Updated a bunch of links

egonw · egonw · commit 7450c15c927c · 2026-03-07T15:38:20.000+01:00
diff --git a/_posts/2009-07-02-bioclipse-for-cdk-developers-2.markdown b/_posts/2009-07-02-bioclipse-for-cdk-developers-2.markdown
@@ -6,9 +6,10 @@ blogger-link: https://chem-bla-ics.blogspot.com/2009/07/bioclipse-for-cdk-develo
 doi: 10.59350/gq1ew-ehp14
 tags: cdk bioclipse
 image: /assets/images/atomTyping.png
+modified_date: 2026-03-07
 ---
 
-I [reported earlier](http://chem-bla-ics.blogspot.com/2009/02/bioclipse-for-cdk-developers-1.html) how [Bioclipse](http://www.bioclipse.net/)
+I [reported earlier <i class="fa-solid fa-recycle fa-xs"></i>](https://chem-bla-ics.linkedchemistry.info/2009/02/15/bioclipse-for-cdk-developers-1.html) how [Bioclipse](http://www.bioclipse.net/)
 allows you to use a script to perceive atom types for the content of the JChemPaint RCP editor. This functionality is now available in the
 outline, and indicates directly if Bioclipse (and the underlying [CDK](http://cdk.sf.net/)) understands the chemistry you are drawing. In a
 future Bioclipse release, these *problems* will be visualized more prominently, likely using the Errors/Problems Views available from Eclipse, or otherwise.
diff --git a/_posts/2009-07-31-new-blogs-11.markdown b/_posts/2009-07-31-new-blogs-11.markdown
@@ -5,10 +5,11 @@ date:   2009-07-31
 blogger-link: https://chem-bla-ics.blogspot.com/2009/07/new-blogs-11.html
 doi: 10.59350/7sbjg-3e122
 tags: blog cb
+modified_date: 2026-03-07
 ---
 
 Not that the last two weeks has seen a boost on blog submissions to [Chemical blogspace](http://cb.openmolecules.net/);
-just that I was not really finished with [New Blogs #10](http://chem-bla-ics.blogspot.com/2009/07/new-blogs-10.html).
+just that I was not really finished with [New Blogs #10 <i class="fa-solid fa-recycle fa-xs"></i>](https://chem-bla-ics.linkedchemistry.info/2009/07/23/new-blogs-10.html).
 
 * [The Realm of Organic Synthesis](http://therealmoforganicsynthesis.blogspot.com/) ([entry in Cb](http://cb.openmolecules.net/blog_search.php?blog_id=201))
 * [Carbon Chemistry](http://carbontube.blogspot.com/) ([entry in Cb](http://cb.openmolecules.net/blog_search.php?blog_id=20))
diff --git a/_posts/2009-08-13-last-call-xep-0244-io-data.markdown b/_posts/2009-08-13-last-call-xep-0244-io-data.markdown
@@ -5,12 +5,13 @@ date:   2009-08-13
 blogger-link: https://chem-bla-ics.blogspot.com/2009/08/last-call-xep-0244-io-data.html
 doi: 10.59350/y1ka2-ad976
 tags: xmpp bioinfo cheminf
+modified_date: 2026-03-07
 ---
 
 Today I received this email, which is a milestone for the [XMPP](http://en.wikipedia.org/wiki/Extensible_Messaging_and_Presence_Protocol)
 (aka Jabber) work Johannes, Ola and I have been working on as SOAP alternative using the intrinsically asynchronous XMPP as transport
 protocol instead of HTTP as SOAP commonly does (see
-[Next generation asynchronous webservices](http://chem-bla-ics.blogspot.com/2008/10/next-generation-asynchronous.html)):
+[Next generation asynchronous webservices <i class="fa-solid fa-recycle fa-xs"></i>](https://chem-bla-ics.linkedchemistry.info/2008/10/31/next-generation-asynchronous.html)):
 
 > This message constitutes notice of a Last Call for comments on XEP-0244 (IO Data).
 >
@@ -32,5 +33,5 @@ protocol instead of HTTP as SOAP commonly does (see
 
