Chemblaics (pronounced chem-bla-ics) is the science that uses open science and computers to solve problems in chemistry, biochemistry and related fields.

One of the goals of my project in Cambridge is to make Oscar available as Taverna plugin (source code, Hudson build). I have progressed somewhat, but still struggling with getting the update site working.

One of the goals of my project in Cambridge


is to make Oscar available as Taverna plugin (source code, Hudson build). I have progressed somewhat, but still struggling with getting the update site working.

Oscar text mining in Taverna

Maastricht University

Part of the scientific program of the ICCS 2022.

The International Conference on Chemical Structures scientific program is online!

Later this year the ninth International Conference on Chemical Structures (ICSS) conference will be held in the Netherlands. I had the pleasure of joining this meeting, I think, eight years ago, when I was doing my PhD in Nijmegen. Mind you, I did not

 attend

the conference;

The 9th International Conference on Chemical Structures (ICCS)

There was a lot of Open Science news this week.

There was a lot of Open Science news this week. The announcement of the Google Dataset Search was one of them:    Of course, I first tried searching for “RDF chemistry” which shows some of my data sets (and a lot more):    It picks up data from many sources, such as Figshare in this image. That means it also works (well, sort of, as Noel O’Boyle noticed) for supplementary information from the Journal of Cheminformatics.

Also new this week: "Google Dataset Search"

Debugging is the process find removing a fault in your code (the etymology goes further back than the moth story, I learned today). Being able to debug is an essential programming skill, and being able to program flawlessly is not enough; the bug can be outside your own code.

Programming in the Life Sciences #19: debugging

About two weeks ago, the ChemConnector blog reported an InChIKey collosion detected by Prof. Goodman . Unlike the previous collision, this one was based solely on the graph and not on stereochemistry.

About two weeks ago, the ChemConnector blog reported an InChIKey collosion


detected by Prof. Goodman


. Unlike the previous collision, this one was based solely on the graph and not on stereochemistry. The two molecules both have the InChIKey OCPAUTFLLNMYSX-UHFFFAOYSA-N: The compounds are really different, the molecular formulas are C

 50

H

 102

O and C

 57

H

 114

O respectively.

InChIKey collision: the DIY copy/pastables

Linus’ law:  Rich of MetaMolecular works on Open Source and closed source cheminformatics solutions. ChemWriter is one product he is working on which uses JavaScript and SVG (two Open Standards), and recently asked feedback on the new version.

ChemWriter, Google Chrome, and Many Eyes in Open Source

RDF and SPARQL are two really useful Open Standards. Bioclipse-RDF is a plugin for Bioclipse that provide RDF functionality, among which using remote SPARQL end points.

RDF and SPARQL are two really useful Open Standards. Bioclipse-RDF is a plugin for Bioclipse that provide RDF functionality, among which using remote SPARQL end points. The MyExperiment team has set up an excellent RDF front end. For example, this is my MyExperiment account in RDF. The storage gets updated once every day (at this moment), but I’m sure that will become more often in the future.

Bioclipse and SPARQL end points #2: MyExperiment

In this series I will introduce the technologies behind my FOAF network.

In this series I will introduce the technologies behind my FOAF network. FOAF means Friend-of-a-Friend and  My FOAF file (draft) will give you details on who I am, who I collaborate with (and other types of friends), which conferences I am attending, what I published etc. That is, I’ll try to keep it updated. BTW, FOAF is a RDF language.

My FOAF network #1: the FOAFExplorer

A bit over two years I posted my first blog item, Chem-bla-ics , introducing the topic of my blog. In January this year I explained why I like blogging .

A bit over two years I posted my first blog item, Chem-bla-ics


, introducing the topic of my blog. In January this year I explained why I like blogging


.

My blog turned 2

Yesterday I blogged about how to include the new del.icio.us tagometer on a www.blogger.com blog , just like Improbulus did last December as I discovered later. Felix asked me how it could be done on the new www2.blogger.com template system. Well, here it is.

Yesterday I blogged about how to include the new del.icio.us tagometer on a www.blogger.com blog


, just like Improbulus did last December as I discovered later. Felix asked me how it could be done on the new www2.blogger.com template system.

