f-1840a92addf8","created":1672531200,"current_feed_url":null,"description":"The Front Matter Blog covers the intersection of science and technology since 2007.","doi":"https://doi.org/10.53731/front_matter","favicon":"https://rogue-scholar.org/api/communities/15a362ea-8138-42b8-917f-1840a92addf8/logo","feed_format":"application/atom+xml","feed_url":"https://blog.front-matter.de/atom","filter":null,"generator":"Ghost","home_page_url":"https://blog.front-matter.de/","issn":"2749-9952","language":"eng","license":"https://creativecommons.org/licenses/by/4.0/legalcode","prefix":"10.53731","relative_url":null,"secure":true,"slug":"front_matter","status":"active","subfield":"1710","title":"Front Matter","updated":1787944127,"use_api":true},"blog_name":"Front Matter","blog_slug":"front_matter","content_html":"This is the August 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.
Three blogs were added in August, with a few more in progress, requiring additional work. Welcome everybody! This brings the number of participating blogs to 172, and the number of archived posts to 46,355.
Personal website of Adriano Rutz.
Natural sciences, English.
https://adafede.github.io
Folgen Sie den neuesten Praxisprojekten aus dem MALIS-Studiengang.
Computer and information sciences, German
https://malisprojekte.web.th-koeln.de/wordpress/
Biological sciences, English.
https://blog.bioconductor.org/
On August 4, Rogue Scholar citation tracking launched to production, with a fully automated workflow and weekly updates of cited blog posts. Currently there are 1,392 citations of 766 blog posts.
On August 12, Rogue Scholar announced that it will disable login via local passwords on September 15. Going forward, authentication requires login via ORCID or the new Rogue Scholar passkey authentication launched in July. This will simplify account management both for Rogue Scholar and for users.
On August 18, Rogue Scholar added internal linking via DOI and ORCID, to show all blog posts by the same author, or to show the blog post, plus all blog posts referencing the same blog post or other scholarly work.
Last week, Front Matter published an updated kcite WordPress plugin to make it easier for WordPress authors to cite other scholarly works via their DOI. The kcite plugin was originally published more than 10 years ago, but it stopped working with current versions of WordPress and PHP.
The Rogue Scholar Slack continues to be helpful for answering support questions and for community feedback. In August we discussed Zulip as an alternative to Slack to allow anonymous read access to messages, but decided that for the time being most users are comfortable with Slack, and switching to Zulip would mean learning to use yet another platform. The Rogue Scholar Slack also had interesting discussions on expanding JSON Feed with extensions, and on CITO, the Citation Typing Ontology.
Please use Slack, email, Mastodon, or Bluesky if you have any questions or comments regarding this monthly newsletter.
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.
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:
![\"\"](\"https://storage.ghost.io/c/c5/33/c533c955-b5f3-4ff1-ae2d-6b52a212e602/content/images/2025/09/Bildschirmfoto-2025-09-11-um-09.41.21.png\")
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.
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.
On April 16, 2025, the Rogue Scholar Advisory Board met for the third time since it started in January 2024. Since the last Advisory Board Meeting on October 24, Rogue Scholar has achieved several important milestones.
In February, the Rogue Scholar Statistics page was relaunched as Rogue Scholar Dashboard, displaying key indicators such as the number of participating blogs and archived blog posts, as well as the percentage of posts with ORCID and ROR identifiers, references, or funding.
![\"\"](\"https://storage.ghost.io/c/c5/33/c533c955-b5f3-4ff1-ae2d-6b52a212e602/content/images/2025/09/data-src-image-5130cdf2-4865-484f-90f0-1b9033ece85d.png\")
The Advisory Board suggested adding filters to better highlight more recent data.
In January and February, Rogue Scholar improved the reference extraction and references display, finding references in about 5% of posts. Using the Crossref Cited-By service, Rogue Scholar also started collecting and displaying citations of Rogue Scholar posts. The kcite WordPress plugin that simplifies the generation of DOI references was very helpful, but hasn't been updated in many years. While the numbers of references and citations are still small, linking to other scholarly content via references and citations further integrates scholarly blogs into the broader scholarly record.
The Advisory Board discussed archiving formats for the full-text of blog posts. Rogue Scholar in 2024 started experimenting with PDF and ePub, but this functionality is not yet integrated with the InvenioRDM repository platform. The Advisory Board felt that the JATS format may not be necessary or beneficial for blog content.
The Advisory Board next discussed starting a webinar series on best practices for science blogs, focusing on specific blogging platforms. A first webinar for WordPress bloggers in German was proposed.
