Updated one more link to Rich' blog and tagged some as to keep

egonw · egonw · commit 142819a61fbf · 2025-12-29T12:14:08.000+01:00
diff --git a/_posts/2008-12-05-cheminformatics-benchmark-project-1.markdown b/_posts/2008-12-05-cheminformatics-benchmark-project-1.markdown
@@ -2,16 +2,16 @@
 layout: post
 title:  "Cheminformatics Benchmark Project #1"
 date:   2008-12-05
+modified_date: 2025-12-19
 blogger-link: https://chem-bla-ics.blogspot.com/2008/12/cheminformatics-benchmark-project-1.html
 doi: 10.59350/wngzb-y3329
-tags: cheminf cdk
-modified_date: 2025-10-11
+tags: cheminf cdk justdoi:10.59350/1ph8m-fj607
 ---
 
 Yesterday's blog about [Who says Java is not fast?!? <i class="fa-solid fa-recycle fa-xs"></i>](https://chem-bla-ics.linkedchemistry.info/2008/12/04/who-says-java-is-not-fast.html)
 caused quite some feedback (thanx to all commenters!) with several good points. Of course, a table like that in the cinfony paper
 (see also the comments in the blogs by [Noel](http://baoilleach.blogspot.com/2008/12/cinfony-paper-published-in-chemistry.html)
-(the author) and [Rich](http://depth-first.com/articles/2008/12/04/choose-java-for-speed)). Many things determine why the CDK
+(the author) and [Rich <i class="fa-solid fa-recycle fa-xs"></i>](https://doi.org/10.59350/1ph8m-fj607)). Many things determine why the CDK
 might be fastest in that table for SDF iterating. Suggestions have been that OpenBabel and RDKit may be doing much more than simple reading; Java might actually take advantage of the second core for caching file content.
 
 [ZZ](http://www.simbiosys.ca/blog/) observed something I overlooked: calculating the molecular mass in CDK is by far slowest
diff --git a/_posts/2009-02-25-rdf-for-chemistry.markdown b/_posts/2009-02-25-rdf-for-chemistry.markdown
@@ -4,14 +4,14 @@ title:  "RDF for chemistry"
 date:   2009-02-25
 blogger-link: https://chem-bla-ics.blogspot.com/2009/02/rdf-for-chemistry.html
 doi: 10.59350/vsb09-mjr40
-tags: google chemistry rdf semweb
+tags: google chemistry rdf semweb justdoi:10.59350/a2w3n-cvb94
 image: /assets/images/sechemticCSHALS.png
-modified_date: 2025-11-29
+modified_date: 2025-12-29
 ---
 
 [C-SHALS 2009](http://www.iscb.org/cms_addon/conferences/cshals2009/io-informatics-news.php) (*Conference on Semantics in Healthcare and Life Sciences*)
 has just started, and has coverage in a [blog](http://cshals.blogspot.com/) and in a [FriendFeed room](http://friendfeed.com/rooms/cshals-2009). It
-nicely coincides with Rich' blog on [What the Heck is the Semantic Web?](http://depth-first.com/articles/2009/02/25/what-the-heck-is-the-semantic-web),
+nicely coincides with Rich' blog on [What the Heck is the Semantic Web? <i class="fa-solid fa-recycle fa-xs"></i>](https://doi.org/10.59350/a2w3n-cvb94),
 and the RDF work I have recently done on [rdf.openmolecules.net <i class="fa-solid fa-recycle fa-xs"></i>](https://chem-bla-ics.linkedchemistry.info/2009/02/17/dbpedia-enters-rdfopenmoleculesnet.html)
 and [Bioclipse <i class="fa-solid fa-recycle fa-xs"></i>](https://chem-bla-ics.linkedchemistry.info/2009/02/22/solubility-data-in-bioclipse-2-handling.html). (Oh, do I wish I could have attended that
 conference.)
diff --git a/_posts/2024-12-08-rich-l-apodaca.markdown b/_posts/2024-12-08-rich-l-apodaca.markdown
@@ -14,19 +14,19 @@ image: /assets/images/depth_first.png
 <img src="/assets/images/depth_first.png" style="width: 40%; display: block; margin-left: auto; margin-right: auto; float: right"
      alt="Screenshot of the first Depth-First blog post" />
 If you are into openscience chemistry or chemistry blogging, then you probably heard of
-[Rich Apodaca](https://orcid.org/0000-0003-3855-9427)'s [Depth-First blog](https://depth-first.com/).
+[Rich Apodaca](https://orcid.org/0000-0003-3855-9427)'s [Depth-First blog](https://depth-first.com/). <!-- keep link -->
 Rich [started blogging in 2006 <i class="fa-solid fa-recycle fa-xs"></i>](https://doi.org/10.59350/xyp0f-9dt42) but this is not
 how I discovered his work originally. I know that we at least already had contact in 2005,
 because that is when he wrote about an integration between his Octet library and the Chemistry Development Kit
 in the [CDK News](https://sourceforge.net/projects/cdk/files/CDK%20News/) (volume 2, issue 2),
 *CDKTools: The CDK-Octet Bridge*. In 2006 he [reviewed our use of the Open Journal System for CDK News <i class="fa-solid fa-recycle fa-xs"></i>](https://doi.org/10.59350/esgte-mv539).
 