The del.icio.us tagometer on www2.blogger.com

On my way back from the Taverna workshop I visited Nature HQ, as Ian reported about on Nascent. It was a (too) short meeting, but very nice to meet Euan (finally;

Lunch at Nature HQ (with Euan, Joanna, Ian and Ålf)

I was very pleased to read today that Kalzium, one of the projects that participate in the Blue Obelisk, got awarded! Cheers, Carsten!

Kalzium Wins Award; Carsten Niehaus Interviewed

Blogs come and go. Sometimes they move from one location to another. However, blogs have not been systematically archived, perhaps for work by efforts by OpenLaboraty.

Archiving blogs

December last year I proposed the use of microformats and RDFa for simple semantic markup of molecular information.

December last year I proposed the use of microformats and RDFa


for simple semantic markup of molecular information.

Chemical RDFa with Operator in the Firefox toolbar

One reason to move my blog from Blogger to a git-backed repository is that I can update links but that the version history shows exactly what change was made.

Updating links to blogs: Peter Murray-Rust

Yeah, it has been hard to miss it (see e.g. Should I join Mastodon? A scientists’ guide to Twitter’s rival). Twitter is experiencing some turbulence and Mastodon has become a very attractive, open source, community-driven, inclusive alternative. It’s been around since 2016 and there is some research literature about it already. I got my account in 2018, but did not start actively using it until earlier this year.

s/Twitter/Mastodon/g

2023 has been a long year in which a lot happens. Two EU projects ended (RiskGONE and NanoSolveIT; more about that in a later post), our group leader Chris Evelo will retire this year, the ELIXIR Toxicology Community started (see this post), the new WikiPathways website launched (see this post), and a lot, lot more.

PhD Defences: Andra Waagmeester and Marvin Martens

My research is into abstract representation of chemical information, important for other research to be performed. Indeed, my work is generally reused, but knowing which research fields my work is used in, or which societal problems it is helping solve, is not easily retrieved or determined.

Join me in encouraging the ACS to join the Initiative for Open Citations

Already 3 months ago I visited Dagstuhl for the second time. The weather was much better than in the January right before the start of the pandemic.

Biology, ACPs, lipids, cheminformatics, and Dagstuhl

Screenshot of the Open Science History group on CiteULike.

Screenshot of the

 Open Science History

group on CiteULike. Open Science has been around for some time. Before Copyright became a thing, knowledge dissemination was mostly limited by how easy you could get knowledge from one place to another. The introduction of Copyright changed this.

History of the term Open Science #1: the early days

The Royal Society of Chemistry and Wikipedia just released an interesting press release:

The Royal Society of Chemistry and Wikipedia just released an interesting press release:  This leaves me with a lot of questions. I asked these in a comment awaiting moderation:  Details on how to apply to access can be found here.

"Royal Society of Chemistry grants journals access to Wikipedia Editors"

Update 2021-02: this post is still the second-most read post in my blog. Welcome!

Update 2021-02

: this post is still the second-most read post in my blog. Welcome! Some updates: Ammar Ammar in our BiGCaT group has set up a new SPARQL endpoint. Please use and tweet. blog, or otherwise let others now how you use the ChEMBL RDF. Since this post I have blogged a lot more about ChEMBL.

 Update

: this work is now written down in this paper. I’m having a really bad month, as you can see from the number of posts.

ChEMBL 09 as RDF

AJCann posted a blog today about what he doesn’t like about Mendeley. Abhishek replied that he does not like people complain about one tool, instead of pointing out a good alternative. Mendeley has two alternatives, Zotero and CiteULike (there is also Connotea, but got behind in evolution).

AJCann posted a blog today about what he doesn’t like about Mendeley. Abhishek replied that he does not like people complain about one tool, instead of pointing out a good alternative. Mendeley has two alternatives, Zotero and CiteULike (there is also Connotea, but got behind in evolution).  Agreeing with @citeulike and @abhishektiwari, as a service provider any bad news is good news too: they provide opportunities to improve.

A list of things I miss in CiteULike

FOAF rulez: it’s RDF. With RDF comes SPARQL. SPARQL needs a query engine, however. And there comes OpenRDF which created Sesame.