Finally, the Advisory Board discussed Rogue Scholar funding. Rogue Scholar is a Diamond Open Access infrastructure with no costs to authors and readers. Seeking grant funding is an option, and Rogue Scholar has so far archived more than 30,000 blog posts, including some highly visible science blogs. One challenge with seeking grant funding is the missing non-profit status for Front Matter, the organization behind Rogue Scholar.
","doi":"https://doi.org/10.53731/taha2-fvd76","guid":"https://doi.org/10.53731/taha2-fvd76","image":"https://images.unsplash.com/photo-1525384197403-b43d320d748a?crop=entropy&cs=tinysrgb&fit=max&fm=jpg&ixid=M3wxMTc3M3wwfDF8c2VhcmNofDMwfHxhcHJpbHxlbnwwfHx8fDE3NTg3MDk4MDV8MA&ixlib=rb-4.1.0&q=80&w=2000","language":"en","license":"https://creativecommons.org/licenses/by/4.0/legalcode","published_at":1758672000,"rid":"vwwxv-mgf29","summary":"On April 16, 2025, the Rogue Scholar Advisory Board met for the third time since it started in January 2024. Since the last Advisory Board Meeting on October 24, Rogue Scholar has achieved several important milestones.","tags":["Rogue Scholar"],"title":"Report Rogue Scholar Advisory Board Meeting April 16, 2025","updated_at":1787973889,"url":"https://blog.front-matter.de/posts/report-rogue-scholar-advisory-board-meeting-ap-16-2024/","version":"v1"}}],"items":[{"authors":[{"affiliation":[{"id":"https://ror.org/00f2yqf98","name":"Medizinische Hochschule Hannover"}],"contributor_roles":[],"family":"Fenner","given":"Martin","url":"https://orcid.org/0000-0003-1419-2405"}],"blog":{"authors":[{"name":"Martin Fenner","url":"https://orcid.org/0000-0003-1419-2405"}],"community_id":"15a362ea-8138-42b8-917f-1840a92addf8","created":1672531200,"current_feed_url":null,"description":"The Front Matter Blog covers the intersection of science and technology since 2007.","doi":"https://doi.org/10.53731/front_matter","favicon":"https://rogue-scholar.org/api/communities/15a362ea-8138-42b8-917f-1840a92addf8/logo","feed_format":"application/atom+xml","feed_url":"https://blog.front-matter.de/atom","filter":null,"generator":"Ghost","home_page_url":"https://blog.front-matter.de/","issn":"2749-9952","language":"eng","license":"https://creativecommons.org/licenses/by/4.0/legalcode","prefix":"10.53731","relative_url":null,"secure":true,"slug":"front_matter","status":"active","subfield":"1710","title":"Front Matter","updated":1787944127,"use_api":true},"blog_name":"Front Matter","blog_slug":"front_matter","content_html":"Cancer is caused by genetic changes. Oncogenes harbor activating mutations that cause or promote cancer, whereas tumor suppressor genes protect from cancer. In this model, genetic changes in one copy of an oncogene, but both copies of a tumor suppressor gene are required to initiate cancer. This simple model is complicated by the fact that more than one genetic change is usually required to initiate cancer, and that other so called epigenetic changes (such as promoter hypermethylation) are also important.
Myelodysplastic syndromes are malignant disorders of the bone marrow that show insufficient production of blood cells and harbor the risk of progressing to acute myeloid leukemia. The 5q syndrome is a distinct subtype that is characterized by loss of genetic material at chromosome 5q31, a characteristic morphology of the bone marrow, and a fairly benign clinical course. We would expect to find a tumor suppressor gene in the deleted region on chromosome 5, but no genetic changes on the other allele of chromosome 5 could be detected. The traditional strategies to identify the genetic changes responsible for the 5q syndrome therefore didn't work.
Research by Benjamin Ebert et al. presented at the American Society of Hematology meeting in December and now published in Nature claims to have finally identified the genetic change responsible for 5q syndrome. They used RNA interference to in turn knock out each of the 40 genes in the common deleted region on chromosome 5q31. They observed the phenotype of human hematopoetic progenitor cells transfected with short hairpin RNAs. The shRNA targeting the gene RPS14 recapitulated the phenotype of patients with 5q syndrome.
To confirm the role of RPS14 in 5q syndrome, RPS14 was overexpressed in hematopoetic cells from patients with 5q syndrome and indeed reverted the erythroid differentiation effect. Reduced expression or inactivating mutations of the one remaining RPS14 gene in 5q syndrome patients was ruled out by sequencing and gene expression profiling.
