dullhunk PloS Bio Article

Duncan Hull and company have just published a thorough (210 references..) review of the current state of scientific digital libraries. Anyone interested in the changing face of publishing or of the Web in general would likely find the article interesting. Out of the many ideas discussed, these two caught my attention:

"As we move in biology from a focus on hypothesis-driven to data-driven science, it is increasingly recognized that databases, software models, and instrumentation are the scientific output, rather than the conventional and more discursive descriptions of experiments and their results."

and

"We suggest that the main obstacles to warmer libraries are primarily social rather than technical in nature. Identity, trust, and privacy are all potential stumbling blocks to better libraries in the future."

To the first quote, I will say simply, hear hear!  The idea that the units with which scientific progress is published and thus measured should correspond more directly to discrete, integratable chunks of knowledge and to sharable processes for knowledge generation rather than (often unparsable) stories is one whose time has clearly come. 

The second one stuck out because it is so similar to something I played a part in writing a while back.  In another review article (with a paltry 93 references) we suggested that ".. the primary hindrances to the creation of the SWLS [Semantic Web for Life Sciences] may be social rather than technological in nature ..".  In a sense, the SWLS that we were thinking about way back then could be said to subsume the digital libraries of Dr. Hull et al.'s article.  But... looking more closely at the first quote above, I realize that relation isn't subsumption, but equivalency.  Though they are writing specifically about 'libraries', they clearly consider databases, software, etc. as parts of the new incarnations of libraries and thus are writing about exactly the same thing that we were writing about.   

Its interesting that we came to similar conclusions to some extent, both articles suggest that the main challenges in moving science forward on the Web are in handling problems that have people at their center, not technology.  

The main problem with LSIDs

As one of the authors of a paper that espoused LSIDs as a great idea and complained about their lack of adoption by the community, I feel obliged to come out and say that I've come to the conclusion that we should not be using them at all (for the time being).

The fundamental problems with LSIDs are the first two symbols in the acronym. If they were simply The Identifier System and thus were not constrained from the beginning to operate in the comparatively small world of the life sciences, the proposal might have stood a chance of working. I think they were really just not ambitious enough. It really is a fantastic bit of work, this paper describing the need for and the implementation of the spec is one of the best works on data integration that I have come across. But, the fact remains that, with a few exceptions, no one has adopted the spec because (IMHO) developers prefer to work with the most widely accepted standards (e.g. those from the W3C) so they don't end up having to re-implement everything when new standards replace the old ones. (There is also the issue of the need for registries but I think that is secondary).

So, until we get to the point where Sun provides a built-in Java class called LSID with methods like getMetaData and getData that I can call with the same ease as the HTTP get method, I think I'll wait with everyone else.