 There remains quite a lot to do, and you are more than welcome to join in the project. There is a Java library and we've
 integrated the specs into [Bioclipse](http://www.bioclipse.net/) and [Taverna](http://taverna.sf.net/) (see
-[Details behind the "Calling XMPP cloud services from Taverna2"](http://chem-bla-ics.blogspot.com/2009/01/details-behind-calling-xmpp-cloud.html)),
+[Details behind the "Calling XMPP cloud services from Taverna2" <i class="fa-solid fa-recycle fa-xs"></i>](https://chem-bla-ics.linkedchemistry.info/2009/01/21/details-behind-calling-xmpp-cloud.html)),
 but there is no support for BioCatalogue yet, and no libraries for other programming language yet.
diff --git a/_posts/2009-08-17-bioclipse-enters-social-web.markdown b/_posts/2009-08-17-bioclipse-enters-social-web.markdown
@@ -2,7 +2,7 @@
 layout: post
 title:  "Bioclipse enters the social web"
 date:   2009-08-17
-modified_date: 2026-02-21
+modified_date: 2026-03-07
 blogger-link: https://chem-bla-ics.blogspot.com/2009/08/bioclipse-enters-social-web.html
 doi: 10.59350/9zgvr-hfk92
 tags: bioclipse twitter friendfeed
@@ -15,7 +15,7 @@ the data on [FriendFeed](https://www.friendfeed.com/).
 
 When someone asked last week on the [Taverna](https://taverna.sf.net/) mailing list about a Twitter [node](http://twitter.com/),
 I was surely interested. Though this can hardly be called *core research*, I, *fortunately*, had to test
-[the new Bioclipse SDK](http://chem-bla-ics.blogspot.com/2009/08/making-bioclipse-development-easier-new.html) :)
+[the new Bioclipse SDK <i class="fa-solid fa-recycle fa-xs"></i>](https://chem-bla-ics.linkedchemistry.info/2009/08/13/making-bioclipse-development-easier-new.html) :)
 
 So, I hacked up a Twitter plugin for [Bioclipse](https://www.bioclipse.net/) in no time using [JTwitter](https://www.winterwell.com/software/jtwitter.php)
 (license:LGPL), to allow sending tweets to [my Twitter account <i class="fa-solid fa-link-slash fa-xs"></i>](https://twitter.com/egonwillighagen) (but not yet my
diff --git a/_posts/2009-08-29-reminder-my-talk-in-frankfurt-on-monday.markdown b/_posts/2009-08-29-reminder-my-talk-in-frankfurt-on-monday.markdown
@@ -5,13 +5,14 @@ date:   2009-08-29
 blogger-link: https://chem-bla-ics.blogspot.com/2009/08/reminder-my-talk-in-frankfurt-on-monday.html
 doi: 10.59350/mwcz7-gmj05
 tags: openscience openaccess blue-obelisk
+modified_date: 2026-03-07
 ---
 
-Quick and short reminder about my [Open Knowledge: Reproducibility in Cheminformatics with Open Data, Open Source and Open Standards](http://chem-bla-ics.blogspot.com/2009/04/open-knowledge-reproducibility-in.html)
+Quick and short reminder about my [Open Knowledge: Reproducibility in Cheminformatics with Open Data, Open Source and Open Standards <i class="fa-solid fa-recycle fa-xs"></i>](https://chem-bla-ics.linkedchemistry.info/2009/04/08/open-knowledge-reproducibility-in.html)
 talk on Monday. The session is great anyway, with other talks from [Cameron](http://blog.openwetware.org/scienceintheopen/), [John](http://chembl.blogspot.com/) and
 someone from Berlin on a Open Access HTS system (which reminds me to talk about the *Open Access* and that the term is tainted).
 