Further evidence for the importance of RPS14 in 5q syndrome comes from studies of related genes. Expression of RPS14 is required for proper function of the 40s ribosomal subunit. Germline mutations of two other ribosomal proteins, RPS19 and RPS24, have been identified in the congenital disorder Diamond-Blackfan anemia, and the disease in these children has similar features.
As a medical student, I was fortunate enough to listen to Alfred Knudson give a talk about is two-hit hypothesis of tumor suppressor genes, and I was fascinated by cancer genetics ever since. Genetics continues to be a driving force in our understanding of cancer. The next big step in the 5q syndrome story will be a better understanding of why the drug lenalidomide works so well in this disease, and how this relates to RPS14 function. More information about the Ebert paper can be found in this Nature News and Views article.
The Hirsch number tries to quantify the (scientific) productivity of a scientist. The Hirsch number was first described by the physicist J.E. Hirsch in a 2005 PNAS paper: An index to quantify an individual's scientific research output. Hirsch says:
I propose the index h, defined as the number of papers with citation number h, as a useful index to characterize the scientific output of a researcher.
Thus, in contrast to the widely used impact factor, the Hirsch number measures the productivity of an individual scientist and not the journal he publishes in. The Hirsch number tries to factor in both the number of papers and the number of citations of these papers.
Your personal Hirsch number should be equal or greater the number of years you have already spent in science. Again in contrast to the impact factor, you can calculate your Hirsch number with freely available tools. You can look up your papers in Google Scholar and write down the citations for each paper. Or, use online tools such as scHolar index to do the work for you.
Using a simple number to measure the productivity of scientist is a dangerous undertaking. But if numbers are needed (e.g. grant or job applications), the Hirsch number is a good tool. Widespread use of the Hirsch number could have broad implications, as authors would more carefully consider which journals would give them the highest number of citations.
We refactored the R-universe CI workflows to make it possible to run the exact same workflow from your own GitHub repository. This allows you to test or debug the build and check process on your R package, exactly as it will happen on R-universe, but without actually deploying to https://r-universe.dev.
The instructions on r-universe-org/workflows explain how it works: simply create a file /.github/workflows/r-universe-test.yml in your R package git repo with the following config:
name: Test R-universeon: push: pull_request:jobs: build: name: R-universe testing uses: r-universe-org/workflows/.github/workflows/build.yml@v3 with: universe: ${{ github.repository_owner }}That is everything. The workflow will use the fully automated R-universe setup to build and check the package on a range of R versions on Linux, Windows, and MacOS configurations very similar to CRAN.
It is possible to use this workflow in your R package for pushes and/or pull requests alongside those from r-lib/actions. Both will check your R package, but note that the purpose is very different: workflows from r-lib/actions are highly configurable and can test R packages using countless options and environments. The R-universe workflow on the other hand is, just like CRAN, not customizable at all: it uses the exact setup and process as it happens on R-universe, nothing else.
The ability to test-run the build workflow has been recurring feature request, and I hope that it will indeed help package maintainers with debugging problems. I also hope the refactoring might make it a little bit easier to understand the R-universe build process, and enable the community to hack on the workflows and actions to contribute improvements.
","doi":"https://doi.org/10.53731/9r3yj-zwy78","guid":"https://doi.org/","language":"en","license":"https://creativecommons.org/licenses/by/4.0/legalcode","published_at":1767398400,"rid":"vy50z-6dv41","summary":"We refactored the R-universe CI workflows to make it possible to run the exact same workflow from your own GitHub repository. This allows you to test or debug the build and check process on your R package, exactly as it will happen on R-universe, but without actually deploying to https://r-universe.dev.","tags":["R-universe","Infrastructure"],"title":"Testing the R-universe build workflow from your own GitHub repository","updated_at":1787975323,"url":"https://ropensci.org/blog/2026/01/03/r-universe-workflows/","version":"v1"},{"authors":[{"affiliation":[{"name":"Front Matter"}],"contributor_roles":[],"family":"Fenner","given":"Martin","url":"https://orcid.org/0000-0003-1419-2405"}],"blog":{"authors":[{"name":"Martin Fenner","url":"https://orcid.org/0000-0003-1419-2405"}],"community_id":"15a362ea-8138-42b8-917f-1840a92addf8","created":1672531200,"current_feed_url":null,"description":"The Front Matter Blog covers the intersection of science and technology since 2007.","doi":"https://doi.org/10.53731/front_matter","favicon":"https://rogue-scholar.org/api/communities/15a362ea-8138-42b8-917f-1840a92addf8/logo","feed_format":"application/atom+xml","feed_url":"https://blog.front-matter.de/atom","filter":null,"generator":"Ghost","home_page_url":"https://blog.front-matter.de/","issn":"2749-9952","language":"eng","license":"https://creativecommons.org/licenses/by/4.0/legalcode","prefix":"10.53731","relative_url":null,"secure":true,"slug":"front_matter","status":"active","subfield":"1710","title":"Front Matter","updated":1787944127,"use_api":true},"blog_name":"Front Matter","blog_slug":"front_matter","content_html":"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:
The Altmetrics manifesto stated in 2010 that
Altmetrics are fast, using public APIs to gather data in days or weeks. They're open \u2013 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 \u2013 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:
Please use Slack, email, Mastodon, or Bluesky if you have any questions or comments regarding the Rogue Scholar citation tracking service.
