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

Egon Willighagen

Last night I upgraded the software behind Chemical  blogspace, to the version online on Google Code, though I needed the help from Eaun  to get paper titles correctly picked up for ACS journals.

Updated Chemical Blogspace Layout and Software

Some time ago I blogged about the ChildResourceCreator extension point in Bioclipse and hinted as using that for PDB files. which contain 3D molecular models, sequences and bibliographic information.

Complex PDB documents using the Bioclipse ChildResourceCreator

I plan to do a daily coverage of the Chemistry Development Kit Bug Squash Party (BSP). While Stefan was working hard to get the wiki machine back online after a hard-disc crash, Rajarshi, Miguel and me have been working hard. Miguel started to work on missing JUnit tests for bugs reported on SourceForge and Rajarshi fixed PMD, JavaDoc and other problems.

CDK Bug Squash Party - Day 1

Bernard Munos at Eli Lilly &amp; Co. wrote up a lengthy analysis on open source in drug discovery in Nature Reviews Drug Discovery: Can open-source R&amp;D reinvigorate drug research?

"Jmol and the CDK add powerful chemical capabilities", says Munos in Nature Reviews Drug Discovery

Martin Szugat reported that a beta for BioJava 1.5 has been released. New features include: a new biojavax package with extension on the basic functionlity, such as the RichSequence.IOTools and the RichSequence object; a genetic algorithm library; features that allow manipulation of 3D structure files and objects; and non-HMM implementations of the NW and SW alignment algorithms.

BioJava 1.5 beta released

In reply to interesting comments to my previous blog on Strigi and xAttr support in KDE4, I would like to suggest the following mockups, which I would find very useful. The deal with the ability to store keywords, for example, not but necessarily using xAttr. I have no idea on how to implement these mockups, so any help or pointers are appreciated.

KDE4 keyword support mockups

Peter Corbett from Peter Murray-Rust’s group at the Unilever Cambridge Centre for Molecular Informatics visited Christoph Steinbeck’s junior Research Group on Molecular Informatics at the CUBIC today, and spoke about the status of Oscar3, a chemistry text mining program with the Artistic License.

Text mining for chemistry using OSCAR3

This evening I have been looking at with the KNOPPIX customization howto, and ran many of the interesting commands. I’ve setup a environment with Kalzium, OpenBabel, CDK, jython, PyMOL, and for development I included gcj and Eclipse. At some later point I will include kfile_chemical too, but I want to make a deb package first.

The goal: a live chemblaics CD

Maastricht University

Ten simple rules for getting started on Twitter as a scientist

Before we go into the learning bit, let’s just revisit what a

 version of record

is. Wikipedia describes it as “the fully copyedited, typeset and formatted copy of a manuscript as published” (with two references). Basically, in the whole scheme of research output, it is a

 release

. Is is a tagged version of the output, allowing people to discuss that version specifically, so that we do not run into endless “oh, but I meant

Version of record, and what Open Access must learn from Open Science

The announcement of the Panton Principles  is the  big news today, though Peter already spoke about them in May last year (see coverage on FriendFeed and Twitter). The four principles list in their short versions: When publishing data make an explicit and robust statement of your wishes. Use a recognized waiver or license that is appropriate for data.

Open Data: the Panton Principles

Just wanted to make sure this news made it to the Blue Obelisk Planet too: David Strumfels reported that he extended MS-Excel with CDK functionality . I wonder how difficult it would be to do this with Kspread or Gnumeric?

A chemistry extension for spreadsheet(s)

There was some talk about the history of chemoinformatics toolkits by Noel and Andrew, which made me wonder on the exact history of Jmol and JChemPaint.

JChemPaint history: CML patches in 1999

Unit testing is important when developing source code. JUnit provides a library to facilitate this in Java, and Eclipse had the functionality to run JUnit tests. Even better, it allows you to run single JUnit tests, even in debug mode:    Just open the java class in your Package Explorer, right click on the JUnit method you want to run, then pick Run As or Debug As, and then JUnit test.

