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. No longer the question was how to get people to know the new knowledge to how to get people to pay for new knowledge. One misconception, for example, is that publishing is a free market. Yes, you can argue that you can publish anywhere you like (theoretically, at least, but reality says otherwise), but the monopoly is in getting access: for every new fact (and republishing the same fact is a faux pas), there is exactly one provider of that fact.

Slowly this is changing, but only slowly. What this really needs, is open licenses, just like open source licenses. Licenses that allow fixing typos, allow resharing with your students, etc.

But contrary to what has been prevalent in the Plan S discussion, these ideas are not new. And people have been trying Open Science for more than two decades already.

I have been trying to dig up the oldest references (ongoing effort) of the term Open Science (in the current meaning), and had a CiteULike group for that. But CiteULike is shutting down, so I will blog the references I found, and add some context.

A first article to mention is this 1998 article that mentions Open Science: Common Agency Contracting and the Emergence of “Open Science” Institutions The American Economic Review, Vol. 88, No. 2. (May 1998), pp. 15-21 by Paul A. David. Worth reading, but does require reading some of the cited literature.

The follow two magazine articles took the term Open Science to a wider public, and in reply to a conference held at Brookhaven National Laboratory:

• The ‘Open-Source Movement’ Turns Its Eye to Science The Chronicle of Higher Education (5 November 1999) by Vincent Kiernan
• A Natural Home for Open Source 1999 Dr. Dobb’s The World of Software Development (1 October 1999)
• Open Source/Open Science 1999 Linux Journal (1 February 2000) by Stephen Adler

I would also like to note that the openscience.org website by Dan Gezelter went online in the late nineties already, which I have used in various of my source code projects, and, of course, also has been used by the Chemistry Development Kit from the start.

Yeah, that looks like what I asked for :) Thanx, and well done!

One of the things, is that the CiTO data added via a certain account, can be downloaded as triples:

The second is that they are improving the graphics of how it is visualized. E.g. they added an ‘Expand’ link, which I found when they tweeted they had hidden drag-n-drop, which I haven’t found yet, though. Clicking that action, will show you the following:

Because CiteULike takes advantage of the inverse function of the CiTO predictates, they show up with the cited paper too, which is less suitable for the top-down flow graphics:

To make this advertorial a bit balanced, not all my wishes have been implemented yet, and the next up from my perspective should be Linked Data. There is some Linked Data embedded as RDFa, but the latter is not turning out to be the killer I had hoped, and regular RDF entry points should be used.

Each CiteULike entry (post) should get a unique IRI (or URI) and opening that link should give RDF about that post (wish #10). That’s is dereferencibility. The RDF can be, for example, in BIBO but there are many alternatives, and I have not been keeping up with which is the best (please leave a comment, if you have an opinion on that).

But I like where this is going! Thanx, CiteIReallyLikeThis!

Then Google Scholar Citations (GSC) shows up. While it does not look as pretty as competing products, it compensates that with a wide coverage of literature (for example, it supports the JChemInf, which Web-of-Science currently does not; and I happen to publish a lot in that journal recently), books, and reports, while keeping false positives fairly low. Thus, it provides an upper limit of my citations statistics, but one I am pretty happy confident about. And my H-index is quite comparable anyway. This is what my profile looks like:

So, these statistics have two purposes to me: 1. grant applications, and 2. I like to know what people based theirs on my research. (Well, OK, 3. it helps me understand why I work so hard on too many things.)

Now the question is, will GSC take off. Will it replace ORCID? Will they join ORCID? Will GSC get a good API? Who will write the first userscript to make the GUI fancier? Will GSC support CiTO? Will GSC start using microformats or RDFa? What mashups can we expect between bibliographic databases? Will new entries automatically be posted to Google+? Will it have a button to autocreate a blog post when a paper gets cited 100, 500, or a 1000 times? Will GSC support #altmetrics?

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. But finally, here it is. Based on source code I wrote and released earlier, the first use case I represent is the Wordle one, which I showed with manual work in February.

Now that all the data is semantically marked up in CiteULike, I can easily extract all paper titles (or whatever is available in CiteULike) for all papers that cite the first CDK paper (doi:10.1021/ci025584y). Using the JSON interface, I have this Groovy script to extract all titles:

import groovyx.net.http.HTTPBuilder
import groovyx.net.http.Method
import static groovyx.net.http.ContentType.JSON

culUrl = "http://www.citeulike.org/";

citotags = [
  "cito--cites",
  "cito--usesMethodIn",
  "cito--discusses",
  "cito--extends"
// there are more, but these are all
// I use right now
]

papers = [
  "1073448",
  "423382"
]

http = new HTTPBuilder(culUrl)

papers.each { paper ->
  println "# Processing $paper..."
  citotags.each { tag ->
    citation = "$tag--$paper".toLowerCase()
    http.request(Method.valueOf("GET"), JSON) {
      uri.path = "/json/user/egonw/tag/$citation"

      response.success = { resp,json ->
        json.each { article ->
          tripleCount = 0;
          article.tags.each { artTag ->
            if (artTag.startsWith(tag)) tripleCount++
          }
          if (tripleCount > 0) {
            title = article.title
            title = title.replaceAll("\\{","")
            title = title.replaceAll("\\}","")
            println "$title"
          }
        }
      }
    }
  }
}

The output is two blocks which I can easily copy/paste into Wordle. Now, I think I heard one can actually download the java code, so I am tempted to integrate it later, but for now copy/paste will do fine, after the data handling is mostly automated: with a few lines extra I can make such visualizations for any paper I annotated in CiteULike with CiTO.