The Rogue Scholar science blog archive has introduced authentication with passkeys and will disable local accounts on September 15. Reading Rogue Scholar content has always been free and never required user accounts or cookie permissions. This is true both for web and API usage.
Science blogs participating in Rogue Scholar also don't require user accounts, but only a contact email, and the initial registration of the blog is via a web form. The import of new or updated blog posts into Rogue Scholar happens automatically via RSS feed or JSON API integration, and there is no ability to update blog posts archived in Rogue Scholar outside of that workflow.
Rogue Scholar offers user accounts that everyone can sign up for. They are currently only intended for blog authors, and two weeks ago their functionality was expanded. Rogue Scholar blog posts are organized around communities, and there are three community types:
The blog community includes basic information about the blog, such as name, description and logo. This information is automatically extracted from the blog feed, but in some cases manual curation is desired, e.g. to include a description or logo that the feed does not provide. Blog authors with a Rogue Scholar account, and after they have received an invitation as community manager, can now manage this information themselves:
Going forward Rogue Scholar will also allow blog authors to provide more information, such as the blog default OECD Field of Science (currently provided in the blog registration form) and International Standard Serial Number (ISSN), currently provided via email.
Topic communities aggregate blog posts from multiple blogs around a common topic, typically referred to as a tag or category in blogs. These tags/categories have naturally evolved as folksonomy rather than a centrally defined taxonomy, and fully automatic classification of blog posts into topics is neither desired nor easily achievable. For these reasons, manual curation of topics is needed, and currently this requires user accounts. Blog authors who are community managers of their blog can submit blog posts to topic communities, or manage the communities the blog post is included.
The creation of topic communities currently requires an admin account, but if people are interested in becoming Rogue Scholar community managers, creating new topic communities, or adding blog posts to topic communities where they are not the author, please reach out to me.
Subject communities are automatically added to blog posts based on the blog subject area, and user accounts are not relevant here. Going forward, I want to enable automatic classification based on blog post content, and inclusion in more than one subject community. We can take advantage of the new collections feature introduced in InvenioRDM v13 earlier this month.
Now that I have explained that user accounts are not required to use Rogue Scholar, but there are important use cases where they are needed, we can talk about how user accounts are managed in Rogue Scholar. Users can register for a user account with Rogue Scholar in one of two ways:
Authentication via ORCID is a widely used authentication workflow in the scholarly community that is free (no ORCID organizational membership required) and built into the InvenioRDM platform.
Depending on a single external authentication service is not desirable, as not all users will have an ORCID (e.g. group or admin accounts), and this would make it impossible to sign in to Rogue Scholar if the ORCID service is temporarily down. ORCID is primarily a service to provide unique identifiers to scholars, and not an identity provider (IdP) that provides single sign-on services.
One option is to provide authentication via local accounts with username/password, but that is both potentially insecure without additional measures such as multi-factor authentication (MFA) and inconvenient without a password manager. The InvenioRDM platform that Rogue Scholar uses has built-in local account management, but not built-in multi-factor authentication or other more advanced functionalities. Many InvenioRDM instances use an external authentication service that integrates with InvenioRDM.
ORCID authentication is implemented via the OpenID Connect (OIDC) authentication protocol, and OIDC can be used with many other third-party logins, including GitHub, which is built into InvenioRDM. For Rogue Scholar I wanted to implement a local OIDC provider that I can configure and control. The most popular authentication service for InvenioRDM for this use case is probably Keycloak. Keycloak is a powerful and well-tested open-source solution for identity management, but it is almost too complex for smaller instances such as Rogue Scholar. For these reasons, Rogue Scholar went with Pocket ID,
A simple and easy-to-use OIDC provider that allows users to authenticate with their passkeys to your services.
Pocket ID depends on passkeys, a secure and user-friendly authentication method that is (slowly) becoming a new authentication standard.