-I still have a free program, other than I want to see [Google Wave](http://chem-bla-ics.blogspot.com/2009/08/social-web-does-not-wait-for-bioclipse.html)
+I still have a free program, other than I want to see [Google Wave <i class="fa-solid fa-recycle fa-xs"></i>](https://chem-bla-ics.linkedchemistry.info/2009/08/17/social-web-does-not-wait-for-bioclipse.html)
 in action (and while I have receive my invitation, I have not received a login account yet). There is a potentially interesting talk about
 *Second Generation Small Molecule Therapeutics* by 15:00. But no plans otherwise for the afternoon and/or evening.
 
diff --git a/_posts/2009-09-02-google-wave-robot-for-cdk-functionality.markdown b/_posts/2009-09-02-google-wave-robot-for-cdk-functionality.markdown
@@ -6,9 +6,10 @@ blogger-link: https://chem-bla-ics.blogspot.com/2009/09/google-wave-robot-for-cd
 doi: 10.59350/stdr4-6rm16
 tags: cdk cheminf google wave
 image: /assets/images/cdkitty.png
+modified_date: 2026-03-07
 ---
 
-I was really happy to hear early last week that I was invited to take part in the [Google Wave](http://chem-bla-ics.blogspot.com/2009/08/social-web-does-not-wait-for-bioclipse.html) beta,
+I was really happy to hear early last week that I was invited to take part in the [Google Wave <i class="fa-solid fa-recycle fa-xs"></i>](https://chem-bla-ics.linkedchemistry.info/2009/08/17/social-web-does-not-wait-for-bioclipse.html) beta,
 and received my account details this Monday, while at attending (and [speaking at](http://chem-bla-ics.blogspot.com/2009/09/open-knowledge-reproducibility-in.html)) the GDCh
 Wissenschaftsforum Chemie 2009. Yesterday was a travel day, and while working on course material for the [Pharmaceutical Bioinformatics](http://www.pharmbio.org/) course that
 uses [Bioclipse](http://www.bioclipse.net/), I set up an Eclipse environment for development of a wave robot. [Documentation](http://code.google.com/apis/wave/extensions/robots/java-tutorial.html)
diff --git a/_posts/2009-09-02-open-knowledge-reproducibility-in.markdown b/_posts/2009-09-02-open-knowledge-reproducibility-in.markdown
@@ -2,13 +2,13 @@
 layout: post
 title:  "Open Knowledge: Reproducibility in Cheminformatics with ODOSOS"
 date:   2009-09-02 00:10
-modified_date: 2026-02-28
+modified_date: 2026-03-07
 blogger-link: https://chem-bla-ics.blogspot.com/2009/09/open-knowledge-reproducibility-in.html
 doi: 10.59350/t5hgg-stt44
 tags: cheminf doi:10.5281/ZENODO.2652076
 ---
 
 Below are the slides of my presentation of last Monday (see my [earlier](http://chem-bla-ics.blogspot.com/2009/08/reminder-my-talk-in-frankfurt-on-monday.html)
-[blogs](http://chem-bla-ics.blogspot.com/2009/04/open-knowledge-reproducibility-in.html)):
+[blogs <i class="fa-solid fa-recycle fa-xs"></i>](https://chem-bla-ics.linkedchemistry.info/2009/04/08/open-knowledge-reproducibility-in.html)):
 
 [![](/assets/images/frankfurthSlides.png)](https://zenodo.org/records/2652077)
diff --git a/_posts/2009-09-04-nmrshiftdb-enters-rdfopenmoleculesnet-2.markdown b/_posts/2009-09-04-nmrshiftdb-enters-rdfopenmoleculesnet-2.markdown
@@ -5,6 +5,7 @@ date:   2009-09-04
 blogger-link: https://chem-bla-ics.blogspot.com/2009/09/nmrshiftdb-enters-rdfopenmoleculesnet-2.html
 doi: 10.59350/nv925-tje87
 tags: rdf sparql nmrshiftdb cheminf
+modified_date: 2026-03-07
 ---
 