FOAF rulez: it’s RDF. With RDF comes SPARQL. SPARQL needs a query engine, however. And there comes OpenRDF which created Sesame. I have to catch the train in about 15 minutes, so will not elaborate too much, but here are some Sesame 2.0.1 work: &gt; create native. Please specify values for the following variables: Repository ID [native]: foafRepo Repository title [Native store]: FOAF Repository Triple indexes [spoc,posc]: Repository created &gt;

My FOAF network #5: SPARQL-ing my network

Third in a series summarizing literature citing one of the two CDK articles. See also #1 and #2 .

Third in a series summarizing literature citing one of the two CDK articles. See also #1


and #2


. Reviews Two reviews have recently appeared which cite the CDK. Ricard Stefani has written a review in Portuguese of the many NMR-based elucidation tools on computer-aided structure elucidation. The CDK is cited as a general chemoinformatics tool. It also cites SENECA which uses CDK’s structure generators.

CDK Literature #3

Third in the series of blogs about molecules in Wikipedia without an InChI (see also #1 and #2 ). There a certainly false positives, but here’s the updated list:

Third in the series of blogs about molecules in Wikipedia without an InChI (see also #1


and #2


). There a certainly false positives, but here’s the updated list: http://www.en.wikipedia.org/wiki/AZD2171 http://www.en.wikipedia.org/wiki/Alizarin http://www.en.wikipedia.org/wiki/Allantoin http://www.en.wikipedia.org/wiki/Allylamine http://www.en.wikipedia.org/wiki/Alpha-ethyltryptamine http://www.en.wikipedia.org/wiki/Anthraquinone

Molecules in Wikipedia without InChIs #3

I just ran into BioSpider. Unlike ChemSpider, BioSpider crawls the internet (well, this list of sources really) to find information, and depending on what it finds it continues the search.

I just ran into BioSpider. Unlike ChemSpider, BioSpider crawls the internet (well, this list of sources really) to find information, and depending on what it finds it continues the search. Below is a screenshot of an intermediate point after starting with the InChI of methane:    After the search it generates a long HTML page with all the information it found on the molecule you queried for.

BioSpider: another molecule search engine

Getting back on microformats (see yesterday ), I added my hCard to the bottom of my blog:

Getting back on microformats (see yesterday


), I added my hCard to the bottom of my blog: I will likely populate it a bit more soon (after holiday in Sweden). Now, if you had the Firefox plugin Operator installed, you would have my contact information show up in your FF toolbar, like this: Note the ‘Export Contact’ button in the toolbar.

Added my hCard to my blog

A bit over 2 years ago I published a UML diagram showing the dependencies between CDK modules . Since then I lot of new modules have been defined, added or factored out from the extra module (click to zoom):

A bit over 2 years ago I published a UML diagram showing the dependencies between CDK modules


. Since then I lot of new modules have been defined, added or factored out from the extra module (click to zoom): These kind of diagrams help us maintain the library, and apply some design goals, as explained in the first post on this.

CDK Module dependencies #2

Mike released Operator 0.8, which picks up RDF (RDFa en eRDF) from HTML pages, and adds actions to it. I blogged earlier about the beta and wrote a script for it for chemical RDFa . At this moment, Chemical blogspace and RDF for Molecular Space (see this blog ) are using chemical RDFa to semantically markup molecular information.

Mike released Operator 0.8, which picks up RDF (RDFa en eRDF) from HTML pages, and adds actions to it. I blogged earlier about the beta


and wrote a script for it for chemical RDFa


. At this moment, Chemical blogspace and RDF for Molecular Space (see this blog


) are using chemical RDFa to semantically markup molecular information.

Operator 0.8 released: a new Sechemtic user script

I do not care about physical and chemical properties in Wikipedia, as I can easily extract them from other sources. The main value of Wikipedia for molecules is, I think, that it describes the history of a molecule.

Molecules in Wikipedia

Second in a series of articles summarizing articles that cite one of the main CDK articles for CDK News. The first CDK Literature was already half a year ago, so it was about time.