Pocket ID authentication for Rogue Scholar was launched three weeks ago, and the service is hosted at https://auth.rogue-scholar.org. The setup was straightforward, and Pocket ID supports some advanced features currently not needed by Rogue Scholar, e.g. restricting user groups, LDAP integration, or a REST API.
With the launch of Pocket ID authentication, registration for new local accounts has been disabled, and login via username/password will be disabled on September 15. Users with existing local accounts can link their accounts to ORCID and/or passkeys until that date.
Please use Slack, email, Mastodon, or Bluesky if you have any questions or comments regarding Rogue Scholar authentication.
The Rogue Scholar science blog archive has supported ORCID and DOI identifiers for linking to authors and blog posts since its launch. Starting this week, these two identifiers can also be used to navigate within the Rogue Scholar archive.
ORCID, which stands for Open Researcher and Contributor ID, is a free, unique, persistent identifier (PID) for individuals to use as they engage in research, scholarship, and innovation activities.
ORCID for Researchers
One third (32.71%) of science blog posts in Rogue Scholar are linked to the ORCID of at least one of their authors. Searching Rogue Scholar by ORCID returns a list of all blog posts authored by that person, e.g. using my ORCID:
Starting this week, clicking on an author name with an ORCID icon in Rogue Scholar will return all records (co-)authored by that author:
This feature works in both search results and single record views. For authors without an ORCID (e.g. organizational authors), Rogue Scholar continues to return a search result by name, which is the built-in behavior of the InvenioRDM repository platform. Clicking on the ORCID icon continues to link to the ORCID profile page for that author.
All blog posts in Rogue Scholar have a Digital Object Identifier (DOI) assigned to them to uniquely identify the blog post and include relevant metadata. These metadata can optionally include references (currently 5.04% of Rogue Scholar posts) that again can use DOIs. Citations of Rogue Scholar posts (currently 1387 citations of 763 blog posts) using their DOI are also shown in the Rogue Scholar record.
Starting this week, clicking on the title of a DOI reference or citation in the Rogue Scholar record returns all records using that DOI as identifier, reference, or citation, with the Rogue Scholar record on top of the list.
Clicking on the title of the citation returns a search result with the cited Rogue Scholar post and also the citing post. Clicking on the DOI link continues to link to the scholarly work with that DOI.
This also works in the case of references or citations that are not Rogue Scholar posts (most of them):
Clicking on the title of reference #6 returns a search result with all Rogue Scholar records referencing or citing that DOI:
The first search result is the record where I clicked the link. The second search result is another Rogue Scholar blog post referencing the same Scientometrics paper.
Implementing DOI linking within Rogue Scholar poses an interesting user interface challenge. I decided to always return search results instead of directly linking to the Rogue Scholar record. By including references and citations in the search results, Rogue Scholar will always return at least one result, but may show more Rogue Scholar records referencing the same blog post or other scholarly work.
This additional functionality around Rogue Scholar references hopefully encourages more Rogue Scholar bloggers to include formal references with their posts. My goal for 2026 is to have 10% Rogue Scholar posts include references (currently 5.04%). Including formal references in blog posts is straightforward, but so far has not been a best practice. Some Rogue Scholar blogs already have high percentages of posts with references, including Research Group Information Management @ Humboldt-Universit\u00e4t zu Berlin (40 posts, 75%), Henry Rzepa's Blog (518 posts, 61%), or chem-bla-ics (499 posts, 39%), and this blog (590 posts, 33%).
Please use Slack, email, Mastodon, or Bluesky if you have any questions or comments regarding Rogue Scholar ORCID or DOI linking.