 About 6 months ago I [reported](http://chem-bla-ics.blogspot.com/2009/03/nmrshiftdb-enters-rdfopenmoleculesnet.html) about my efforts to RDF-ize the data from the
@@ -29,7 +30,7 @@ binary debs for 5.0.12 on my laptop. With some basic Apache magic, I hooked up t
 ```
 
 Nice thing about this is, that I can set up multiple servers, allowing me to keep incompatibly licensed data sets apart (see
-[Open Data: license, rights, aggregation, clean interfaces?](http://chem-bla-ics.blogspot.com/2009/05/open-data-license-rights-aggregation.html)), which is
+[Open Data: license, rights, aggregation, clean interfaces? <i class="fa-solid fa-recycle fa-xs"></i>](https://chem-bla-ics.linkedchemistry.info/2009/05/18/open-data-license-rights-aggregation.html)), which is
 the same approach Bio2RDF is taking.
 
 The [end point](http://pele.farmbio.uu.se/nmrshiftdb/sparql) now offers about [278887](http://pele.farmbio.uu.se/nmrshiftdb/sparql?default-graph-uri=&query=SELECT+count%28*%29+WHERE+{\%0D%0A++%3Fs+%3Fp+%3Fo+.%0D%0A}&format=text%2Fhtml&debug=on)
diff --git a/_posts/2009-09-05-nmrshiftdb-rdf-1-spectra-by-inchi.markdown b/_posts/2009-09-05-nmrshiftdb-rdf-1-spectra-by-inchi.markdown
@@ -5,9 +5,10 @@ date:   2009-09-05
 blogger-link: https://chem-bla-ics.blogspot.com/2009/09/nmrshiftdb-rdf-1-spectra-by-inchi.html
 doi: 10.59350/7k8wn-jee62
 tags: nmrshiftdb sparql
+modified_date: 2026-03-07
 ---
 
-Originally, I wanted to include a SPARQL query in [my yesterdays blog](http://chem-bla-ics.blogspot.com/2009/09/nmrshiftdb-enters-rdfopenmoleculesnet-2.html)
+Originally, I wanted to include a SPARQL query in [my yesterdays blog <i class="fa-solid fa-recycle fa-xs"></i>](https://chem-bla-ics.linkedchemistry.info/2009/09/04/nmrshiftdb-enters-rdfopenmoleculesnet-2.html)
 showing how to retrieve [NMRShiftDB](http://www.nmrshiftdb.org/) spectra based on an InChIKey, but it horribly failed. I have yet to discover why. This
 morning I discovered that it is specific for that field, and that using the same thing with InChI is no problem:
 
diff --git a/_posts/2009-09-08-updated-bioclipse-sdk-eclipse-35.markdown b/_posts/2009-09-08-updated-bioclipse-sdk-eclipse-35.markdown
@@ -6,11 +6,12 @@ blogger-link: https://chem-bla-ics.blogspot.com/2009/09/updated-bioclipse-sdk-ec
 doi: 10.59350/hx839-f4h59
 tags: bioclipse eclipse java
 image: /assets/images/newBCProject2.png
+modified_date: 2026-03-07
 ---
 
 Last Friday, the Bioclipse 2.1 development series moved to [Eclipse 3.5](http://update.eclipse.org/downloads/drops/R-3.5-200906111540/eclipse-news-all.html),
 so I had to update the [Bioclipse SDK](http://wiki.bioclipse.net/index.php?title=Bioclipse_SDK) too, which
-[we developed earlier](http://chem-bla-ics.blogspot.com/2009/08/making-bioclipse-development-easier-new.html).
+[we developed earlier <i class="fa-solid fa-recycle fa-xs"></i>](https://chem-bla-ics.linkedchemistry.info/2009/08/13/making-bioclipse-development-easier-new.html).
 
 With a new Eclipse version also comes new screenshots to talk you through the process of setting up a new
 [Bioclipse manager](http://wiki.bioclipse.net/index.php?title=How_to_make_a_manager_2) plugin.
diff --git a/_posts/2009-09-10-open-chemical-data-1-nmrshiftdb.markdown b/_posts/2009-09-10-open-chemical-data-1-nmrshiftdb.markdown
@@ -6,11 +6,12 @@ blogger-link: https://chem-bla-ics.blogspot.com/2009/09/open-chemical-data-1-nmr
 doi: 10.59350/g3jct-gta96
 tags: opendata friendfeed chemistry
 image: /assets/images/ocdGroup.png
+modified_date: 2026-03-07
 ---
 
 As I reported earlier, progress is only possible of you can modify and redistribute. This is why Open Data, Open Source, and
 Open Standards are so important to us [Blue Obelisk](http://en.wikipedia.org/wiki/Blue_Obelisk) members. For data,
-[proper licensing](http://chem-bla-ics.blogspot.com/2009/05/open-data-license-rights-aggregation.html) makes these two
+[proper licensing <i class="fa-solid fa-recycle fa-xs"></i>](https://chem-bla-ics.linkedchemistry.info/2009/05/18/open-data-license-rights-aggregation.html) makes these two
 requirements possible, but more importantly, make those rights explicit. [Rich](http://depth-first.com/) is running the
 nice [Zusammen](http://zusammen.metamolecular.com/) blog, but most of his entries are **not** Open Data. Even larger
 chemistry data repositories can be vague and have seemingly contradicting statements.
diff --git a/_posts/2009-11-19-chempedia-rdf-1-sparql-end-point.markdown b/_posts/2009-11-19-chempedia-rdf-1-sparql-end-point.markdown
@@ -2,7 +2,7 @@
 layout: post
 title:  "ChemPedia RDF #1: the SPARQL end point"
 date:   2009-11-19
-modified_date: 2025-02-16
+modified_date: 2026-03-07
 doi: 10.59350/qfhff-gen31
 blogger-link: https://chem-bla-ics.blogspot.com/2009/11/chempedia-rdf-1-sparql-end-point.html
 tags: rdf sparql chempedia justdoi:10.59350/kprj3-gyg97 nmrshiftdb
@@ -44,7 +44,7 @@ json.each { it ->
 ```
 
