Disqus - Latest Comments for bgood

Re: my cloudy evolution

bgood — Wed, 05 Aug 2009 18:00:06 -0000

You are probably right. I'm sure they are all trying to figure this out
internally and many of them have very capable people working for them. I
suppose the other reason for my statement is that I am more interested in
being part of something small and totally new right now than I am in joining
a larger organization - though it sure would be nice to have access to some
of the resources of a company that already has revenue!

Re: my cloudy evolution

bgood — Sun, 02 Aug 2009 14:20:30 -0000

Thanks for the offer Bill, I may take you up on it at some point.
For now, I'm more interested in smaller, perhaps more revolutionary initiatives (with clear financial models). While PloS is doing some great things in general, it still seems to me that they are operating based on what Wilbanks refers to as "document mentality". If you know anyone that really seems to understand and is working to realize the following bit of advice from his post, please let me know:
"If you want to make the article of the future, start with integration and work backwards. Don't start with the article and work forward, because you'll be trapped in document mentality instead of the network mentality."

Re: Sell bgood on twitter ?

bgood — Sat, 27 Jun 2009 01:09:39 -0000

It is very tempting ;). Though right now I'm more in the mode of 'angel funding' then postdoc funding...

How much would you sell something like a twitter name for ?

Re: Sell bgood on twitter ?

bgood — Thu, 25 Jun 2009 17:33:17 -0000

Ya, thats pretty much whats on offer I think. Seems kind of fun.

My only real hesitation is the twitter sensation right now. It occurs to my
penniless capitalist mind that the name might be worth some real money in
another year or so. Or.. the bizarre amount of twitter hype fades out
(perhaps because of google wave..) and then no one cares anymore and I miss
my opportunity for free burgers and a plaque.

will have to sleep on it.

Re: publisher removal

bgood — Fri, 19 Jun 2009 12:07:25 -0000

Thanks Ricardo, I feel the same way. if I ever get my act together I'd love
to set up a simple system to test out the idea for real.

Re: publisher removal

bgood — Tue, 16 Jun 2009 12:36:11 -0000

Thanks Bill. You are right of course, the effect isn't exactly the same.
However.. isn't it really a question of scale?

Taking things to extremes for the sake of argument, lets say that there was
an institution of some sort (we could just group all of them into this)
that paid for access to all scientific articles and that this institution
allowed a robust, user-friendly filesharing network to emerge such that
anyone outside of the boundaries of said institution could easily and
freely retrieve any of the articles (or data..). At that point, it seems
that other institutions and non-institutionalized citizens (like me) would
probably prefer to save their pennies (and time) by using the free archive.
If that situation became reality then it would force revolutionary changes
in the way publishers did their business.

I'm no expert, but this seems to be a lot like what happened in the music
industry. No one lead that particular revolution as far as I can tell - it
seems that the current state of affairs came to be as a direct result of
non-revolutionary people sharing musical publications with each other.

I have this sinking suspicion that scientists younger then me (though I'm
no longer a scientist I suppose) have already created and are using the the
Napster of science but I haven't heard about it yet.

BTW, I'm with you on the review policy, but I think you will need to
convince more powerful people than me if that revolutionary path is to be
taken. Maybe you should start a list of such people - a sort of public
declaration?

Re: publisher removal

bgood — Thu, 11 Jun 2009 02:17:22 -0000

Apologies if I have offended my PDF-supplying comrades by calling them saboteurs, I meant no ill-will by it.

However, you folks did indeed hand me - for free - an item that was not only legally owned by another party but one that was officially for sale.

Whether this action is active sabotage of a system that many (of you) claim is broken or not is a question that I suppose I should not be trying to answer for you. But, the effect of that action and many more like it is the same whether you are just trying to be friendly to me or are trying to be revolutionary.

Re: publisher removal

bgood — Fri, 05 Jun 2009 14:14:45 -0000

Hi Jamie, yes indeed. This follow-up was mostly in response to the emails I received with the PDF that didn't appear as comments here - people are still a bit shy about doing p2p file sharing in the open.

Re: licenses and linked data

bgood — Tue, 02 Jun 2009 18:46:23 -0000

Hmm. Thanks everyone for responding so fast. Within a few hours I have now had three different people send me the PDF. Guess I will have to read it!!

While satisfying from an academic, freedom of information, down-with-the-man, perspective I have to say that this is a little bit troubling when considering current career choices..

I'm wondering to myself if there is anything digital that people would actually pay for these days? How might one make a living as an independent information engineer if not? Does the now expected free flow of knowledge mean that all knowledge creation must be government (or advertising) sponsored ?

Is it time to start working on real physical things if I am to escape working for a government in one way or another?

Re: bad day programming

bgood — Mon, 27 Apr 2009 15:56:43 -0000

Yes, I mentioned it in the last bullet there. The problem I had with it was that the file was very large; I couldn't find the string I was after by browsing through it and there was no search option in the plist editor.

Re: holy mashup, mashup man!

bgood — Fri, 17 Apr 2009 17:27:30 -0000

From sister: this shows "the joy of unintentional collaboration". Like that way of putting it.