The CDK I paper

The CDK II paper

Interesting differences… more statistics will soon follow. See Further statistics on the papers citing the CDK for the kind of analyses I have in mind.

Agreeing with @citeulike and @abhishektiwari, as a service provider any bad news is good news too: they provide opportunities to improve. So, as encouraged to do so, I reported my long list of things I miss in CiteULike:

• @citeulike ok, one more. wish #18: get readermeter.org to also support citeulike
• @citeulike wish #17: allow people linking between papers in their libs using CiTO to annotate how they cite papers, see http://ur.ly/lBUO
• @citeulike wish #16: I think I saw images from some papers, right? how about doing that for #biomedcentral journals too?
• @citeulike wish #15: at the same http://ur.ly/lIGn page, the tag cloud should reflect tag use with font sizing
• @citeulike wish #14: upon ‘post url’, the first page with extraced information should allow marking as ‘I am author’ (cannot find that)
• @citeulike (new) wish #12: clicking an account name should get me to a public portal, rather than just his paper list
• @citeulike good point, wish #13: be more strong on requiring people to tag papers… and use article keywords as default tags
• @citeulike wish #11: remove ‘no-tag’ from tag clouds
• @citeulike wish #10: support #RDF export with BIBO and/or PRISM
• @citeulike wish #9: use #foaf for the RDFa for account pages, and to mark up friends
• @citeulike wish #8: and more generally, make #citeulike part of the #linkeddata network (provide an #rdf API)
• @citeulike wish #7: start using RDFa, e.g. with the PRISM ontology
• @citeulike wish #6: on an article page (like http://ur.ly/lvWk) summarize the network that bookmarked that article, not just the acc names
• @citeulike wish #5: don’t show the ‘copy’ button for papers that are already in my archive (really a bug)
• @citeulike indeed, but don’t or do it right… wish #4: allow people to have that link automatically point to an external blog
• @citeulike wish #3: provide summaries of lists, like article count per journal and article count per year
• @citeulike well, I’ll use the blog functoinality to summarize… wish #2: do not try to be a blogging platform
• @citeulike (new) wish #1: put automatically focus on text field after clicking search and select all text for easy deletion

The reports are now also available in the fora of CiteULike.

Searching

Searching literature is traditionally done in systems like Chemical Abstracts and Web-of-Science. The open nature of a growing number of repositories (e.g. the Dutch DARE) and indexing facilities like PubMed make these proprietary tools obsolete.

It is incorrect to assume that these payed services are the only trustworthy sources. Even WoS fails to make the all links between entries in the database. For example, I am aware of two missing citations to articles I have written, even though both the cited and the citing article is available in the system. One of the citing articles was in the Angewandte Chemie!

Additionally, some search services, like Google Scholar, have the advantage that they find copies and close variants of articles in proprietary articles on home pages and in open repositories. Today, I learned about Scientific Commons which indexes and links to a staggering 1.5M publications, using, among others, PubMed and university repositories. Where possible it makes direct links to PDF versions of the article.

Ranking

Mitch set up ChemRank, to which Peter , the ChemBlog and I replied . Afterwards, I learned that other services are available too, that allow, in addition to setting up an online personal literature database, voting and commenting on articles.

Apparently, CiteULike (CUL) supports this too. In contrast to ChemRank, CUL requires a login, which I personally see as an advantage, because I can browse literature bookmarked by other accounts I trust. There is also Connotea but I never liked that site that much (e.g. is allows bookmarking any web page); Rich has his comments too . I would also like to mention BioWizard which is based on the PubMed content, which actually covers a good deal of chemistry literature nowadays too.

Local Storage

These above mentioned systems can be used as alternative to offline bibliographic database systems, like EndNote and JabRef. The latter is my favorite, being based on BibTeX which I use for my LaTeX based publications, and is opensource and contains a few patches from yours truly. Jungfreudlich wondered how people organized their PDF archive and I commented how I do it:

• a directory hierarchy based on journal name and year
• file names that include last name of the first author and year
• JabRef for the bibiographic database
• Strigi for full text search

Jörg and the power of goo replied too.

Mashups

I have accounts on several online tools now (with some duplication which I don’t like), and I have no idea which of the options will stay around. Time will learn. Good news is that the open characters of many of these allow making mashups, and generally integrate tools. For example, JabRef allows downloading citations from PubMed, and Noel suggested to use Greasemonkey scripts to link to the supplementary information for his articles, instead of using the mechanisms journals have. I can see the advantage of this, as, for example, Wiley takes full copyright of the data in SI material , while Noel’s mechanism would keep the data open.

For now, however, I would very much like to see a meta service where I can query rankings and comment for articles using any or all of the above tools.