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Allyson Lister › Comments
@allysonlister Clearly, a bioinformatician is a cool, awesome person who deserves respect, praise and love :-)
Nir London, Rajarshi Guha, Allyson Lister and 4 other people liked this
...and now we've got that out of the way...get on and sort out my Word files ;-)
- Cameron Neylon
Cameron, that was not even funny! I finally begin to appreciate when people send me an Excel file with their data. I mean, it could have been a Word file.
- Lars Juhl Jensen
At least a cheminformatician deals with chemical information, not 80% IT problems...
- Egon Willighagen
Lars, consider the following: Last night I tried to load a badly formatted XML file in excel so I could see what was going on...the scary thing is it almost worked...but the formatting and comprehension issues do go in both directions. I just wanted to see what was in the file...but I do at least avoid Word. Besides isn't the file format illegal now anyway? ;-)
- Cameron Neylon
My first attempt would be to open an XML file in a validating XML editor... not excel ?!?! Try jEdit...
- Egon Willighagen
I have heard stories about bioinformaticians being sent word docs with sequence in them... very odd. :)
- Allyson Lister
...actually I probably should have just opened it in a web browser and viewed source in retrospect...
- Cameron Neylon
@allyson screenshots of the NCBI sequence page pasted into a word document are even better :)
- Endre Sebestyen
Neil, you are definitely right: bioinformatics, though difficult to define, is important, as are the "icians"!
- Allyson Lister
@Endre - eeek, really? That's amazing...
- Allyson Lister
@allyson :D, and i've also seen scientists _editing_ pictures in word. getting just simple sequences in word documents is quite usual for me now.
- Endre Sebestyen
Integrating with integrity - http://www.citeulike.org/user...
tim liked this
Nature Genetics, Vol. 42, No. 1. (01 January 2010), pp. 1-1. Data worthy of integration with the results of other researchers need to be prepared to explicit export standards, linked to appropriate metadata and offered with field-specific caveats for use. Data exchange may need to be taught and discussed in handshaking workshops.
- Allyson Lister
eek - Feel better soon!! And don't get anywhere near me! :)
- Allyson Lister
Duncan Hull to Duncan's feed, The Life Scientists, Semantic Web for Health Care and Life Sciences IG
The Semantic Biochemical Journal experiment « O'Really? - http://duncan.hull.name/2009...
Bora Zivkovic, Mickey Schafer, Hope Leman and 20 other people liked this
"There is an interesting review [1] (and special issue) in the Biochemical Journal today, published by Portland Press Ltd. It provides (quote) “a whirlwind tour of recent projects to transform scholarly publishing paradigms, culminating in Utopia (http://www.getutopia.com) and the Semantic Biochemical Journal experiment”. Here is a quick outline of the publishing projects the review describes and discusses: Blogs for biomedical science Biomedical Ontologies – OBO etc Project Prospect and the Royal Society of Chemistry The Chemspider Journal of Chemistry The FEBS Letters experiment PubMedCentral and BioLit [2] Public Library of Science (PLoS) Neglected Tropical Diseases (NTD) [3] The Elsevier Grand Challenge [4] Liquid Publications The PDF debate: Is PDF a hamburger? Or can we build more useful applications on top of it? The Semantic Biochemical Journal project with Utopia Documents [5] The review asks what advances these projects have made and what obstacles to progress still exist....
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- Duncan Hull
from Bookmarklet
Am I missing something here? I only seem to see a few popups when mousing over references?
- Cameron Neylon
Interesting though getting started wasn't entirely transparent. Figs are interactive (pink background and menu) so, for example, data from Fig 9 can be replotted. Tended to spawn popups at an alarming rate. Fig. 13e appeared unable to load into popup.
- Peter Miller
@Cameron, you need to download the Utopia client to get the full effect http://www.getutopia.com the animations are embedded in the PDFs and viewable within the client. It's not a browser based thing (yet).
