Science Online '09: Saturday AM My very much delayed notes from the sessions I attended Saturday.

Open Access
Moderated by Bill Hooker and Bjoern Brembs

http://www.scienceonline09.com/index.php/wiki/Open_Access_publishing/

What’s open access – green vs. gold models…
for university and disciplinary repositories, they can be listed in directories and have machine harvestable/federated searchable content

citation advantage and acceleration of the research cycle.
also allows for text mining
example: iHOP, information hyperlinked over proteins – works amazingly well, but can only work on the abstracts, and needs to be able to work on the full text

serials crisis – costs rising >> consumer price index

Can’t access own article

member of audience – databases in NAR database issue, exponential growth (published in Scitable open access) – duplicating efforts – how to you prevent duplication

6 major publishers control most of scholarly publishing

my point – if journals are dead, why proliferating? Societies as well as (or perhaps more so than) commercial publishers

journals go on your cv – where you’re published
- journal quality as a proxy for researcher quality or research quality
- is using journals for assessment such a good idea
- do you want to delegate that filter to someone?

- idea separate the research that we’re doing – dissemination – vs. making judgments of people for promotion. separate those things out
- this was already done in particle physics – pre-publish, even before the net by hand dissemination through the mail, then through e-mail, ArXiv… everything in particle physics is open access, but this didn’t change the market in scientific publishing – didn’t have anything to do with making the science available, but for the point of reputation, credit, etc. Market wasn’t created by evil companies, it was created by the people working in universities – everyone has to find a place to published – even if the work is very poor. Overlap btwn ArXiv and the journals is 100%, but need the certification, etc., comes from the published edition.
- criticism of making money – business model – vs. spirit of open access.

business model
- is open access really more expensive in total because management decentralized vs. centralized within the library, who has more or less figured out how to manage licenses based on subscriptions

- shifting the cost from the library to the individuals is sometimes resisted, but sometimes ok – depends on the field and if they’re accustomed to paying page charges

So, this session covered a bit that was really appropriate to the impact factor discussion. Unsurprisingly, there were still those in the audience who wouldn't publish OA because their advisor bought the line about OA != quality. This is just like the advisors saying ejournals != quality when in fact nearly all journals are in electronic format and the format has nothing to do with the quality.

Another time this week someone who works at a big evil society tried to get me to make some absolute statement about OA and I just wouldn't take the bait. I think for certain communities, it works quite well (for example, HEP and biomed) while for others there are a lot of very real barriers. I don't think libraries are necessarily the place to manage the article payments, but some libraries have taken on this task and have been able to support their researchers this way. There's a question about scalability.

There was a very interesting contribution to LIB-LICENSE this week from someone who actually went to Kenya and talked to some users of the literature. He found that they were getting just about all they needed from HINARI. So the LDC or developing countries argument might not be the best one - the argument might have more weight for smaller institutions in developed countries -- they seem to be the ones who can't get what they need.

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Not just text – image, sound and video in peer-reviewed literature
http://www.scienceonline09.com/index.php/wiki/Not_just_text/

This session was very helpful in distinguishing for me the difference between these two things and how they might be valuable.

Two versions: You Tube, and Journal Like

Moshe P, from JOVE
journal articles are very inefficient at transferring tacit or craftsman like knowledge, such as how to do certain experimental techniques
“golden hands”
he had to fly to the original lab to get expertise and then bring it back.
need video publication – show me
like cooking – small things omitted from the recipe that you can get through watching someone prepare it or by watching a cooking show

questions:
- what incentives are there to publish science on videos
- what format would be most useful?
- what equipment is required

incentive – make it a publication, a scientific journal, peer review, indexed in PubMed
tools – they do it for the scientists. Distributed network. Specialized outsourced video production companies with expertise and equipment to capture.

each article begins with a schematic representation, then an introduction of the scientist
(questions – Java – can I embed – have to do it by e-mail them, bcs, they had people ripping off the entire content of their site)

are the authors given help in speaking to the camera?
(real question – about widening audience – but this isn’t about this at all, this is for an expert audience which should indeed be full of expert language, somewhat incomprehensible outside of the exact area)

Scivee.tb
- science video sharing web site – synchronize video, literature, slides – within the browser
- more discussing a paper, vs. showing an experiment
- profiles and community to connect scientists to each other
- changed – people wanted to upload stand alone science videos (lions on the savannah or conference presentation)
- poster casts, slide casts

questions to scivee:
- requirement that poster already be accepted/published elsewhere first?
- they contact conference organizers to have a private community where these are available to conference attendees by password for some period of time and then open later

questions to JOVE
- do they get the text with what the equipment is and where the consumables came from and such answer is yes
- is this new methods – or is this methods that already exist in the literature – could be both
- how does peer review work – goes to 2 or three reviewers who give time stamped comments
- is this multiple or duplicate publication? not really because you’d have a methods paper vs. the results paper

funding models:
- sci vee- trying to go to conference organizers
- jove: advertising, author fees ($1k) when they produce for you

question about animal research
- they review carefully special board
- nevertheless face associated with animal research – firebombings, attacks etc.
- they’re concerned about self-censure and the science being put out.

(question that occurs to me now - people judge other people by their names and institutions and stuff, of course, but also about personal attributes - when you know CK Pikas is a white woman in her 30s, does that make your think any differently about her work? so here's the question: is there value or what difference/impact whatever, does it make to see and hear the scientist with the protocol? Ideally using Mertonian norms of universalism, it makes no difference whatsoever... but people are really funny.... if you had the same or equivalent protocols done by an older white man and a younger minority woman, would the reaction and the use be the same? I really hope so! Maybe it's horrible that I even speculate? The choice to have a little intro of the scientist before the protocol is an interesting one - presumably to help the viewer trust the protocol.)

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Semantic web in science: how to build it, how to use it

John Willbanks

semantic web rdf
triple – subject, relationship (directed arc, with label), object
literals vs reification (“has category”)
bootstrap using grddl (“griddle”) – extract rdf, using parser, from sql database or whatever

owl stuff- types of relationships (symmetric,
sparql (queerly language)
unlike xml, pull statement out and it still makes sense – can remix
licenses are really nasty – even if intended to be open, can prevent some remixing bcs eventual user might be corporate?

need a public domain- in US databases can be public domain (not so in Europe)
cc zero – zone of certainty for semantic web – certify types of reuse that are ok.

viral licensing actually causing problems… need this new way to make things usable in a semantic web

neurocommons – their proof of concept
- e pluribus unim
- this domain bcs pubmed/nlm non-copyrighted data
uses:
dns for life sciences
api to the public domain of data
enhanced document markup
activity center analysis

working with Microsoft to like spell check articles as they are written so all of the connections to the data are in tact
(all life sciences all the time - actually, I think astro and earth/planetary sciences have some goodies like this, but the people who work on these sorts of things apparently don't show up at this meeting --- it would be great from someone from ADS to show up and talk next year)

Labels: scio09

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