nodalpoint.org - open access - Comments

Open Access?

Duncan — Wed, 05 Sep 2007 12:42:39 -0400

It seems we're not quite there yet, even with the Open Access journals. See This post from Peter Murray-Rust on "Open" Access.

Unintentional hilarity

Neil — Mon, 27 Aug 2007 01:36:24 -0400

I've had that poster above my desk for years (in fact I think you alerted me to it about 6 or 7 years ago).

Unintentional hilarity is right. The swift, incisive comment by the OA community has labelled this group as clowns from day one. They're doomed to ridicule and disdain until they take down their site.

Thank God

nuin — Sun, 26 Aug 2007 19:09:43 -0400

It is "only" in America so far.

A snip at $250,000

Duncan — Tue, 07 Aug 2007 09:12:03 -0400

Nice camera, but a little expensive for my pocket at $250,000. The sales guy told me he'd cut me a deal of 10 cameras for $1m if I wanted.

Don't forget the hotel bar

mndoci — Mon, 06 Aug 2007 17:22:09 -0400

Where else can you get a presentation on the coolest 3D camera in the world

According to their access

pwnedd — Sun, 22 Apr 2007 17:21:18 -0400

According to their access options chart (http://www.sciencemag.org/subscriptions/access_chart.dtl), "Full text of research articles one year after publication back to 1997" is available for free to registered (via free registration) users. Both the ones about are more than a year old so perhaps that is what you are seeing? That's wierd that you would see the same thing though even when you are not logged in. I Actually never saw any mention of "free" full texts. I either could see the full-texts (on-campus with institution subscription), or could not see them (e.g. if i visited the site through a proxy). That's neat though that they do offer those articles for free :)

Keith

That paper is a technical

Greg — Fri, 20 Apr 2007 22:37:14 -0400

That paper is a technical comment so it looks like according to science that is free.

Interesting, I didn't notice the "My Access Rights" link, however it still doesn't make sense as the referred articles are reports and reviews. Maybe they have made a mistake on the permissions of this article ?

Technical Comments are free

PedroBeltrao — Fri, 20 Apr 2007 10:09:05 -0400

I checked the link "My Access Rights" and it says that I have access to the paid content and also to the free content of the site that includes:

* Science, Science Classic, STKE, SAGE KE Table of Contents of current issues and back issues
* Science, Science Classic, STKE, SAGE KE, abstracts and summaries
* Science Supporting Online Material
* Science Technical Comments
* ScienceCareers.org including Next Wave and GrantsNet
* ScienceNOW stories published within the past four weeks
* Searching

That paper is a technical comment so it looks like according to science that is free.

Sorry about the original

Greg — Fri, 20 Apr 2007 09:32:27 -0400

Sorry about the original post+image being a little screwed up, I guess the system for posting images in blogs needs a little tweaking.

As far as free the free access to this article and its referenced articles, I can read them all without logging in. I did a little digging for some kind of open access announcement, but nothing turned up via site search ?

Databases in Peril

Duncan — Fri, 12 Jan 2007 10:48:39 -0500

Thanks for all your comments, here are some thoughts...

Quantity is a significant problem we're not just talking about individual databases getting bigger and bigger like GenBank, we're talking about more different types of databases. Potentially we want to allow the combination of data from any of these different databases and others that will appear in the future. Obviously, any given researcher probably isn't going to want to search all 900+ databases, but it would be beneficial to the wider scientific community if all these databases can easily interoperate. The more databases there are, the more challenging easy interoperation becomes, because there is more heterogeneity, more API's, more schemas etc.

Peer-reviewed publication can help assess quality this is what peer-review is for. The editors of this issue claim to look for good quality data as well as a good quality interface. As pointed out in the comments above “anyone with a modicum of knowledge can put a database or web app online”. By itself, this is not enough for publication. It is no good having great data with an awkward non-standard interface and vice versa. The NAR database issue may well be an “easy” publication, but it doesn't make it any less important. The Databases in Peril article, wouldn't have been possible if NAR hadn't been faithfully recording all this information in the first place. I suspect publication in the NAR database issue is harder than some suggested, it's not just a case of shoving a database on the web then writing a paper about it, you have to convince the reviewers the database is worthy: novel, useful and usable.

