It turned out that planets do still exist, so I started a small corner on Wikidata: Q121134938, and a number of existing blog planets:

The software used to run these planets is ancient, though. We need a new generation of software, replacing things like Planet. And I want something people can easily host on GitHub or GitLab Pages or the likes.

I created a minimal shape expression but the Wikidata items for the planets still lack a lot of information that can be added. First, we can think of them as venues, perhaps, where people “publish” their work. Second, we can annotate the blog planets with ‘main subject’ for the topics the cover. Or we can list the people that are “author” on the planet; most planets are very transparent about which blogs they aggregate.

Love to see where this is going. Who knows? Maybe we will see Postgenomic (see doi:10.1186/1471-2105-8-487) and Chemical blogspace resurface :)

• Chemical Abstracts Service Committee (CCAS) (entry in Cb )
• Agilemolecule’s Blog (entry in Cb )
• The Allotrope (entry in Cb )

If you know good chemistry blogs, please contact the author and ask them to email me for inclusion.

• Paul Dobson Research (entry in Cb )
• Loose Morels » science (entry in Cb )
• The plate is bad (entry in Cb )
• Laborantje (entry in Cb )
• alchemoinformatics (entry in Cb )
• Andy’s Blog - Oral Roberts University (entry in Cb )
• UU Cheminformatics Journal Club (entry in Cb )
• Is this going to be on the exam? (entry in Cb )
• Asad’s Blog » Work (entry in Cb )
• Chemical Calisthenics (entry in Cb )
• Chemistry & Cooking (entry in Cb )
• Master Organic Chemistry (entry in Cb )
• Imaging Chemistry (entry in Cb )
• Click Chemistry (entry in Cb )
• Dr. Joaquin Barroso’s Blog (entry in Cb )
• Tripod Development (entry in Cb )

Happy reading!

BTW, some WordPress feeds are weird, causing the blog post titles to not show up properly in Cb. I’ll investigate this soon.

PLoS ONE is a new journal that changes the way science is published: it publishes anything that is scientifically sound and does not make any judgement on impact and lets the community deal with that. Cameron Neylon recently had him taped to discuss article-level metrics used at PLoS ONE (see also this).

And, PONE (as they affectionately call it) seems to be steadily growing to, at least, become a BIG publisher. Clearly, not dedicating yourself to a small discipline helps. And the IT we have had around for the past 10 years make this large scale publishing possible. The impact of a paper becomes clear through those article level metrics.

Finding interesting papers, however, may be a bit more difficult. There are dedicated RSS feeds listed at the front page:

And I recently subscribed to the Chemistry feed (RSS).

One of the sources taken into account for the article-level metrics is Postgenomic.com, and you may be aware that Chemical blogspace is using the same software. However, us ~60 active have not been paying attention this PONE feed. Well, there have appeared only 84 papers yet in this subsection:

… but only one has been cited in Chemical blogspace, which is a bit disappointing:

So, what are your reasons you do not read this journal yet?

I have spotted one paper which I will soon read and review: How Large Is the Metabolome? A Critical Analysis of Data Exchange Practices in Chemistry (doi:10.1371/journal.pone.0005440).

• The Realm of Organic Synthesis (entry in Cb)
• Carbon Chemistry (entry in Cb)
• OChemOnline (entry in Cb)
• polymer processing (entry in Cb)
• Metallome (entry in Cb)
• BKBlog (entry in Cb)
• Sam’s notes (entry in Cb)
• Zusammen (entry in Cb)
• Kashthealien’s Blog (entry in Cb)
• Chemjobber (entry in Cb)
• Henry Rzepa (entry in Cb)
• ChemCafé (entry in Cb)
• Phosphorus carbide (entry in Cb)
• Molecular Modeling Basics (entry in Cb)
• /chemical/structure Blog (entry in Cb)
• Indiana University Cheminformatics News (entry in Cb)
• Accelrys | Blog (entry in Cb)

Happy reading!

• Graphene Literature Reviews (entry in Cb)
• RajcaLab Weblog (entry in Cb)
• Making Graphite Work (entry in Cb)
• infiniflux! (entry in Cb)
• PMGB (entry in Cb)
• The road less travelled (entry in Cb)
• PaulingBlog (entry in Cb)
• InkSpot. Science. On Demand (entry in Cb)
• kilomentor (entry in Cb)
• Chemistry in silico (entry in Cb)
• So much to do, so little time (entry in Cb)
• Der Molekülblog (entry in Cb)
• Selenocisteïna (entry in Cb)
• ChEMBL (entry in Cb)
• A Chemistry Question, Daily (entry in Cb)
• Macromolecular Modeling Blog (entry in Cb)
• Practical Fragments (entry in Cb)
• Bridgehead Carbons (entry in Cb)

Data Rich Publishing

Peter had a detailed blog about why he joined the editorial board:

I take this position with some trepidation as I have grave reservations about the current practice of cheminformatics. It suffers from closed data, closed source and closed standards, and thereby generally poor experimental design, poor metrics and almost always irreproducible results and conclusions which are based on subjective opinions.