Running single JUnit tests in Eclipse

Because I was struggling hard with default values for cdk.interfaces fields, I did not have time to write up the Bug Squash Party report for day 3 (see also day 1 and day 2). But here it is. Day 3   Kai worked hard on getting the cdk.interfaces API cleaned up, as agreed upon earlier. Christian added a test for the RMSD calculator (see getAllAtomRMSD()), and cleaned up his code a bit.

CDK Bug Squash Party - Day 3 and 4

Mix one of the oldest and one of the latest computer technologies, and you get FoX (BSD license), a Fortran library for reading and writing Chemical Markup Language, and thus XML.

Fortran and XML: FoX reads and writes CML

Recently, a second beta of Java 6 was released, which triggered a patch for the Debian java-package package. It was a Bioclipse bug report today, however, which made me patch my java-package setup and install the beta. So, next thing was to try to get the CDK compile with the Java 6 beta.

CDK and the Java 6 beta

Technorati is nice in several ways, one being the feature to set up a watchlist. I have set watches on

 chemoinformatics, Jmol, Bioclipse

and a few more. This allows me see the latest blog items on these topics. Often, the point to Asian blogs, mostly Chinese and Japanese, which I mostly find hard to read.

BlueObelisk components in Japanese

With chemometrics in mind (QSAR, data mining, …), I have started working on matrix support in Bioclipse, because the matrix is the important step between (bio-)molecular content and statistical analysis. I implemented this such that the actual matrix implementation can be freely chosen, that is, bc_statistical provides a IMatrixImplementation extension point.

Matrix support in Bioclipse

CompLife’06 started today in Cambridge, UK. About 80 people are attending the meeting, and topics range from systems biology to QSAR. This evening there was a free software session mostly focussing on opensource software.

CompLife'06 - Day 1

NanoWiki 5

GPML files for Homo sapiens pathways

ChemPedia as RDF

Metabolite BridgeDb ID Mapping Database (20240903)

MOESM1 of PubChemRDF: towards the semantic annotation of PubChem compound and substance databases

MOESM1 of XMetDB: an open access database for xenobiotic metabolism

The ChEMBL database as linked open data

PSnpBind: a database of mutated binding site protein–ligand complexes constructed using a multithreaded virtual screening workflow

Open Science doesn’t make publishing easier. That that’s all for the better: our research efforts are complex, so why should the publishing be. Sure, I am

 not

talking about references formatting or moving the Methods section to the right location, or some silly statement that all authors agree with the manuscript when you are the only author. No, let’s talk about data. What should you publish? How, and when?

Additional files, data, datasets, databases, and published data

Research Output Management

A large collection of bioinformatics question-query pairs over federated knowledge graphs: methodology and applications

Jerven Bolleman

 et al.

recently published a great preprint about how to use RDF to give SPARQL queries context by linking it (semantically) with metadata. The context includes keywords, the SPARQL endpoint the query can be run against, and a human-oriented description of the query.

SPARQL examples: SIB model, software, and patches

David Strumfels posted news about the Useful Chemistry CMLRSS feed . He explains how this feed can be accessed using Jmol and Bioclipse. The latter are accompanied by two AVI movies: one about creating a new OPML file, and one about accessing the CMLRSS file from the OPML.

AVI movies of CMLRSS howto in Bioclipse

The x-odus continues and there is a wave of researchers moving from X to another walled-garden called Bluesky. This is good and bad. First, it is good that people are leaving X (imho) and it is good that they move to a platform that supports open standards, the AT Protocol. But I am less sure, about moving to another closed source platform. I prefer Mastodon.

Mastodon, RSS, BlueSky

I noted earlier this week that

 [d]uring the week [in Oxford ], someone (name and address is know at the editorial office) commented on the fact that my blog posts are somewhat difficult to follow;

The Molecular Chemometrics Principles #2: be clear in what you mean

ケムインフォマティクスに虚空投げ runs a story on how to calculate geometrical properties of a 3D structure using CDK’s ForceFieldTools. This class contains a few methods to calculate distances between atoms and angles between bonds. This tools class is special as it uses vecmath GVector objects, which just contain atomic coordinates, likely suitable for extensive computation, as expected in CDK’s force field implementation.