Re: So long 26th grade!

bgood — Tue, 14 Apr 2009 12:34:48 -0000

Thanks Egon. Honestly I really didn't have a good answer on the
spot. To clarify, most of the discussion oriented around ways to
crowdsource knowledge acquisition in the name of ontology creation and
semantic annotation. The only thing that came to mind when he asked
the question was improved natural language processing - but I don't
really think that was what he was hoping to hear nor do I think we
will see any paradigm shifting improvements in the area for a while.
(Plenty of incremental improvements all the time of course.) He
mentioned better voice-based interfaces with computers but I'm not
really sure if they would help. Since then, I've been thinking about
it and, if given the chance to answer the question again, I would
probably say something about Mobile devices -> which could might
connect directly to his ideas about voice-based interfaces. In the
end, I don't think we need any new technology to effect dramatic
change - just better use of existing human and technical resources.

The revised thesis will be up online via the UBC library (open
access!) within about a week. I'll post a link to it when its ready.

Re: So long 26th grade!

bgood — Wed, 08 Apr 2009 13:18:38 -0000

Thanks everyone! We will see about the next steps..

Shirley, yes the grass is indeed greener over here on the other side, but it is also a strange and uncharted land. It feels like I've been pushing for years to reach the top of this mountain and now that I made it I find myself in the middle of a seemingly endless plateau - most of which is hidden from my view. The only solution? - pick a direction and start walking I guess.

Re: semantic dissonance in uniprot

bgood — Thu, 26 Mar 2009 00:10:22 -0000

Chintan, thank you for your comment,

As you seem to be going against the general consensus so far
(including that of a representative from UniProt), perhaps you could
elaborate on the "classic mistake" that you speak of. I am not
familiar with it as you express it here.

Re: semantic dissonance in uniprot

bgood — Mon, 02 Mar 2009 11:30:44 -0000

Hi Richard, I honestly don't know enough about the two ontologies to make a judgment about your suggestion. It seems likely that this isn't an isolated problem and that any attempt to improve on the 'sort of related to' relationship would really require an extensive mapping exercise between the different ontologies - which would certainly be valuable but may be beyond the interest of a third-party like uniprot to pursue. Regarding sameAs and trust, it seems like a reasonable and useful thing to do to check with both owners when considering making a sameAs assertion; however, if I needed it to solve a particular problem and the other party was unresponsive (which would happen a lot) I would not hesitate from using it. 'Publish then filter' works here as well - until the assertion is made in the open its much harder to get external feedback.

Re: semantic dissonance in uniprot

bgood — Mon, 23 Feb 2009 17:52:36 -0000

I wasn't arguing against the use of owl:sameAs, just the misuse of it. Obviously this is a misuse. Suggesting that this is an example to illustrate the point of owl reasoning seems like a bit of stretch to me but ok sure - if they bothered to run a reasoner (assuming they found one that was happy with their OWL-full representation) they would no doubt be surprised at some of the inferences it generated and perhaps make adjustments. I suppose the lesson is perhaps that developers that make use of constructs for which reasoners exist should probably assume that those reasoners will eventually be used and test accordingly. Perhaps this would make people more aware of the semantics of the languages that they are using.

Re: semantic dissonance in uniprot

bgood — Mon, 23 Feb 2009 17:08:07 -0000

Hi Mike, thanks for the links. No, I hadn't known about the thread. I honestly didn't know how pervasive the sameAs problem seems to be. I guess I should not have been surprised when I found it in uniprot! I read through your comment there and I think we are definitely thinking in the same direction - you have my vote when the election comes ;).

Re: semantic dissonance in uniprot

bgood — Mon, 23 Feb 2009 12:52:18 -0000

Feel free to use this as a starting point and go forth ;). I'm not really excited about writing papers these days.

You could do the same thing for bio2rdf and probably contribute significantly to both projects. Linked data is a great start, now lets make the links a little more meaningful!

Re: semantic dissonance in uniprot

bgood — Mon, 23 Feb 2009 12:49:39 -0000

Yes. Looks like they have some useful concepts. In particular http://umbel.org/umbel#with... and http://umbel.org/umbel#isLi...

Is there any indication of how widespread UMBEL uptake is? This is the key chicken and egg problem of course. It needs to be widely used to convince people to use it....

Re: semantic dissonance in uniprot

bgood — Sun, 22 Feb 2009 12:30:17 -0000

Yep, I agree with your assessment. Though I do like their current interface, I wish uniprot would also put up a SPARQL endpoint - it would be much more powerful and mashable. We created a local version of a slice of their data with Virtuoso for a project of mine and it is very fun to work with. Have a look if you like here and put in 'uniprot' (no quotes) as the default graph URI.

I thought about rdfs:seeAlso which is a lot like skos:related, but I think the relationship should be stated more explicitly. They use seeAlso in many cases where I think they should be more explicit about what the relationship is (e.g. between proteins and sequence motifs) but at least it isn't ~wrong.

Re: Notes from Everything is Miscellaneous

bgood — Thu, 12 Feb 2009 17:45:15 -0000

I'd be happy to lend it out. The only thing that I can think of right
now that I disagree with but still like is my wife ;).

Re: testing disqus friendfeed sync

bgood — Tue, 10 Feb 2009 15:57:34 -0000

hmm looks like this is a one-way sync for the moment. Comments from friendfeed appear here but not in the other direction. Also I'm not receiving email notifications of new comments now despite enabling this feature on both disqus and blogger. hmm

Re: testing disqus friendfeed sync

bgood — Tue, 10 Feb 2009 12:29:30 -0000

testing again

Re: testing disqus friendfeed sync

bgood — Tue, 10 Feb 2009 12:19:44 -0000

testing blogger/friendfeed integration via disqus