 After uploading it into [Virtuoso](http://virtuoso.openlinksw.com/dataspace/dav/wiki/Main/VOSIndex) (now using `DB.DBA.TTLP` instead of
-[DB.DBA.RDF_LOAD_RDFXML_MT](http://chem-bla-ics.blogspot.com/2009/09/nmrshiftdb-enters-rdfopenmoleculesnet-2.html)), we can now have our
+[DB.DBA.RDF_LOAD_RDFXML_MT <i class="fa-solid fa-recycle fa-xs"></i>](https://chem-bla-ics.linkedchemistry.info/2009/09/04/nmrshiftdb-enters-rdfopenmoleculesnet-2.html)), we can now have our
 regular SPARQL fun with the data from ChemPedia. For example, list the 10 names with the most votes:
 
 ```sparql
diff --git a/_posts/2025-06-29-curation-is-an-essential-part-of-doing-research.markdown b/_posts/2025-06-29-curation-is-an-essential-part-of-doing-research.markdown
@@ -2,7 +2,7 @@
 layout: post
 title:  "Curation is an essential part of doing research"
 date:   2025-06-29
-modified_date: 2025-11-29
+modified_date: 2026-03-07
 doi: 10.59350/c4k5q-h8849
 tags: curation openscience justdoi:10.1038/455047A doi:10.1021/CI050400B nmrshiftdb
   europepmc
@@ -80,7 +80,7 @@ of:
   [the ERM indentifier database](https://nanocommons.github.io/erm-database/)
 * made RDF for supplementary information (e.g. [this NanoE-Tox spreadsheet](http://chem-bla-ics.linkedchemistry.info/2018/09/16/data-curation-5-inspiration-95.html),
   full databases, like [ChEMBL](https://chem-bla-ics.linkedchemistry.info/2011/04/21/chembl-09-as-rdf.html) and
-  [NMRShiftDb](https://chem-bla-ics.blogspot.com/2009/09/nmrshiftdb-enters-rdfopenmoleculesnet-2.html)
+  [NMRShiftDb <i class="fa-solid fa-recycle fa-xs"></i>](https://chem-bla-ics.linkedchemistry.info/2009/09/04/nmrshiftdb-enters-rdfopenmoleculesnet-2.html)
 * organized [an online ChemCuration event](https://chem-bla-ics.linkedchemistry.info/2019/10/14/chemcuration-2019-poster-conference.html) (inspired by the ISB annual meetings!)
 
 I am also curation my blog, which was [originally in blogger.com but being ported to Markdown with extra annotation](https://chem-bla-ics.linkedchemistry.info/2023/08/18/last-post-here-freebie-model-online.html).
diff --git a/_posts/2026-01-17-chemical-blogs-history.markdown b/_posts/2026-01-17-chemical-blogs-history.markdown
@@ -9,6 +9,7 @@ comments:
   host: social.edu.nl
   username: egonw
   id: 115911624045354212
+modified_date: 2026-03-07
 ---
 
 Like many awesome internet phenomena, [blogging started in the late nineties](https://en.wikipedia.org/wiki/Blog).