Calculating geometrical properties with the CDK

Just before the end of the year, the

 Wikidata subsetting: approaches, tools, and evaluation

paper by Seyed Amir Hosseini Beghaeiraveri

 et al.

got published (doi:10.3233/SW-233491). I am really excited our group (i.e. Ammar and Denise) has been able to contribute to this. I think it also is a great example of the power of hackathons to bring together people.

New paper: “Wikidata subsetting: approaches, tools, and evaluation”

Joerg Wegner recently blogged about

 Chemogenomics: structuring the drug discovery process to gene families

by C.J. Harris and A. P. Stevens in Drug Discov Today (DOI: 10.1016/j.drudis.2006.08.013). This review article provides a nice overview of a trend in mathematical modelling of the interaction of small organic molecules with proteins, often referred to as QSAR.

Are chemogenomics and proteochemometrics the same?

We all know chemical space; Chemical blogspace (Cb) is different: it is the chemistry discussed in blogspace. Cb is build on the opensource software of Postgenomic.com which I bloged on before. The now running Cb aggregates 19 blogs and, like the original, extracts linked (cited or reviewed) articles from literature. The system is beta, but I am happy about it already that I mention it now.

Chemical blogspace

Chemical Archeology (see Christoph’s comment) is the process of extracting chemical information from old journal articles. Some time ago, Peter Corbett from the group of Peter Murray-Rust visited the CUBIC to talk to us about Oscar3 which can do just that. That day, we already hooked OPSIN into Bioclipse .  Oscar3, however, is capable of more then the name2structure of OPSIN (see also 10.1039/b411033a;

Chemical Archeology: OSCAR3 to NMRShiftDB.org

Recently, a new generation of Chemical Markup Language CML users seem to hit the learning-curve-wall; there seems to be a niche in explaining the use of CML, so here goes. My new (third) blog will discuss frequently and less frequently asked questions about the use of CML.

CML Explained

I started a spin-off blog earlier this week: kemistry desktop environment. It will deal with integration of chemistry on opensource desktops, with KDE as one of them. Today, it features an overview of earlier blogs on the subject in this new blog.

New chemistry-on-the-desktop blog

Timo Hannay blogged  in Nature’s Nascent blog  about the Open Text Mining Interface (OTMI), which is “a suggestion from Nature about how we might achieve text-mining and indexing purposes”. The idea is that each article has a link pointing to a machine readable file containing raw data about (and from?) the article.

Open Text Mining Interface and Bioclipse

Rajarshi Guha  has set a nightly build service  for the Chemistry Development Kit (CDK). The output is pretty, but information rich: it includes results for the JUnit test, DocCheck, and PMD. The compiled jar and the corresponding JavaDoc can be downloaded, offering a cutting edge distribution for users.

Nightly CDK builds now available

Together with Christoph, Christian and Jerome, I will be representing the Blue Obelisk movement on the first First Workshop on Chemoinformatics in Europe with the topic

 Research and Teaching

. Though I wonder what this theme excludes? Development? Can’t imagine that commercials companies will not be represented as usual. Moreover, it will likely include some bioinformatics too, unless you consider that to deal with sequences only.

Blue Obelisk in Obernai at Chemoinformatics in Europe

If you have read my previous post and visited that other blog, you might have noted the Technorati keywords . Or tags, really, as explained in this rel=“tag” microformat. Adding them to blog items, will enable indexing by Technorati, one of the bigger blog search engines. So, from now on, you’ll see these tags in my items too, hoping they don’t get annoying.

Tagging blog items

Update: this work is now described in this paper.

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

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

One of the things I had not fully figured out up to today, was how to configure my Kubuntu system to easily view DVDs on our TV, using my NVIDIA’s TV-OUT. I’ve seen xorg.conf files that define a X11 server for the monitor and a second for the TV, and files that use TwinView. Now, I did not really like the way first option worked, so tried the second.