Second in a series of articles summarizing articles that cite one of the main CDK articles for CDK News. The first CDK Literature


was already half a year ago, so it was about time. Bioclipse Nothing much I have to say about that. Just browse my blog and you’ll see that it heavily uses CDK, JChemPaint and Jmol. See also the Bioclipse blog.

CDK Literature #2

Some time ago I wrote a small Perl script to convert a decision tree created with Weka in the ARFF format to Java source code, for use in the ionization potential prediction in CDK. The advantage is that Weka is no longer used are runtime, and that there is no model that needs to be loaded and interpreted. Instead, it is simple Java code that does the work, much faster.

Weka Decision Trees to Java Conversion

The 2nd German Conference on Chemoinformatics started yesterday, with two chemoinformatics tutorials: one on industrial chemoinformatics (I saw this presentation before… not sure when), with a good overview on integrating different information sources;

German Conference on Chemoinformatics 2006: Day 1 and 2

The Self-organizing map (SOM) is a popular (again) and intuitive non-linear mapping method: it transforms a multidimensional space into two dimensions (normally: they are so easy to visualize). Latino and Aires-de-Sousa published a paper that uses this method to analyze the whole KEGG pathway database: Genome-Scale Classification of Metabolic Reactions: A Chemoinformatics Approach (DOI: anie.200503833).

The Self-organizing map (SOM) is a popular (again) and intuitive non-linear mapping method: it transforms a multidimensional space into two dimensions (normally: they are so easy to visualize). Latino and Aires-de-Sousa published a paper that uses this method to analyze the whole KEGG pathway database:

 Genome-Scale Classification of Metabolic Reactions: A Chemoinformatics Approach

(DOI: anie.200503833). The method is based on earlier

Mining the KEGG pathway database with self-organizing maps

The OD part of ODOSOS is getting more and more attention, and it seems that Peter’s Open Data battle is paying off (see his original OpenData article in Wikipedia): an open data specific license has reached the beta stage (see this announcement).

The OD part of ODOSOS is getting more and more attention, and it seems that Peter’s Open Data battle is paying off (see his original OpenData article in Wikipedia): an open data specific license has reached the beta stage (see this announcement).  The idea behind this licenses seems to come down to:  I am looking forward how this license will be picked up by the community. PubChem may be a good candidate to use this license;

Open Data getting more recognition

A few days back, Classpath 0.90 was released, the first release after the 0.20 release. Earlier Classpath releases could run the rendering engine , but running the application failed so far .

A few days back, Classpath 0.90 was released, the first release after the 0.20 release. Earlier Classpath releases could run the rendering engine


, but running the application failed so far


. Today it hit Debian unstable, so upgrade my sid32 chroot and had Cacao run Jmol. I had some memory issues opening a small molecule (4-methyl-2-pentyne), and the rendering speed was a factor 100 or so slower than Sun’s JVM, but it runs!

Classpath 0.90 makes the Jmol application run

The beta has been using Jmol as one of the viewers for ages already, but this beta is no longer: it’s the new interface for the PDB database.

The PDB protein database uses Jmol

Yesterday I reviewed an article which published a QSPR model which looked something like:

Yesterday I reviewed an article which published a QSPR model which looked something like: \[y = 151 + 50p1 - 12p2 - 0.006p3\]  with quite OK prediction results (R=0.9880). But I was not quite comfortable with the coefficient for the \(p3\) variable. The article did not calculate significances for the coefficients, so it was not obvious from the article wether is was useful to include them. I then looked at the range for p3, which was 110-150;

When to stop including QSAR model variables...

About two years ago a student started with me to work on the use of 1D NMR and IR spectra in quantitative structure-activity relationship (QSAR) work, with the goal to show that these spectra contain 3D information relevent to QSAR models. It is known that these spectra depend on the 3D conformation of the molecule.

1D NMR Spectra do not work in QSPR

I drop in on the #classpath channel of freenode.net IRC network, where the #cdk channel runs too. The #classpath channel is for the Classpath project which is developing the free Java libraries used by most open source virtual machines.

