In the spirit of the holidays…a time in which we ask for everything our hearts desire…here’s a few wishes, hopes, and dreams for open science in 2008 (after the jump).

- NIH archiving mandate language in the omnibus appropriations bill. It’s past time that US taxpayer funded research goes into an archive where we can all read it without paying fees. The primary licensing issues appear to be worked out and it’s just a matter of creating the incentive for scientists to actually comply. This one’s a no-brainer.

- PRISM goes away. I’m not even going to link to these people. It’s an industry-sponsored lobbying group that spouts incredible statements like “public access equals government censorship” (the so-called logic behind this is more twisted than a complex protein structure). PRISM doesn’t help the dialogue in the Open Access world any more than attacks on traditional publishers help the dialogue. We’re in this one together in the end.

- the OECD Biological Resource Centers take flight. We need these repositories to get to a world where published research can seamlessly spark new discoveries, and that doesn’t happen when individual scientists have to fulfill orders and manufacture materials.

- the Society for Neuroscience peer review experiment works out. Anything that starts to make peer review less sclerotic is worth a shot…

- Traditional publishers open up their backfiles for extensive entity recognition, text mining, and semantic indexing. We have to do a lot of reformatting of knowledge to make the web work better for research, and just letting google index citations and keywords isn’t enough. We need as many smart people as possible crunching the literature and connecting it into the web of data (in life sciences alone, there’s almost 1000 primary databases ). We can do this while we figure out the OA policy for the backfile, this is common ground.

- Web 2.0 advocates overcome what appears to be a reflexive distaste for the Semantic Web – when it comes to biology at least, the Semantic Web not only works but is incredibly useful. There’s plenty of certified, standard ontologies and the problems you face are very amenable to semantic solutions. I’m sorry, as I know this produces enormous cognitive dissonance for many people, but seriously – we have existence proof, and mirrors are going up. Time to recognize that the Semantic Web may indeed be useful to some people, and time to exploit the opportunity represented by the intersection of Social Web and Research Web.

- Open database licensing comes of age. Watch the Science Commons and Creative Commons space for announcements…it’s time to start thinking about the “Freedom To Integrate” when it comes to databases in science.

- Pharmaceutical companies start to think about building common pools of toxicity data. The big costs in pharma are clinical trials, and the reason they cost so much is that we don’t understand toxicity. A vanishingly small number of people (i.e., the ones who work inside the pharma company that did a clinical trial) get to see failed clinical data. It simply cannot be the most efficient way to figure out tox to have the data decay, unexplored and unconnected. If we can simply take the mouse data about failed trials on a single target like P38 and let the smartest minds in the world take on the challenge of figuring out tox mechanisms – could it possibly do a worse job than the current strategies are doing?

- New business models for pharma emerge, based on strategies far more virtual than we see today. I’d like to see a gang of smart, funded people be able to organize research through outsourced contracts and informatics, and dramatically lower at least the cost of the biological discovery aspects of pharma. Until we crack tox, that’s probably the best we can do (so I guess this wish is tied to the one above).

- and to be a home-teamer, I hope Science Commons gets a new bike…er, a big grant.