Kubuntu, XRandR and TV-OUT

The code clean up after CDK’s interfaces transition is in progress, and two CDK modules are now independent of the

 data

module. After doing the

 core

module , the standard was next, and I finished this yesterday. The dependencies in CVS now look like (click it to get a larger view): IMAGE LOST This UML diagram was made with Umbrello, and the source is in XMI in CVS.

UML diagram of CDK module dependencies

OK, just back from the first German Chemoinformatics Conference, which I enjoyed very much. A rather interesting program, and lots of interesting posters too. You can read the programme online, and will not spend too many words on that (at least not now). But what I will do is point out some interesting posters here. One poster was on the Molecular Query Language (MQL) by Ewgenij Proschak from Frankfurt.

Back from the 1st GCC

Method for the computational comparison of crystal structures

This sunday starts the first German Chemoinformatics Conference  in Goslar. It’s an interesting programme , with presentations on the InChI, PubChem, 25 years of chemoinformatics, the chemical semantic web, and much more. Among these presentations is mine, on comparing crystal structures (PDF ) and deducing cell parameters. But I’m having a poster on QSAR too.

Going to the German Chemoinformatics Conference

The Jmol FAH team  has just entered the Top 800 of most active Folding@Home  teams. And they started monitoring contributions on a user level. Thus, I can now see how active I am within the team. And so can you! Join the team, and let’s get into the Top 500!

Jmol's FAH team in Top 800

The Dutch version of the Google Summer of Code, Programmeerzomer.nl, announced today the five students participating. I was happy to see that Rob Schellhorn was selected with his project proposal for a Ghemical plugin for Bioclipse. Like in the Google original, both the student and the mentoring organization are funded, 3600 and 400 euro respectively.

Dutch Summer of Code sponsors a Bioclipse project

With some help, I got the kfile stream analyzer for Strigi working. This means that Strigi will now index the meta data fields defined by the kfile-chemical plugins. The problem why it was not working earlier, was that it segfaulted on every creation of KDE classes. That’s something I really hate about C/C++: the lack of stack traces, though valgrind was helpful. It turned out that adding the below line fixed all.

Strigi gets kfile plugin support

Classpath 0.91 is released with 1.45 million lines of code and with 98.96% coverage of Java 1.4.2, and 99.82% of java.swing. Or, as Dave calls it: 0.91 rocks! JChemPaint runs again  (they fixed the XML parsing problem), and  Jmol still runs  , but slow. I also tested Taverna which now also starts up, but has an XML parsing error too: Exception occured whilst loading RDFS!

Taverna runs with Classpath 0.91

November last year, I reported my plans  to develop a live CD with all our favorite chemo- and bioinformatics software. Bioclipse requires Java5 and sort of still depends on the Sun JVM (I will experiment with classpath-generics later), but is now distributable with operating systems.

A live life-sciences CD

Conference season is nearing. And just in time, Postgenomic.com  added a conferences map  showing locations of upcoming and recently finished conferences. Oh boy, do I want to set this up for chemoinformatics too! Postgenomic.com makes use of the rel=“conference” attribute  for the  element.

Postgenomic.com maps upcoming conferences

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

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.

CiTO / CiteULike: publishing innovation

Yesterday I arrived in Oxford, after a 3.5 hour bus transfer from London Stansted. Long, boring ride (though I might have seen a few red kites , but seeing that they were near extinct, I am wondering what other large bird of prey has strong split tail like a swallow). Showed once more that the UK infrastructure has hardly changed since the 19th century. Enjoying an undergraduate room at one of the colleges.

Oxford...

Like yesterday I will give short overview of things done at the Chemistry Development Kit Bug Squash Party (BSP). I think Stefan was the only to fix and close a bug report yesterday.

CDK Bug Squash Party - Day 2

The meetings in and around Oxford were great! I already wrote that the Predictive Toxicology workshop was brilliant (see Oxford… #1 ) and Oxford… #2 ), but I also very, very much enjoyed meeting up with Dan and Nico! During the week, someone (name and address is know at the editorial office) commented on the fact that my blog posts are somewhat difficult to follow; that is, it’s often not clear why I am posting what I am posting.