I drop in on the #classpath channel of freenode.net IRC network, where the #cdk channel runs too. The #classpath channel is for the Classpath project which is developing the free Java libraries used by most open source virtual machines. A Slashdot.org item was mentioned “Java Is So 90s”. It lead to a funny discussion about what that would make C/C++ and Fortran.

Math libraries for Java?

One thing I was still missing in BioHackrXiv was a place with an overview of: 1. all biohackathons, 2. all preprints linked to a biohackathon, 3. an RSS feed for new papers of a biohackathon.

All BioHackrXiv preprints and BioHackathon RSS feeds

A lot is happening. If you have been following this project more closesly, you may have already seen some interesting updates, but I will post it here too. First, a quick recap. In March I started a new Blue Obelisk project to collect CCZero IUPAC names from primary literature (paper still pending). It turned out we can automate that, while legally not violating any laws or licenses.

One Million IUPAC names #4: a lot is happening

Source: Wikipedia. CC-BY-SA April this year I blogged about an important SPARQL query for many chemists: getting CAS registry numbers from Wikidata.

Source: Wikipedia. CC-BY-SA April this year I blogged about an important SPARQL query


for many chemists: getting CAS registry numbers from Wikidata. This is relevant for two reasons: CAS works together with Wikimedia on a large, free CAS-to-structure database Wikidata is CCZero The original effort validated about eight thousand registry numbers, made available via Wikipedia and the Common Chemistry website.

New Edition! Getting CAS registry numbers out of WikiData

I arrived at the EBI last night for the Taverna workshop, during which the design of Taverna2 is presented and workflow examples are discussed. Several ‘colleagues’ from Wageningen and the SARA computing center in Amsterdam are present, along with many other interesting people. This afternoon is my presentation.

Taverna Workshop, Hinxton, UK

Johannes joined a Bioclipse Workshop a long time ago, and introduced the participants to the idea of using XMPP (aka Jabber) for asynchronous web services. SOAP is commonly user to run webservices over HTTP, but via (SMTP) email and XMPP is possible too (see SOAP over XMPP). Using HTTP as transport layer has problems. The biggest problem, is possibly that HTTP connections are timed out, e.g. by intermediate router.

Next generation asynchronous webservices

The MetWare components are slowly coming together. The RAW data upload facility prototype went into beta stage, while the SKOS has proven really useful for various things.

The MetWare components are slowly coming together. The RAW data upload facility prototype went into beta stage, while the SKOS has proven really useful for various things. Because of being compatible with various Java libraries and tools, we decided some time ago to use Java. We also wanted to start of with a HTML GUI to MetWare, which led us to Java Server Faces.

MetWare, SKOS and Java Server Faces

I just want to drop this here. There are various ways to make BridgeDb identifier mapping files.

Making BridgeDb Derby files with Groovy

As part of our Dutch Research Council (NWO) Open Science grant, we organized a Chemistry Development Kit User Group Meeting (#CDK25UGM), of which yesterday was the “conference” day, and today a hackathon.

As part of our Dutch Research Council (NWO) Open Science grant, we organized a Chemistry Development Kit User Group Meeting (#CDK25UGM), of which yesterday was the “conference” day, and today a hackathon. I opened the session with a few slides welcoming everyone at Maastricht University (and our Dept of Translational Genomics, and explaining the NWO grant.

cdk2024 #4: Chemistry Development Kit User Group Meeting - Day 1

About a year ago I started migrating my blogger.com blog to a git-version-controlled, Markdown-based blogging platform. I have to say, it has been a happy year. It actually is awesome to port old blog posts (follow that here) and to see what I have been working on some 17, 18 years ago.

About a year ago I started migrating my blogger.com blog to a git-version-controlled, Markdown-based blogging platform. I have to say, it has been a happy year. It actually is awesome to port old blog posts (follow that here) and to see what I have been working on some 17, 18 years ago. I do have a nasty bug to fix that causes the conversion of the Markdown to HTML is scaling badly.

GoatCounter, Rogue Scholar and more new things

Today I received news on the Jmol user list that Lubert Stryer’s Biochemistry replaced the proprietary Chime with the open source Jmol. The third edition from which I learned biochemistry in my first year at the university did not feature a CD with live figures, but I am very thrilled to see a program on which I have actively programmed hit a text book I used myself in the past.