Fenner, M. (2025, August 4). Rogue Scholar citation tracking launches to production. Front Matter. https://doi.org/10.53731/zyg15-qv911
","doi":"https://doi.org/10.53731/yjq4w-5yr32","guid":"https://doi.org/10.53731/yjq4w-5yr32","image":"https://images.unsplash.com/photo-1694596747902-626600534e80?crop=entropy&cs=tinysrgb&fit=max&fm=jpg&ixid=M3wxMTc3M3wwfDF8c2VhcmNofDU0fHxsaW5raW5nfGVufDB8fHx8MTc1NTQxNzYxNnww&ixlib=rb-4.1.0&q=80&w=2000","language":"en","license":"https://creativecommons.org/licenses/by/4.0/legalcode","published_at":1755475200,"reference":[{"id":"https://doi.org/10.53731/zyg15-qv911","unstructured":"Fenner, M. (2025, August 4). Rogue Scholar citation tracking launches to production. Front Matter."}],"rid":"4sfxs-drd44","summary":"The Rogue Scholar science blog archive has supported ORCID and DOI identifiers for linking to authors and blog posts since its launch. Starting this week, these two identifiers can also be used to navigate within the Rogue Scholar archive.ORCID One third (32.71%) of science blog posts in Rogue Scholar are linked to the ORCID of at least one of their authors.","tags":["Rogue Scholar","Metadata"],"title":"Rogue Scholar links records via ORCID and DOI","updated_at":1787973900,"url":"https://blog.front-matter.de/posts/rogue-scholar-links-records-via-orcid-and-doi/","version":"v1"},{"authors":[{"affiliation":[{"name":"Front Matter"}],"contributor_roles":[],"family":"Fenner","given":"Martin","url":"https://orcid.org/0000-0003-1419-2405"}],"blog":{"authors":[{"name":"Martin Fenner","url":"https://orcid.org/0000-0003-1419-2405"}],"community_id":"15a362ea-8138-42b8-917f-1840a92addf8","created":1672531200,"current_feed_url":null,"description":"The Front Matter Blog covers the intersection of science and technology since 2007.","doi":"https://doi.org/10.53731/front_matter","favicon":"https://rogue-scholar.org/api/communities/15a362ea-8138-42b8-917f-1840a92addf8/logo","feed_format":"application/atom+xml","feed_url":"https://blog.front-matter.de/atom","filter":null,"generator":"Ghost","home_page_url":"https://blog.front-matter.de/","issn":"2749-9952","language":"eng","license":"https://creativecommons.org/licenses/by/4.0/legalcode","prefix":"10.53731","relative_url":null,"secure":true,"slug":"front_matter","status":"active","subfield":"1710","title":"Front Matter","updated":1787944127,"use_api":true},"blog_name":"Front Matter","blog_slug":"front_matter","content_html":"References are an important element of scholarly metadata, and that is also true for science blog posts. Currently 5.06% of all Rogue Scholar posts include at least one reference, which are then registered with Crossref metadata.
Citations are the counterpart of references. When other scholarly works are cited in the references of a scholarly work, this citation information can be communicated to the cited work.
Citations are the links that knit together our scientific and cultural knowledge. They are primary data that provide both provenance and an explanation for how we know facts. They allow us to attribute and credit scientific contributions, and they enable the evaluation of research and its impacts. In sum, citations are the most important vehicle for the discovery, dissemination, and evaluation of all scholarly knowledge.
Initiative for Open Citations (I4OC)
The first step is making the references metadata openly available in Crossref metadata, and thanks to the Initiative for Open Citations (I4OC) and the work of many publishers, nearly 100% of all references are now open by default.
The next step is aggregating all these references by the cited work. Crossref members receive this information via the Crossref Cited-By service, other aggregators are OpenCitations and OpenAlex, and of course a number of commercial services.
Rogue Scholar is collecting citations to its blog posts via the Crossref Cited-By service every week and makes that information available with each record, and with a search filter. As of today, there are 1,392 citations of 766 Rogue Scholar posts (1.65%). You can get basically the same information from OpenAlex or other aggregators.
DataCite references and citations add several challenges to this. A small number of Rogue Scholar blogs register their own DOI metadata and use DataCite for this. DataCite metadata use related_identifiers with a number of relation_types instead of references, which adds ambiguity, e.g. what relation_types should be treated as references (probably Cites and References, but maybe also IsSupplementedBy). There are also relation_types for the inverse relation (IsCitedBy, IsReferencedBy) with the challenge that a repository has to update these metadata after publication as citations happen. And aggregators face the same problems. In addition, services such as OpenAlex are still building up workflows to index DataCite metadata at scale.
For science blogs where Rogue Scholar registers the DOI metadata, the above is not relevant. The challenge is to provide reference metadata in a format Rogue Scholar can understand. Besides experimental support for a JSON Feed extension (as RSS, Atom.,or blogging platform JSON APIs don't support references), this means extracting the references from the full-text content.
Luckily references in scholarly documents follow an established format: a section called references (or similar) at the end of the document, followed by one or more references. The recommendation by Rogue Scholar is to format these references as an ordered or unordered HTML list (<ol> or <ul> tag), as this is easier to parse than a list of <div> or <p>. The citation style (there are thousands) doesn't matter, but the reference should include a link to the DOI or URL of the cited resource.