The Molecular Chemometrics Principles #1: access to data

Something I have not completely comfortable with about the CDK in the past, is the way Atom’s are constructed:   IAtom carbon = new Atom("C");  Not that it is horrible code, but the CDK has an Element too. Why not reuse that?

new Atom(Elements.CARBON);

About four weeks ago the Fall 2023 American Chemical Society meeting (#ACSFall2023). I have attended a few ACS meetings in person and even organized a symposium at the 2010 ACS meeting in Boston. This time too, I did not participate in person, tho visiting San Francisco again would have been nice. I gave two presentations (slides doi:10.5281/zenodo.8255394), but have not uploaded my slides of the first presentation to Zenodo yet.

American Chemical Society Fall 2023 meeting

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

There are many ways to contribute to opensource software (OSS), programming only being one of them. I develop OSS, but use OSS too. For example, I am a big user of the Linux kernel, the KDE desktop, Kubuntu, Debian (I have unstable in a chroot), Firefox, Eclipse, Classpath, and many, many others. What these have in common, is that I generally have no time to look into the source code of these projects.

Being a good opensource user

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

Google has set up a new search enginge specifically for source code: /* Code Search */. Important difference with their normal search engine is that it allows restricting your search by programming language, license and filename and package. I have not been able to figure out how to use ‘package’ yet, but the others are pretty clear.

Google's new search engine: /* Code Search */

CDK News  2.3 is scheduled for this month, and origanally planned to be distributed on the CDK5AW event. So, it’s a bit late. But the editorial process is converging… I realized that I forgot to mention the requirement for InChI’s whenever molecules are given.

CDK News 2.3 and InChI's

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

I’ve just uploaded kfile_chemical 0.9 . It has new translations for ES and DA, and plugins for InChI files. It will extract the InChI string as meta data (and will thus be used by the KDE desktop search Kat , and the InChI version number. Thinking about this, it might be useful to extract all layers as meta data, so that one can search on chemical formula and even connectivity, and find all matching structures.

InChI meta data with kfile_chemical

My research is about the interaction of (machine) representation and the impact on the success of data analysis (matchine learning, chemometrics, AI, etc). See the posts about molecular chemometrics. This got me into FAIR: making data interoperable and being able to (really) reuse data is the starting point of doing research.

Reusing data: two new papers

This new blog will deal with chemblaics in the broader sense, and will not be restricted to research in this field in which I am involved personally. Chemblaics (pronounced chem-bla-ics) is the science that uses computers to address and possibly solve problems in the area of chemistry, biochemistry and related fields. The general denomiter seems to be molecules, but I might be wrong there.

Chem-bla-ics

I just read that the Kubuntu team wants to include Kat in the dapper release (scheduled for April 2006). Kat is (to be) the KDE equivalent of Google’s desktop search bar.  This is great news for us chem-bla-icians, as Kat has support for full text searching of chemistry files! Let’s see if I can get the Kubuntu team to package up kfile_chemical too, which will extend Kat (and KDE in general), with extraction of meta data from chemical documents.

Ubuntu Dapper will include chemistry features

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?

Some days ago, I started added boiling points to Wikidata, referenced from Basic Laboratory and Industrial Chemicals (wikidata:Q22236188), David R. Lide’s ‘a CRC quick reference handbook’ from 1993 (well, the edition I have). But Wikidata wants pressure (wikidata:P2077) info at which the boiling point (wikidata:P2102) was measured. Rightfully so. But I had not added those yet, because it slows me and can be automated with QuickStatements.

Boiling points in Wikidata

Roland Krause  discussed today in his blog Notes from the Biomass an interesting website: postgenomic.com . This website, still marked BETA, mines blogs in the field of genomics and extract noteworthy statistics from it: which articles are cited in those blogs. For example, the most discussed article is Kai Wang’s Gene-function wiki would let biologists pool worldwide resources  in Nature.

Hot articles; mining the semantic web

I have not posted a lot about our Virtual Human Platform for Safety Assessment (VHP4Safety) project yet. Actually, more generally I do not post frequently about the funded projects. This is likely that few of them are Open Science by contract and often they have some formal process in place to approve output. That makes open notebook science-style posting about these projects hard. One is restricted to previously cleared material.