Today I received news on the Jmol user list that Lubert Stryer’s Biochemistry


replaced the proprietary Chime


with the open source Jmol. The third edition from which I learned biochemistry in my first year at the university did not feature a CD with live figures, but I am very thrilled to see a program on which I have actively programmed hit a text book I used myself in the past.

Open source Jmol hits student text book Biochemistry

This is the best news I heard in weeks! The US Patent and Trade Offfice spoke with open source representatives about ways to deal with open source software as prior art. Apparently, their problem was how to be sure about release dates of open source, and authoritative sites like SourceForge.net, FreshMeat.net help a lot here, which extensive logging of releases.

USPTO considers open source software prior art

One of the Classpath developers pointed me to their CVS statistics when I asked them how actively their project is currently developed, i.e. the number of active developers.

One of the Classpath developers pointed me to their CVS statistics when I asked them how actively their project is currently developed, i.e. the number of active developers. The pages are generated with StatCVS, and I ran it one the CDK too. I knew I did a lot of work on the CDK, but never realized that 62.7% of the commits were mine! Keep in mind, though, that a lot of these commits are for code maintainance!

StatCVS on CDK

For some weeks now I have been thinking about bug 1309731: “ModelBuilder3D overwrites Atom IDs”. The ModelBuilder3D is a complex piece of source code, reusing many other parts of the CDK, including atom type perception.

For some weeks now I have been thinking about bug 1309731: “ModelBuilder3D overwrites Atom IDs”. The ModelBuilder3D is a complex piece of source code, reusing many other parts of the CDK, including atom type perception. Somewhere in October, however, I found that Taverna could not create 3D models and convert these into reasonable CML because the Atom ID’s were messed up. So the question is, where did the ModelBuilder3D do this?

CDK Debug classes and fixing the ModelBuilder3D bug

Tobias commited Jumbo 5.0 to CDK CVS, so that the CDK is now again up to date with the latest CML library. Note that Jumbo 5.0 requires Java 5.0.

Tobias commited Jumbo 5.0 to CDK CVS, so that the CDK is now again up to date with the latest CML library. Note that Jumbo 5.0 requires Java 5.0.  At first all JUnit tests seems to work, but apparently the CML2Writer tests were skipped because they were only run when Java 1.4 was found. I updated the test for the a appropriate Java version, and then it turned out that most tests fail.

Jumbo 5.0 and CML support in CDK

Stefan has done an excellent debugging week on JChemPaint, while I have been late with a 2.1 release. Anyway, I’ve just uploaded a Java 1.4 compiled JChemPaint 2.1 series release. I was told the (reported) bug count is down to one, so I expect to see the next stable branch to be released soon (2.2 series).

Stefan has done an excellent debugging week on JChemPaint, while I have been late with a 2.1 release. Anyway, I’ve just uploaded a Java 1.4 compiled JChemPaint 2.1 series release. I was told the (reported) bug count is down to one, so I expect to see the next stable branch to be released soon (2.2 series).  But what after JChemPaint 2.2 gets released? Will a 2.3 developers branch be opened?

About JChemPaint's future and todays 2.1.5 release

KDE 3.5 was released with lots of changes. SuperKaramba is now a standard KDE application and is neatly integrated. It allows embedding themelets on your desktop background.

KDE 3.5 was released with lots of changes. SuperKaramba is now a standard KDE application and is neatly integrated. It allows embedding themelets on your desktop background. It shows several themelets: the weather, a calender, a toolbar with applications, a FoldingAtHome monitor


, the contents of the clipboard, the music that is playing (Cake) and a simple todo list. All customizable up to the pixel.

KDE 3.5 is out

Doesn’t happen often, but my machine crashed two hours ago. Not a big deal, because I have my important files in SVN. Oh wait, SVN had a commit in progress during the crash. So, svn recover. Mmmm… doesn’t work either. OK, SVN FAQ: try db_recover. That worked. No, it did not: svn commit still not working for the files I was trying to commit.

