nodalpoint.org - Yahoo! Research! Laboratories! - Comments

Yeah, need to update my

ejain — Tue, 22 Jan 2008 19:47:42 -0500

Yeah, need to update my blog...

700?

nuin — Tue, 22 Jan 2008 13:18:11 -0500

At 700 a pop for an Action Figure?

Dude, Where's My NAR?

Duncan — Tue, 22 Jan 2008 13:09:27 -0500

Hello Maximillian, I wasn't attacking NAR, was just wondering about what proportion of the data is dead. It is an interesting technical challenge to find this out. It would also be useful to measure the cost of gathering noisy, redundant and poorly understood data in terms of wasted resources (people, time, money, computers, false positives etc). Perhaps somebody has done something like this already? Especially with all the irresponsible sequencing just for sake of it that goes on...

As for the physicists, I mentioned them for comparison. Like you, I doubt they will use 100% of their data either, but will probably use much more of it. However, they keep delaying switching their big machine on, which means they are still waiting for the data. That is, unless when they finally flip the switch on the LHC, we all disappear into a black hole, tombs and all :)

It doesn't matter, they got published

lbbros — Tue, 22 Jan 2008 06:46:50 -0500

Does it matter that large quantities of this data will probably never be used?

Probably not, as their authors are already happy enough to have those published, and then they can ~~stop mantaining~~ move on to another ~~project~~ publication. It is indeed a sad state of affairs.

Swiss Prot Databases / Action Figures

Duncan — Mon, 21 Jan 2008 18:12:33 -0500

Hi Eric, yeah even more redundancy there. Talking of SWISS Prot people, I'm just wondering when your Amos Bairoch action figure will be available in shops?!?! What are you up to now that you've moved on from SWISS Prot to Seattle?

Why NAR

maximilianh — Sun, 20 Jan 2008 10:59:14 -0500

I add the usual defense of the NAR databases: At least they are indexed by pubmed, so as there are biologists that are not used to checking in google if there are websites about their subject, they will find them quicker via NAR. The data is not dead, websites can always be exported. (I've made the experience that for smaller databses it's usually quicker to scrape the data from an html page with something like HTTP::Recorder than writing to the person responsible for the data to send you an sql dump.) In addition, people get papers for their databases like this and other people can cite the database properly, so NAR makes the web citable and advances someone's career a little bit. It already eases the transition from a traditional paper-based science to a more web-orientated world. Databases are peer-reviewed, so they don't contain complete crap, a paper in NAR assures some minimal quality. And a write-only database is better than none at all, at least someone has collected something and you can scrape it from its tomb.

I would just love to see a minimal requirement for a publication in NAR: They should all offer some simple text-based export, e.g. tab-delimited flatfiles. That could save me a lot of time...

Of course, large quantities of these data are never used and never read. But, heck, this is research, right? 90% will not be used in the end. It's not too different from those 500 alignments algorithms, 200 genomic analyses, hundreds of papers that describe "new" cloning strategies, yet another new gene, etc. I don't believe that the physisists use 100% of their 1,5 GB / sec either.

Also, think of all the

ejain — Fri, 18 Jan 2008 20:12:16 -0500

Also, think of all the redundant effort that goes into setting up the basic technical infrastructure each database needs (data storage, user interfaces etc)...

Neil — Tue, 20 Dec 2005 23:23:41 -0500

I must admit, discussions about the semantic web leave me baffled. I get the idea - that we use metadata to deliver relevant content rather than relying on keyword searches. However, reading articles like those mentioned leaves me with no sense of how this is being achieved (if it is). It seems to be an almost deliberately abstruse and jargon-riddled field - jargon for jargon's sake - which, for people whose goal is information delivery seems rather absurd.

I'd like to see some practical demonstrations, proof of concept, particularly with relevance to biology. Perhaps such sites exist? Set up a server with some content, write a prototype client and show me how it works and the advantages over what I already use. Otherwise it's all just so much highbrow intellectual arm-waving.

Rather interesting piece. It

Greg — Tue, 20 Dec 2005 07:05:26 -0500

Rather interesting piece. It is nice that Rob McCooool has offered up his reasons why the semantic web won't work, I mean *who hasn't* criticized the semantic web at some point ? It is becoming like a club or something, "The semantic web is a pipe dream and won't work because of...". Funny thing is I don't think TBL at any point has said the semantic web will be an easy thing to achieve... of course Rob has a solution, doesn't everyone have a solution to the semantic web ? but I think the contribution is not so much his solution but *how* the solution is presented.

Think about it, the article is entitled "Rethinking the Semantic Web part 1" and the solution is presented in the "To be continued..." part II. Pure genius, you just can't help yourself begging for more ? So from this point on I plan to publish all papers in in either two parts or three. Part one will will have the introduction, materials and methods and a results teaser... just to keep you on the edge of your seat for part II, full results and discussion. I haven't figured out the trilogy format yet.

Seriously though.

I am curious about his proposed solution as I agree with many of the failings he states e.g. how OWL deails with exceptions and context. This is close to my current issue with the semantic web, that people miss the point that It Takes an Agent to be Semantic. It is not just about controlled vocabularies and reasoners.

However for someone claims to have a solution to the semantic web's problems there are some odd statements in the article. For example "RDF triples must be maintained, either as separate files or within separate blocks inside HTML files." What about in a triples database ?

"The ontological data model makes representation of any nontrivial factual information difficult because it can’t represent context of any kind." What about named graphs ? What about the fact that context (in the semantic sense and not just the provenance of the triple) is dependent on shared meaning (common knowledge) ?

See Kashori (John Black) for more on how the semantic web is likely to emerge.