New paper: The Virtual Human Platform for Safety Assessment (VHP4Safety)

An InChI (or see the FAQ) is a line notation for a molecular structure that was recently developed by the NIST and the IUPAC. Principally they can be applied to protein too (see below), but because proteins would give lenghty InChI’s and are quite well defined in terms of connectivity anyway, those can better be described by their amino acid sequence.

InChI's in LaTex and CDK News

Dan (the original Jmol author) has an interesting blog series: How to make money from Open Source scientific software I, II and III. Three more blog items are in the planning. The deal with how to make money from open source scientific software. He wants to be able to skeptically review the software in his field, hence open source.

How to make money from Open Source scientific software

After Kalzium and kfile_chemical , KDE has now be extended with kparts for 3D structure and spectrum display: Kryomol . It is written in C++ and licensed GPL. It supports several chemistry formats, among which quantum chemical formats like Gaussian03, NwChem and ACES, and 3D structures as MDL molefile and XYZ.

More chemistry in KDE

Division 1 of our Institute of Nutrition and Translational Research in Metabolism (NUTRIM) held a meeting last week which had a panel discussion on the use of patents to bring research to the market, aimed at PhD candidates of the institute. Patents are one of the routes to make research output more sustainable. For example, the research output into a new method to study something or make something often needs the development into a product.

Patents, societal impact, and sustainability

This summer I am trying to finish up some smaller projects that I did not have time for to finish, with mixed successes. I am combing this with a nice Dutch staycation, and I already cycled in Overijssel and in south-west Friesland and learning about their histories. But this post is about an update on my Citation Typing Ontology use cases. And I have to say, a mention by Silvio Peroni is pretty awesome, thanks! First, the bad news.

CiTO updates: Wakefield and WikiPathways

Publishing grant proposal is still not very common. The proposal published in Research Ideas and Outcomes) (doi:10.3897/rio.10.e124884) for the NWO Open Science grant for the CDK is, however, not the first and hopefully not the last. Interestingly, it is already cited in (the German) Wikipedia. It is used there to support a statement which tools use the Chemistry Development Kit.

cdk2024 #2: publishing grant proposals

I am still catching up with a lot of work, and found out I actually had forgotten to blog about this cool article by Denise Slenter: “Discovering life’s directed metabolic (sub)paths to interpret human biochemical markers using the DSMN tool” (doi:10.1039/D3DD00069A). This paper explains how various open science resources (Wikidata, Reactome, WikiPathways) are used to visualize the biological story of the data from two metabolomics experiments

New paper: "Discovering life's directed metabolic (sub)paths to interpret human biochemical markers using the DSMN tool"

Ammar is finishing up his PhD thesis with his research on the use of FAIR towards predictive toxicology. Or, “AI ready”, as the term FAIR is now sometimes explained. Any computational method needs good data, and just FAIR is not enough. It needs to meet community standards, as formalized in R1.3. To me, this includes meeting community standards like minimal reporting standards.

New paper: FAIR assessment of nanosafety data reusability with community standards

Noting that in the coming week I am not attending the ELIXIR All Hands in Uppsala. Having lived in (and around) Uppsala for more than three years, I am disappointed and with the first stories from colleagues coming in even more. But it has been a way too busy year, I have much to finish up, and I need to take care of myself too. I am not 32 anymore. But in the past two weeks I did attend two workshops.

Two meetings: ELIXIR Toxicology and FAIR4ChemNL

Making something FAIR is hard, particularly when you do more than making something findable. We’ve seen before that making something usefully findable requires deep indexing, and already that continues to be difficult, because we are not seeing it enough. So, when I thought convert a paper led by Hoet’s lab in Leuven into machine-actionable RDF to make it FAIR, I gravely underestimated the amount of work.

New paper: From papers to RDF-based integration of physicochemical data and adverse outcome pathways for nanomaterials

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...

During the Open Science Retreat I organized a short session where we looking into typing citation intentions using a new nanopublication template. First, let’s describe nanopublications (originally used in doi:10.3233/ISU-2010-0613) a bit. Scholia gives a nice overview of (macro?)publications on the topic.