Machine crash; SVN went along

Some weeks back there was the CDK5AW , the CDK 5th anniversiry workshop. A small group of international open source chemo-, bioinformatics software developers met, among which two from Sweden.

Some weeks back there was the CDK5AW


, the CDK 5th anniversiry workshop. A small group of international open source chemo-, bioinformatics software developers met, among which two from Sweden. It was then decided to generalize their work resulting in Bioclipse: https://www.bioclipse.net/ It’s heavily using the Eclipse Rich Client Platform


, making additional plugins trivial.

Bioclipse: the chemo-/bioinformatics workbench

Some time ago Rajarshi Guha introduced R bindings for the CDK (see his CDK News articles), and today I tried to install his rcdk package that makes it happen.

Some time ago Rajarshi Guha introduced R bindings for the CDK (see his CDK News articles), and today I tried to install his rcdk package that makes it happen. However, it requires SJava which compiled fine on other machines, but not on my AMD64 machine. The problem seems to be related to the GNU GCC 4.0 compiler I have installed.

R/CDK install fails on GCC 4.0 systems

Less then three months before the end of my contract of my PhD project. And not nearly done yet. Weekends are now spend on wrapping up bits of experimental research into something like a coherent article. And even lot’s of calculations to do to answer the open questions. FreeMind is helping me organize thoughts.

Less then three months before the end of my contract of my PhD project. And not nearly done yet. Weekends are now spend on wrapping up bits of experimental research into something like a coherent article. And even lot’s of calculations to do to answer the open questions. FreeMind is helping me organize thoughts. Opensource chemoinformatics is a welcomed diversion now and then.

Wrapping up...

This week there was an interesting article in the Dutch Intermediar about viagra. They cite an article in Environmental Conversation and state that it saves the environment as it greatly reduced the market for animal parts from the traditional chinese medicine that address the same problem as viagra does.

This week there was an interesting article in the Dutch Intermediar about viagra. They cite an article in Environmental Conversation and state that it saves the environment as it greatly reduced the market for animal parts from the traditional chinese medicine that address the same problem as viagra does.

 Viagra: good for the environment, good for you! ;)

You don’t see this often, though.

Viagra saves the environment

This is a series of two posts repeating some content I wrote up back in the Bioclipse days (see also this Scholia page). They both deal with something we were facing: restructuring of version control repositories, while actually keeping the history. For example, you may want to copy or move code from one repository to another.

Bioclipse git experiences #2: Create patches for individual plugins/features

Found my way back to my room a few kilometers from the San Francisco city center, after a third day at the WikiPathways 2018 Summit at the Gladstone Institutes in Mission Bay, celebrating 10 years of the project, which I only joined some six and a half years ago. The Summit was awesome and the whole trip was awesome. The flight was long, with a stop in Seattle.

Two presentations at WikiPathways 2018 Summit #WP18Summit

Slice of the spreadsheet in the supplementary info.

Data Curation: 5% inspiration, 95% frustration (cleaning up data inconsistencies)

It takes effort to move scholarly publishing forward. And the traditional publishers have not all shown to be good at that: we’re still basically stuck with machine-broken channels like PDFs and ReadCubes. They seem to all love text mining, but only if they can do it themselves.

It takes effort to move scholarly publishing forward. And the traditional publishers have not all shown to be good at that: we’re still basically stuck with machine-broken channels like PDFs and ReadCubes. They seem to all love text mining, but only if they can do it themselves. Fortunately, there are plenty of people who do like to make a difference and like to innovate. I find this important, because if we do not do it, who will.

Two conference proceedings: nanopublications and Scholia

Doing searches in RDF stores is commonly done with SPARQL queries. I have been using this with the semantic web translation of WikiPathways by Andra to find common content issues, though sometimes combined with some additional Java code. For example, find PubMed identifiers that are not numbers.

Two Apache Jena SPARQL query performance observations

In 2010 Samuel Lampa and I started a pet project: collecting pKa data: he was working on RDF extension of MediaWiki and I like consuming RDF data. We started DrugMet. When you read this post, this MediaWiki installation may already be down, which is why I am migrating the data to Wikidata. Why?

