Open Access works; articles matter not journals

As part of our Open Biblio project Jim and I were looking for lists of journal references to turn in BibJSON. I thought that I’d take some of our article listing from “Visions of a Semantic Molecular Future” ( ) in J. Cheminformatics, an Open Access journal published by Biomed Central. To make clear, an Open Access journal is one where all the articles are individually OA, usually under a CC-BY licence so free to read and re-use and do whatever you like with.

So VoaSMF had 15 articles and they’ve just been published a few days ago. I was looking for a way to emit them as an RDF / RSS feed so that we could turn them into BibJSON. It would contain records for each article with name/title/journal etc. and we’d see how they fitted into the BibJSON schema. Anyway the RSS isn’t ready yet, but I did find one for heavily accessed articles (which would include one of our groups – ChemicalTagger).

So I went to and started to read down:

 Top 10 most accessed articles for last 30 days / past year / all time         [more info]


Open Babel: An open chemical toolbox
Noel M. O’Boyle, Michael Banck, Craig A. James, Chris Morley, Tim Vandermeersch, Geoffrey R. Hutchison
Journal of Cheminformatics 2011, 3:33 (7 October 2011)

1367 accesses in … wow! 20Oct – 7 Oct = 13 days = 100 hits/per day. Well done the Open babel team. Of course OB is a wonderful program, open source and part of the Blue Obelisk. Wow!

1329 Preliminary communication    
Linked open drug data for pharmaceutical research and development
Matthias Samwald, Anja Jentzsch, Christopher Bouton, Claus Stie Kallesøe, Egon Willighagen, Janos Hajagos, M Scott Marshall, Eric Prud’hommeaux, Oktie Hassanzadeh, Elgar Pichler, Susie Stephens

journal of Cheminformatics 2011, 3:19 (16 May 2011)

That’s presumably hits for the month = 40/day. Extremely good. And the subject is about OPEN drug data. People must really want open data.

1247 Commentary    
Openness as infrastructure
John Wilbanks
Journal of Cheminformatics 2011, 3:36 (14 October 2011)
[Abstract] [Full Text] [PDF] [PubMed] [Related articles]

WOW! That’s only 6 days old, and from our symposium! 200 hits/day! These hits are not because of where it appeared. John has no connection with Chemistry. The point is that people want to read John’s work. And they will find it in DAYS regardless of where it’s published. It’s the top article in our symposium.

1168 Software    
PubChem3D: A new resource for scientists
Evan E Bolton, Jie Chen, Sunghwan Kim, Lianyi Han, Siqian He, Wenyao Shi, Vahan Simonyan, Yan Sun, Paul A Thiessen, Jiyao Wang, Bo Yu, Jian Zhang, Stephen H Bryant
Journal of Cheminformatics 2011, 3:32 (20 September 2011).

Well done Pubchem. Pubchem is an OPEN data base of 30 million structures. Some closed organization some years ago tried aggressively to close it down as unfair competition. But Openness prevailed (ca 40 hits a day)

868 Research article    
Open Data, Open Source and Open Standards in chemistry: The Blue Obelisk five years on
Noel M O’Boyle, Rajarshi Guha, Egon L Willighagen, Samuel E Adams, Jonathan Alvarsson, Jean-Claude Bradley, Igor V Filippov, Robert M Hanson, Marcus D Hanwell, Geoffrey R Hutchison, Craig A James, Nina Jeliazkova, Andrew SID Lang, Karol M Langner, David C Lonie, Daniel M Lowe, Jerome Pansanel, Dmitry Pavlov, Ola Spjuth, Christoph Steinbeck, Adam L Tenderholt, Kevin J Theisen, Peter Murray-Rust
Journal of Cheminformatics 2011, 3:37 (14 October 2011)

Zowie! Another from the VoaSMF. (and I’m an author). 6 days = 140 hits/day. Fantastic. But, as they say, there’s more

672 Research article    
Open Bibliography for Science, Technology, and Medicine
Richard Jones, Mark MacGillivray, Peter Murray-Rust, Jim Pitman, Peter Sefton, Ben O’Steen, William Waites
Journal of Cheminformatics 2011, 3:47 (14 October 2011)

ANOTHER from our symposium! 110 hits/day. And nothing directly to do with chemistry. So people have discovered this article because of what it is rather than where it is!

… and …

598 Editorial    
Semantic science and its communication – a personal view
Peter Murray-Rust
Journal of Cheminformatics 2011, 3:48 (14 October 2011) – 100 hits/day


So what’s the message from this? It’s that journals are no longer relevant to discovery. If they were, no one would have discovered John’s article and probably not the Open Bibliography. There are other mechanisms. I don’t know what they are, but I suspect John’s has been blogged or tweeted. Because it’s OA people know they will be able to read it. It’s also clear that article metrics are real. This isn’t robot activity. Of course John might have written a fleet of bots to knock up his accesses but since the bean-counting-weenies don’t count accesses there wouldn’t be any point (and of course John wouldn’t even think of doing it).

So it’s real. People will find articles of value regardless of where they are published as long as they are Open.

Don’t get me wrong – I am not arguing against editors. The scientific editors and the technical editors have done a great job. But it doesn’t need to be done in a journal.

And although article metrics – like any metrics – can be gamed they are far more valuable than the mindless citations. After all, all the papers have ZERO citations – which would make them worthless.

Here’s a secret not many people know. The way to find out how good a paper is, is to read it. Try it.


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One Response to Open Access works; articles matter not journals

  1. Mike Taylor says:

    VERY interesting analysis. I wonder if there is a way to move this beyond the anecdotal, and somehow quantify the relative importance of writing a good article and placing it in a good journal.
    I recently wrote ( that “If you work in an institution where they count up the IFs of the journals where your papers are published, then it may be advantageous to forego actually getting read and cited, for the benefit of rubbing up against other papers that, despite the disadvantage of being in a walled garden, still accumulate many citations. Promotion by the company that you keep rather than by your own achievements.” I’m hugely encouraged to think that we may be further along to road to fixing that system than I’d realised.

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