Digital Science launches

Digital Science, a "sibling" of Nature Publishing under the parentage of Macmillan Publishers looks like it could be an interesting new company in the scientific publishing domain.  Interesting because it looks like they are really setting themselves up as a software company and perhaps more interesting because they seem to be doing so primarily through partnerships.  Seems like it could be grand opportunity if you are trying to get the ball rolling with a scientific software company.

Where is the API?

Yes.. I am procrastinating. I should be sleeping, working on the OntoLoki automatic ontology evaluation system, or preparing for our meeting with the SWAN team tomorrow morning; but instead, I am perusing Project Prospect and thinking about what a journal should look like. This is largely because of my disappointment in reading this nascent blog post in which Ian Mulvaney (a person who I think I respect and leader of a project I obviously find fascinating) suggests that enforcing the application of naming standards for chemical entities at the time of publication would a) be too hard for authors, b) not provide much benefit, c) that it would be better to let this be a voluntary step - all of which I absolutely disagree with.

This, and comments on the post, lead me to Project Prospect - which seems to be the first real publisher to take the idea of semantic enhancements of online manuscripts seriously.

Project Prospect provides semantic annotation (e.g. labeling GO terms etc. in manuscripts) and uses this to provide some enhanced navigation patterns and some additional information (e.g. definitions) for any of the annotations. Doing a pretty nice job at this was apparently enough to win them the 2007 ALPSP/Charlesworth Award for Publishing Innovation. While this is certainly a nice addition and a step in what I think is the right direction, it is 1) overwhelmingly similar to the much older and much more flexible, Conceptual Open Hypermedia ServicE (COHSE) from the University of Manchester and 2) does not seem to provide any capacity for semantic integration of the manuscripts in the collection.

Is this really the best we can do?

What I would like to see is a journal with an API. An API that would let me ask it questions like "what genes are present in articles published in this journal that contained both go:0005576, or any of its children , the word 'vaccine', and are described in the article as being upregulated". Right now, we can approach this sort of question with text-mining, but, with extensions to work like that done to enable the hypermedia browsing defined above (which fundamentally depends on solid entity identification and annotation within the document), this question (which spans multiple manuscripts) could be answered with a relatively straightforward query.

Its time for journals to step up an stop wasting talented researchers time writing text mining algorithms. Lets build a journal with a proper API, one with standards compliant methods for both writing content to it and querying the content inside it programmatically. Such a journal would not only improve human navigation and understanding of its independent textual documents, but would also enable entirely new modes of interaction with the integrated knowledge spanning all of its semantic content.

Nature Preceedings verse the blog(b)!

OK, its been a few weeks since I posted my latest piece of work on my blog (Sept. 4, 2007) and on Nature Precedings (Sept. 7, 2007). I think that is enough time to give a little summary of my experiences with both.

	number of comments	number of ambiguous votes	number of potential job offers
Blog	10	0	1
N. P.	0	4	0

Based on these metrics, the blog post is clearly the winner; however, the preceedings version does have a few plusses not listed. It does appear to be a tiny bit more professional looking, there is a consistent versioning system, they offer a standardized way to cite the draft, the voting system has some potential, and it is frankly cool to get yourself onto their home page in any way possible..

In my humble opinion, N.P. could be improved by:

1. enabling both positive and negative votes


2. improving their submission system such that content not suitable for inclusion in a PDF such as large images, movies, and so on could easily by added


3. notifying the authors of submitted manuscripts when comments or votes are added to their manuscripts

So, why did I get comments on my blog and not the N.P. post?
I think it is mostly because of the personal, social nature of the blog as a media. Many of the comments, (though not all) came from people that I think are signed up to a feed for my blog, the majority of which are personal friends (again, not all). These are the people that are most likely to a) be interested in what I have to say and b) to take the time to provide a useful response. If a post is interesting enough, these same people will tell their friends about it and they will tell their friends about it and all of a sudden it will have reached the right segment of the Internet population before Google Karma has even had a chance to act.

Nature is a broad spectrum journal with Nature Precedings even broader. If the Precedings idea is to take hold and thus reach a large enough participating audience to become interesting, I suggest that they need to figure out how to better accomodate the social side of this equation. (and don't think they aren't working on that..)