In 2010 Samuel Lampa and I started a pet project: collecting pK

 a

data: he was working on RDF extension of MediaWiki and I like consuming RDF data. We started DrugMet. When you read this post, this MediaWiki installation may already be down, which is why I am migrating the data to Wikidata. Why?

Migrating pKa data from DrugMet to Wikidata

If you are a scientist you have heard about the ORCID identifier by now. If not, you have been focusing on groundbreaking research and isolated yourself from the rest of the world, just to make it perfect and get that Nobel prize next year.

Chemistry Central and the ORCID identifier

I previously wrote about the JavaScript Object Notation (JSON) which has become a de facto standard for sharing data by web services. I personally still prefer something using the Resource Description Framework (RDF) because of its clear link to ontologies, but perhaps JSON-LD combines the best of both worlds.

I previously wrote about the JavaScript Object Notation (JSON) which has become a de facto standard for sharing data by web services. I personally still prefer something using the Resource Description Framework (RDF) because of its clear link to ontologies, but perhaps JSON-LD combines the best of both worlds. The Open PHACTS API support various formats and this JSON is the default format used by the ops.js library.

Programming in the Life Sciences #20: extracting data from JSON

I think the authors of the Open PHACTS proposal made a right choice in defining a small set of questions that the solution to be developed could be tested against. The questions being specific, it is much easier to understand the needs. In fact, I suspect it may even be a very useful form of requirement analysis, and makes it hard to keep using vague terms.

I think the authors of the Open PHACTS proposal made a right choice in defining a small set of questions that the solution to be developed could be tested against. The questions being specific, it is much easier to understand the needs. In fact, I suspect it may even be a very useful form of requirement analysis, and makes it hard to keep using vague terms. Open PHACTS has come up with 20 questions (doi:10.1016/j.drudis.2013.05.008;

Programming in the Life Sciences #17: The Open PHACTS scientific questions

Yesterday, I received a letter from the Association of Universities The Netherlands (VSNU, @deVSNU) about Open Access. The Netherlands is for research a very interesting country: it’s small, meaning we have few resources to establish and maintain high profile centers, we also believe strong education benefits from distribution, so we we have many good universities, rather than a few excelling universities.

On Open Access in The Netherlands

I am happy that I got my first research grant awarded (EU FP7), which should start after all the contracts are signed, etc, somewhere early 2014. The project is about setting up data needs for the analysis of nanosafety studies. And for this, I have the below two position vacancies available now.

Looking for a PhD and a Postdoc to work on Open Science Nanosafety

Never underestimate the power of lack of coding standards in code obfuscation. Just try randomly to read code you wrote a year ago or four years ago. You’ll be surprised with what you find. Coding standards are like the grammar in writing: they ensure that our message gets understood.

Programming in the Life Sciences #8: coding standards

The “Emerging practices for mapping and linking life sciences data using RDF” (doi:10.1016/j.websem.2012.02.003) is now available online, where I contributed a section on the original workflow for creating ChEMBL triples, and contributed to the section about open licensing, referring to CCZero and the Panton Principles. Happy reading!

"Emerging practices for mapping and linking life sciences data using RDF"

Update

: this work is now described in this paper


. Last week, ChEMBL 13 was released, with even more data, data fixes, etc. Since my RDF for ChEMBL 09


my workflow has become more solid and uses more common ontologies, started using more common ontologies and ontologies I just like, such as CHEMINF and CiTO.

ChEMBL 13 as RDF

Readers of my blog know I have been using the Citation Typing Ontology, CiTO (doi:10.1186/2041-1480-1-S1-S6). I allows me to see how the CDK is cited and used . CiteULike is currently adding more CiTO more functionality, which they started doing almost one and a half years ago.

Readers of my blog know I have been using the Citation Typing Ontology, CiTO (doi:10.1186/2041-1480-1-S1-S6). I allows me to see how the CDK is cited and used


. CiteULike is currently adding more CiTO more functionality, which they started


doing almost one and a half years ago.

chem-bla-ics

Jmol's FAH team in Top 800

InChI meta data with kfile_chemical

CDK-Taverna fully recognized

CIA statistics for Blue Obelisk

Chem-bla-ics

Single PDFs for CDK News articles