Reference metadata can be generated by copy/paste from your favorite reference manager, or can be automatically generated. From the popular blogging platforms only Quarto can generate references (what they call citations, a common confusion). With Wordpress, the most popular blogging platform in Rogue Scholar, you can use a plugin to automate reference generation. Either Zotpress, which tightly integrates with the reference manager Zotero, or kcite.
Kcite works by collecting reference metadata for DOIs, PubMed, or random web resources via the Greycite service. Greycite was discontinued years ago, and the plugin was last updated 12 years ago, so that the plugin is no longer working with current PHP and Wordpress versions.
The plugin makes it very easy to cite DOI resources, just use a Wordpress shortcode in a blog post:
[cite]10.59350/xqerh-wam97[/cite]The Rogue Scholar blogger (and Advisory Board member) Henry Rzepa has made heavy use of the plugin for many years, and ultimately convinced me to update the plugin. Last week, I did that and released a fixed kcite version. You can download the latest version (1.7.97) here as zip file, that you can upload to your Wordpress instance:
A more streamlined installation via the plugin installer requires this fork to become the official kcite plugin, something I am working on.
The focus on the initial work was compatibility with recent versions of PHP (8.4) and Wordpres (6.8.2). The included citeproc.js Javascript file was updated to the latest version (1.4.61), and the citation styles and locales used are the latest versions.
The plugin by default works in server mode, where references are formatted with a generic template. In client mode, the built-in citeproc.js processor is used to generate references with richer metadata. I included a fix to properly show the name of Rogue Scholar blogs. An example reference list in client mode generated by the plugin is shown below:
A lot more work is needed with testing the plugin, and potentially adding more functionality, especially the following:
Please use Slack, email, Mastodon, or Bluesky if you have any questions or comments regarding references, citations, or the kcite plugin.
","doi":"https://doi.org/10.53731/326tr-95k32","guid":"https://doi.org/10.53731/326tr-95k32","image":"https://images.unsplash.com/photo-1584266049120-f8c39aaaccb1?crop=entropy&cs=tinysrgb&fit=max&fm=jpg&ixid=M3wxMTc3M3wwfDF8c2VhcmNofDQzfHxyZWZlcmVuY2VzfGVufDB8fHx8MTc1NjExNjMzMHww&ixlib=rb-4.1.0&q=80&w=2000","language":"en","license":"https://creativecommons.org/licenses/by/4.0/legalcode","published_at":1756080000,"reference":[{"id":"https://doi.org/10.59350/xqerh-wam97","unstructured":"Rzepa, H. (2024, March 21). Internet Archeology: reviving a 2001 article published in the Internet Journal of Chemistry. Henry Rzepa's Blog."}],"rid":"9rtkj-36y78","summary":"References are an important element of scholarly metadata, and that is also true for science blog posts. Currently 5.06% of all Rogue Scholar posts include at least one reference, which are then registered with Crossref metadata. Citations are the counterpart of references. When other scholarly works are cited in the references of a scholarly work, this citation information can be communicated to the cited work.","tags":["Rogue Scholar","Metadata"],"title":"Adding references to Wordpress posts: updated kcite plugin","updated_at":1787973896,"url":"https://blog.front-matter.de/posts/adding-references-to-wordpress-posts-updated-kcite-plugin/","version":"v1"},{"authors":[{"affiliation":[{"name":"Front Matter"}],"contributor_roles":[],"family":"Fenner","given":"Martin","url":"https://orcid.org/0000-0003-1419-2405"}],"blog":{"authors":[{"name":"Martin Fenner","url":"https://orcid.org/0000-0003-1419-2405"}],"community_id":"15a362ea-8138-42b8-917f-1840a92addf8","created":1672531200,"current_feed_url":null,"description":"The Front Matter Blog covers the intersection of science and technology since 2007.","doi":"https://doi.org/10.53731/front_matter","favicon":"https://rogue-scholar.org/api/communities/15a362ea-8138-42b8-917f-1840a92addf8/logo","feed_format":"application/atom+xml","feed_url":"https://blog.front-matter.de/atom","filter":null,"generator":"Ghost","home_page_url":"https://blog.front-matter.de/","issn":"2749-9952","language":"eng","license":"https://creativecommons.org/licenses/by/4.0/legalcode","prefix":"10.53731","relative_url":null,"secure":true,"slug":"front_matter","status":"active","subfield":"1710","title":"Front Matter","updated":1787944127,"use_api":true},"blog_name":"Front Matter","blog_slug":"front_matter","content_html":"This is the August 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.
Three blogs were added in August, with a few more in progress, requiring additional work. Welcome everybody! This brings the number of participating blogs to 172, and the number of archived posts to 46,355.
Personal website of Adriano Rutz.