@@ -46,7 +47,7 @@ You can also just visit many of these blogs to relive the dynamics at the time:
 * [New Blogs #7](https://chemicalblogspace.blogspot.com/2007/06/these-are-new-blogs-that-entered.html)
 * [New Blogs #8](https://chemicalblogspace.blogspot.com/2007/10/new-blogs-8.html)
 * [New Blogs #9](https://chemicalblogspace.blogspot.com/2008/04/new-blogs-9.html) (2008)
-* [New Blogs #10](https://chem-bla-ics.blogspot.com/2009/07/new-blogs-10.html) (2009)
+* [New Blogs #10 <i class="fa-solid fa-recycle fa-xs"></i>](https://chem-bla-ics.linkedchemistry.info/2009/07/23/new-blogs-10.html) (2009)
 * [New Blogs #11](https://chem-bla-ics.blogspot.com/2009/07/new-blogs-11.html)
 * [New Blogs #12](https://chemicalblogspace.blogspot.com/2009/11/new-blogs-12.html)
 * [Cb: New Blogs #13](https://chem-bla-ics.linkedchemistry.info/2010/07/15/cb-new-blogs-13.html) (2010)
diff --git a/_posts/updateLinks.groovy b/_posts/updateLinks.groovy
@@ -16,7 +16,13 @@ mappings = [
   "2021/06/conflict-of-interest-or-why-i-am.html": "2021/06/11/conflict-of-interest-or-why-i-am.html",
   "2020/11/cito-updates-1-first-research-paper-in.html": "2020/11/01/cito-updates-1-first-research-paper-in.html",
   "2010/07/cb-new-blogs-13.html": "2010/07/15/cb-new-blogs-13.html",
+  "2009/09/nmrshiftdb-enters-rdfopenmoleculesnet-2.html": "2009/09/04/nmrshiftdb-enters-rdfopenmoleculesnet-2.html",
   "2009/08/bioclipse-and-sparql-end-points.html": "2009/08/16/bioclipse-and-sparql-end-points.html",
+  "2009/08/social-web-does-not-wait-for-bioclipse.html": "2009/08/17/social-web-does-not-wait-for-bioclipse.html",
+  "2009/08/making-bioclipse-development-easier-new.html": "2009/08/13/making-bioclipse-development-easier-new.html",
+  "2009/07/new-blogs-10.html": "2009/07/23/new-blogs-10.html",
+  "2009/05/open-data-license-rights-aggregation.html": "2009/05/18/open-data-license-rights-aggregation.html",
+  "2009/04/open-knowledge-reproducibility-in.html": "2009/04/08/open-knowledge-reproducibility-in.html",
   "2009/03/nature-chemistry-improves-publishing.html": "2009/03/19/nature-chemistry-improves-publishing.html",
   "2009/03/open-nmr-data-raw-curves-and-annotated.html": "2009/03/04/open-nmr-data-raw-curves-and-annotated.html",
   "2009/02/dbpedia-enters-rdfopenmoleculesnet.html": "2009/02/17/dbpedia-enters-rdfopenmoleculesnet.html",