Churn is inevitable but the overall trend is still upward Databases (and tools) are not immortal, some are bound to wither and die eventually. Since last year 11 databases have gone this way, and the article, discusses why. The general trend is still upward and will probably keep going. In the long run, the longevity of database can be an indicator of its quality because somebody cares and is skilled enough to maintain and fund it for a long period of time. As for the databases that are “struggling financially” (according to Nature) how is this news? Struggling could mean anything. Haven't you always had to fight for sustained funding of any scientific project?

Standards are boring (but important) it can be difficult to get standards work funded, done and published, what John Quackenbush calls Blue-collar science. It is unglamorous but essential work, and nobody is going to win a nobel prize for creating a standard schema, ontology or whatever. What is the research contribution of creating a standard? Novelty? Discovery of new knowledge? This is partly why we have chaos, creating standards, in itself is often not considered “science” or “research”. But without them, science is much harder.

Integrated Search is hard We would all like integrated search “from one box”, but the way to do this is still very much an open research question, not just in bioinformatics, but for computer science also. What is more, this is not merely an “IT problem”, there are novel and serious scientific challenges in achieving this. If it was easy and straight forward to provide integrated search to all these databases, don't you think somebody would have done it by now? Until that time, we have Entrez Global Query...

Quantity not the problem

Neil — Sun, 07 Jan 2007 08:10:00 -0500

Not drowning. More data are good - the more, the better. Only a few of those databases are relevant to an individual researcher.

As others have already commented, the problems are (1) the quality of the databases, (2) their diverse, "higgledy-piggledy" nature (no standards, APIs, integration) and (3) their longevity, or lack thereof. Frankly, anyone with a modicum of SQL and CGI knowledge can put a database or web app online. So they do. You can't legislate against bad web resources.

I would question whether these annual issues still serve any useful purpose, other than to make the journal appear authoritative or provide an avenue for an easy publication. If I'm looking for an online resource I start with Google, not an outdated journal article.

Need standards

Animesh — Sun, 07 Jan 2007 05:02:36 -0500

Great article Duncan, thanks for bringing this on.
I have seen lot of people accessing low quality data from many well-known db's and high quality data in not-so-well-known ones.
For eg, GBK files mostly does not talk about quality while it's ASN.1 counterpart might offer it [ http://getentry.ddbj.nig.ac.jp/cgi-bin/get_entry.pl?AF207953 ].
Regarding algorithms to analyze these data, any comment will be like a troll.
To minimize this, I feel, something like Bioinformatics oriented DIGG will be great.

Vaporware

lindenb — Fri, 05 Jan 2007 16:23:41 -0500

Each time a new annual issue of NAR is published I remember this paper from Nature.

http://www.nature.com/nature/journal/v435/n7045/full/4351010a.html

Databases in peril
Zeeya Merali and Jim Giles
Nature 435, 1010-1011 (23 June 2005)
doi: 10.1038/4351010a

Nature contacted 89 databases listed in the Molecular Biology Database Collection (Nucl. Acids Res.28 1−7; 2000) to see how many still have funding five years on. Of these, 51 reported that they are struggling financially. Seven of these have closed; the rest are being updated sporadically in their owners' spare time.

Pierre

Drowning!!!

mndoci — Fri, 05 Jan 2007 16:12:25 -0500

I think that we're going to drown at this rate. Not because there are too many databases. Those can, and perhaps should be spread far and wide. My concerns

Quality. How do we know whether the results in our hands are any good? Can we glean meaningful knowledge from them?
Integrated search. I don't want to go to every database and search there. I want to search from one box
Standards. I want the data to follow certain minimum standards.

What was that about airlines :-)?

My Blog: http://mndoci.com