 But I did find we have been blogging about our work a lot. [Searching for Rich](https://www.google.com/search?q=site%3Achem-bla-ics.blogspot.com+rich)
-gives false positives, but plenty of discussions of his work. At the same time, [my name shows up multiple times](https://www.google.com/search?q=site:depth-first.com+egon)
+gives false positives, but plenty of discussions of his work. At the same time, [my name shows up multiple times](https://www.google.com/search?q=site:depth-first.com+egon) <!-- keep link -->
 in Depth-First too. Looking back at our shared history, we find, for example, Rich has blogged a lot about using the
 [Chemistry Development Kit in Ruby <i class="fa-solid fa-recycle fa-xs"></i>](https://doi.org/10.59350/50ebs-4zq55).
 
-Rich [blogged about a lot of cheminformatics innovation](https://depth-first.com/articles/). For example,
+Rich [blogged about a lot of cheminformatics innovation](https://depth-first.com/articles/). For example, <!-- keep link -->
 in 2006 [he was working on multi-atom bonding <i class="fa-solid fa-recycle fa-xs"></i>](https://doi.org/10.59350/pz3p6-fv247),
 such as in ferrocene, something that is even today not routinely used in cheminformatics. I replied
 to that in [this post](https://chem-bla-ics.linkedchemistry.info/2006/12/30/modern-chemistry-in-cdk-beyond-two.html).
@@ -57,5 +57,5 @@ was very active in open science and [held many patents](https://patents.google.c
 His latest work was about *Balsa: A Compact Line Notation Based on SMILES*
 (see doi:[10.26434/chemrxiv-2022-01ltp](https://doi.org/10.26434/chemrxiv-2022-01ltp)).
 
-The [Depth-First blog](https://depth-first.com/) has a CC-BY 2.0 license and perhaps [Rogue Scholar](https://rogue-scholar.org/)
+The [Depth-First blog](https://depth-first.com/) has a CC-BY 2.0 license and perhaps [Rogue Scholar](https://rogue-scholar.org/) <!-- keep link -->
 can archive it? It helps us remember Rich and his contributions to open science cheminformatics.
diff --git a/_posts/2024-12-30-fair-blog-to-blog-citations.markdown b/_posts/2024-12-30-fair-blog-to-blog-citations.markdown
@@ -49,14 +49,14 @@ So, when [Martin Fenner](https://blog.front-matter.io/author/martin/) and
 [I](https://chem-bla-ics.linkedchemistry.info/2024/12/08/rich-l-apodaca.html)
 [started](https://chem-bla-ics.linkedchemistry.info/2024/12/27/archiving_blogs.html)
 [archiving](https://doi.org/10.53731/3c6pm-xbp04)
-the [Depth-First blog of Rich Apodaca](https://depth-first.com/) to digitally preserve his blog,
+the [Depth-First blog of Rich Apodaca](https://depth-first.com/) to digitally preserve his blog, <!-- keep link -->
 it also automatically gave the blog posts DOIs. This makes the blog more FAIR, just like it does
 for my blog. And being more FAIR, we can use the DOIs for other things too, like blog to blog
 citations with CiTO intent annotation, as nanopublications.
 (Technically, any Springer Nature journal can do this, but they found reasons to not do it.)
 
 So, let's take [this blog post](https://chem-bla-ics.linkedchemistry.info/2024/12/08/rich-l-apodaca.html).
-I have today updated this to not use `depth-first.com` URLs but, following Martin's example, use the DOIs
+I have today updated this to not use `depth-first.com` URLs but, following Martin's example, use the DOIs <!-- keep link -->
 for those posts instead.
 
 And when I make a nanopublication out of this, I can add the citation intent, and then it looks like