Open Science Retreat #2: CiTO Nanopublications

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

Update

: Mark wrote up a blog post on the RDF that the ChEMBL team itself. Yesterday, the paper “The ChEMBL database as linked open data” (doi:10.1186/1758-2946-5-23) by Andra Waagmeester (@andrawaag), Ola Spjuth (@ola_spjuth), Peter Ansell (@p_ansell), Antony Williams (@chemconnector), Valery Tkachenko, Janna Hastings, Bin Chen (@binchenindiana), David J Wild (@davidjohnwild), and me appeared in the OA JChemInf journal.

New Paper: "The ChEMBL database as linked open data"

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"

I reported earlier how to I uploaded the ChemPedia (RIP) data onto Kasabi. But for ChEMBL-RDF I have used the pytassium tool, not just because it has a cool name :) I discovered yesterday, however, that I did not write down in this lab notebook, what steps I needed to take to reproduce it. And I just wanted to uploaded new triples to the ChEMBL-RDF data set on Kasabi.

ChEMBL-RDF: Uploading data to Kasabi with pytassium

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

Some time ago, the brilliant GitHub people gave me the following tip. Rajarshi is lazy, and might find it interesting. By appending .patch to the commit URL, a commit can easily be downloaded as patch. That way, developers can easily download it with wget or curl and apply it locally with git am, without having the fetch the full repository.

GitHub Tip: download commits as patches

Last month I reported a few things I missed in CiteULike. One of them was support for CiTO (see doi:https://doi.org/10.1186/2041-1480-1-S1-S6), a great Citation Typing Ontology. I promised the CiTO author, David, my use cases, but have been horribly busy in the past few weeks with my new position, wrapping up my past position, and thinking on my position after Cambridge.

CiteULike CiTO Use Case #1: Wordles

I have blogged about two Molecular Chemometrics principles so far: McPrinciple #1: access to data McPrinciple #2: be clear in what you mean Peter’s post #solo10: Green Chain Reaction; where to store the data? DSR? IR? BioTorrent, OKF or ??? gives me enough basis to write up a third principle:

 Molecular Chemometrics Principles #3

: We make scientific progress if we build on past achievements. Sounds logical, right?

The Molecular Chemometrics Principles #3: stand on shoulders

The Predictive Toxicology  meeting is over. It was a great meeting, by any standard. Very much recommended, and many thanx to Barry for the organization! The meeting was a true workshop, with a mix of presentations and getting work done. I participated in a group that looked at mutagenicity of potential anti-malaria drugs from the datasets of GSK and Novartis recently release as Open Data.

Oxford... #2

This week was the CDK5AW  event, a workshop for users and developers of the Chemistry Development Kit (CDK). After talking with other developers we agreed on creating PDF and HTML versions of single articles that appeared in the CDK News  newsletter. Well, I haven’t figured out how to create nice HTML (the latex2html does not give nice results, anyone ideas?), but for the PDF version I now have a pipeline.

Single PDFs for CDK News articles

Bioclipse 1.0 is to be released in May, and the cartoon on script command is still not working in the Jmol viewer. For those who do not know yet, Bioclipse is a cool Eclipse RCP based Java chemo-and bioinformatics workbench. To have a better idea what goes on inside Bioclipse, I wrote a new BioPolymer tree to show me the strands in the protein.

Getting Jmol's 'cartoon on' to work in Bioclipse

Scholarly articles provide context to the factualness of statements in Wikidata, similar to the [citation needed] in Wikipedia. And just like the cited references in each scholarly article itself. The citation network is general seen as an essential part of (doing) science, even without citation intention annotation.

Adding citations between existing articles in Wikidata

Scholia is a visual layer on top of Wikidata providing a rich user experience for browing scholarly research related knowledge. I am using the combinatie for various things, including exploring new research topics (a method, compound, or protein I do not know so much about yet), indexing notable research output (including citations), progress of Citation Typing Ontology uptake, etc.

chem-bla-ics

CIA statistics for Blue Obelisk

Chem-bla-ics

Single PDFs for CDK News articles