I strongly agree with this observation, and have discussed my view on this in my thesis (send me an email if you want a copy).

So, what has the journal to say about this (see Instructions to the Author, emphasis mine):

Journal of Cheminformatics recommends, but does not require, that the source code of the software should be made available under a suitable open-source license that will entitle other researchers to further develop and extend the software if they wish to do so.

Regarding data, they even less revolutionary; recommended figures formats (EPS, PDF, PNG) focus on nice graphics instead of reuse of data. I also note that I cannot upload data in the Open Document Format, or, hey, let’s really push things, in RDF. Well, not according to the Instructions. And surely, I can put the [O|R]DF in the supplementary information, anyway. It would also be nice if I could use Jmol as an applet to enrich the graphics, and improve data reusability of the paper, like the RSC recently started to allow .

Regarding the supplementary information, there is a section on additional files, which, unconveniently are capped at 20MB size. No mention of chemical formats at all, neither any recommendation on semantic formats like CML (I wonder when this was discussed with the Editorial Board, and where Peter was at the time). How am I going to put online my 500 molecular structure CML file now? (Though it’s good to know it is virus scanned ;)

So, why do I vent my concerns about these limitations? I had not blogged about the launch of the journal earlier, because I have not made up my mind about it. On one side, I am happy to see a journal that promotes (scientific) use of papers, and a journal that allows me to keep copyright on the material. However, on the other side, what the current Instructions suggest, the data I could use from the papers is available only in an old-fashion way. That’s a lost opportunity and could have killed competition for sure. Instead, the unique selling point is now restricted to using an open access license. Nature Chemistry, on the other hand, chose data rich publishing as a selling point (though in competition with things done at the RSC).

The other thing I want to mention about the journal is the following. Rajarshi blogged about Bachrach’s paper on Chemistry publication - making the revolution (DOI:10.1186/1758-2946-1-2). Firstly, by adding a link like that for the DOI I just gave, Chemical blogspace can pick it up; we need this later. Secondly, the paper actually suggests that “[b]y publishing lots of data, available for ready re-use by all scientists, we can radically change the way science is communicated and ultimately performed”; this is in strong contrast to what I have seen in the Instructions so far.

Starting the Scientific Communication

Rich replied to Rajarshi about the requirement to log in before someone could make a comment, which he did not like. He suggested alternative ways to prevent SPAM and sorts. The choice for this commenting approach may also originate from having an Open discussion, where everyone takes responsibility for what he says. The use of OpenID, as Rich suggests would only partially address that; on the other hand, setting up a fake email address is quite common in the blogosphere too.

If Rajarshi would have used the DOI to link to the Steven’s paper, as said, Chemical blogspace would have recognized it. Instead, he chose to link directly to the PDF. This is a typical case of hamburgers in action. However, others did when they discussed the first research paper in the journal (DOI:10.1186/1758-2946-1-3). These blogs were picked up by Cb and are listed on this page.

Now, I only need to remind you of Userscripts for the Life Sciences (DOI:10.1186/1471-2105-8-487) that we have the methods to link these comments back to the journal website. The Quotes from Chemical Blogspace and Postgenomic script in particular, does the hard work (needs GreaseMonkey, the script can be downloaded here; see also Noel’s original post). This way, we can read the comments when we visit the papers homepage:

Now, the script has not yet been updated for the new journal (Noel, can you please upload the revision?), so you need to edit the source right now and add http://*.jcheminf.com/* to the list of website the script acts on:

Drugs are still missing, but will add those too, and since not all entries had InChIs, SMILES were converted using CDK 1.1.5 .

The blogosphere oversees all major Open discussion

• Open Text Mining Interface and Bioclipse
• USPTO considers open source software prior art
• New InChI software beta: license issues resolved and InChIKey
• SMILES to become an Open Standard

The blogosphere cares about data

• Uncertainty in NMR based 3D protein models
• re: ACS RSS feeds are messed up
• Molecules in Wikipedia without InChIs

Important bad science cannot hide

I do not feel much like pointing to bad scientific articles, but want to point to the enormous amount of literature being discussed in Chemical blogspace: 60 active chemical blogs discussed just over 1300 peer-reviewed papers from 213 scientific journals in less than 10 months. The top 5 journals have 133, 78, 68, 57 and 48 papers discussed in 22, 24, 10, 11 and 18 different blogs respectively. (Peter, if you need more in depth statistics, just let me know…)

Two examples where I discuss not-bad-at-all scientific literature:

• Automatic Classification of thousands of Crystal Structures
• CDK Literature #2

Open Notebook Science

I regularly blog about the chemoinformatics research I do in my blog. A few examples from the last half year:

• CDK Workshop - Days #3 and #4
• Weka Decision Trees to Java Conversion
• RDF-ing molecular space
• Atom typing in the CDK
• Further Bioclipse QSAR functionality development

For now, you will have to do with this page:

An additional flaw is that it also shows molecules for other blogs.

Update: the RSS feed for a specific category was already available, but just not from the FireFox URL bar. Instead, it is given on the right side of the posts page when you selected a category. Here a shortcut for the RSS for posts from the Blue Obelisk category.