Natural sciences, English.
https://adafede.github.io
Folgen Sie den neuesten Praxisprojekten aus dem MALIS-Studiengang.
Computer and information sciences, German
https://malisprojekte.web.th-koeln.de/wordpress/
Biological sciences, English.
https://blog.bioconductor.org/
On August 4, Rogue Scholar citation tracking launched to production, with a fully automated workflow and weekly updates of cited blog posts. Currently there are 1,392 citations of 766 blog posts.
On August 12, Rogue Scholar announced that it will disable login via local passwords on September 15. Going forward, authentication requires login via ORCID or the new Rogue Scholar passkey authentication launched in July. This will simplify account management both for Rogue Scholar and for users.
On August 18, Rogue Scholar added internal linking via DOI and ORCID, to show all blog posts by the same author, or to show the blog post, plus all blog posts referencing the same blog post or other scholarly work.
Last week, Front Matter published an updated kcite WordPress plugin to make it easier for WordPress authors to cite other scholarly works via their DOI. The kcite plugin was originally published more than 10 years ago, but it stopped working with current versions of WordPress and PHP.
The Rogue Scholar Slack continues to be helpful for answering support questions and for community feedback. In August we discussed Zulip as an alternative to Slack to allow anonymous read access to messages, but decided that for the time being most users are comfortable with Slack, and switching to Zulip would mean learning to use yet another platform. The Rogue Scholar Slack also had interesting discussions on expanding JSON Feed with extensions, and on CITO, the Citation Typing Ontology.
Please use Slack, email, Mastodon, or Bluesky if you have any questions or comments regarding this monthly newsletter.
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.
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.
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.
On April 16, 2025, the Rogue Scholar Advisory Board met for the third time since it started in January 2024. Since the last Advisory Board Meeting on October 24, Rogue Scholar has achieved several important milestones.
In February, the Rogue Scholar Statistics page was relaunched as Rogue Scholar Dashboard, displaying key indicators such as the number of participating blogs and archived blog posts, as well as the percentage of posts with ORCID and ROR identifiers, references, or funding.
The Advisory Board suggested adding filters to better highlight more recent data.
In January and February, Rogue Scholar improved the reference extraction and references display, finding references in about 5% of posts. Using the Crossref Cited-By service, Rogue Scholar also started collecting and displaying citations of Rogue Scholar posts. The kcite WordPress plugin that simplifies the generation of DOI references was very helpful, but hasn't been updated in many years. While the numbers of references and citations are still small, linking to other scholarly content via references and citations further integrates scholarly blogs into the broader scholarly record.
The Advisory Board discussed archiving formats for the full-text of blog posts. Rogue Scholar in 2024 started experimenting with PDF and ePub, but this functionality is not yet integrated with the InvenioRDM repository platform. The Advisory Board felt that the JATS format may not be necessary or beneficial for blog content.
The Advisory Board next discussed starting a webinar series on best practices for science blogs, focusing on specific blogging platforms. A first webinar for WordPress bloggers in German was proposed.
Finally, the Advisory Board discussed Rogue Scholar funding. Rogue Scholar is a Diamond Open Access infrastructure with no costs to authors and readers. Seeking grant funding is an option, and Rogue Scholar has so far archived more than 30,000 blog posts, including some highly visible science blogs. One challenge with seeking grant funding is the missing non-profit status for Front Matter, the organization behind Rogue Scholar.
","doi":"https://doi.org/10.53731/taha2-fvd76","guid":"https://doi.org/10.53731/taha2-fvd76","image":"https://images.unsplash.com/photo-1525384197403-b43d320d748a?crop=entropy&cs=tinysrgb&fit=max&fm=jpg&ixid=M3wxMTc3M3wwfDF8c2VhcmNofDMwfHxhcHJpbHxlbnwwfHx8fDE3NTg3MDk4MDV8MA&ixlib=rb-4.1.0&q=80&w=2000","language":"en","license":"https://creativecommons.org/licenses/by/4.0/legalcode","published_at":1758672000,"rid":"vwwxv-mgf29","summary":"On April 16, 2025, the Rogue Scholar Advisory Board met for the third time since it started in January 2024. Since the last Advisory Board Meeting on October 24, Rogue Scholar has achieved several important milestones.","tags":["Rogue Scholar"],"title":"Report Rogue Scholar Advisory Board Meeting April 16, 2025","updated_at":1787973889,"url":"https://blog.front-matter.de/posts/report-rogue-scholar-advisory-board-meeting-ap-16-2024/","version":"v1"}],"out_of":638,"page":1,"per_page":10,"total-results":638}