- Duncan Hull
Done that, looking at both the paper online in enhanced version and pdf I'm not seeing any visual cues or anything that take me anywhere much. Do I need to have the utopia client running as well? Ok you need to open the pdf in Utopia. That's really not immediately obvious I have to say, particularly with the "enhanced online version" getting billing front and centre. Ok I could have read the instructions but its only the mention that Utopia is a "pdf reader" that tells you what to do. Could be clearer.
- Cameron Neylon
Have to say that the idea of a semantically enhanced pdf I have to download and open up in a particular viewer seems to be somewhat missing the point :-)
- Cameron Neylon
Also seems odd that the enhanced online version doesn't at least include the links that are in the enhanced pdf
- Cameron Neylon
@Cameron I see your point, I'd like to see a more web friendly version but there are some limits to what you can do in a web browser (especially when it comes to sequence alignment and molecular visualisation)
- Duncan Hull
Yes, and that is all fair enough - you need to start somewhere but you'd think the links could be translated across pretty easily (e.g. Caspase-3 in paper 1, fig-1 legend is linked in the PDF to a wikipedia entry, why not in the online version?). Bring on HTML5 is what I say :-)
- Cameron Neylon
@Cameron ... and yes, its an "experiment" too (normaly caveats apply!). The thing to look for is the little Utopia Documents icon embedded in the text once you've opened up an article (e.g. the review) in Utopia documents. Thanks for the rapid feedback...
- Duncan Hull
Yep, found it eventually. I'd suggest changing the instructions to be much more explicit. i.e. Download Utopia, then download pdf, then open in Utopia. Most people will have pdfs set to autoload in something else so its not an obvious path - particularly to people used to plugins and overlays. Heh, next quetions can I leave a comment on the journal article to suggest this....mmmm.....that would be a "no" then... ;-)
- Cameron Neylon
Dear Santa, Please can you provide Utopia for Ubuntu/Debian/Linux. Thanks :)
- Allyson Lister
I just skimmed it initially - didn't note the requirement for this odd piece of software. Puts paid to it for me, I'm afraid.
- Neil Saunders
From Philip McDermott: "ubuntu version in the works but just slightly delayed for launch. I'd have thought it'll be available next week sometime"
- Allyson Lister
The idea of a specialized PDF reader for this means it's just a proof of concept at this stage. I'll mention it to the Mendeley people and see if they might like to incorporate some of this into their internal PDF reader.
- Mr. Gunn
@Mr. Gunn thanks...
- Duncan Hull
@Mr. Gunn thanks. Be interesting so know what they think of it, feel free to put them in touch with us :o)
- Philip McDermott
I think that the initial confusion of PPLs website has confused a lot of web-oriented users. Try grabbing the app, the paper, and working through it, and you should get a feel for what we're trying to do. We're not saying web-based is bad, it's just that this is a little different.
- Philip McDermott
@Philip see also commentary here http://digitalcuration.blogspot.com/2009...
- Duncan Hull
As I understand it the PDF reader software is just an initial client for the backend which lets you annotate whatever - and from where all the annotations are fetched. If (when?) it gets opened up you could extend the existing client to read other files, write your own client, write a Firefox plugin, whatever...
- Euan
@Euan yes that's right (and you put it much better than me). As for opening it up, you'd have to ask the Utopia team... it would make a lot of sense.
- Duncan Hull
I like the concept of the Utopia reader. But the integration of references could have been done better. Why not use DOIs instead of linking to a Google Scholar search?
- Martin Fenner
Dear Santa, like @Allyson I really hope your reindeer's can still pull the Linux version, too.
- joergkurtwegner
Besides, how does it compare to the interactive ICM in PLoS ? http://ff.im/acHs9
- joergkurtwegner
@Martin yes references linking to Google Scholar is just an example really for the first release, since the DOI is known the links could be configured to go anywhere -you're Institutional Repository, university libary, pubmed, etc.
- Philip McDermott
@Allyson @Joerg are Linux hacker is lost in the Black Forest right now, but when he gets back a Linux build will be high up on his list :o)
- Philip McDermott
Comment on Short Tutorial on using Pellet + OWLAPI + SWRL Rules by themindwobbles - http://themindwobbles.wordpress.com/2009...
I'm not quite sure what you're trying to accomplish with the above rule - it seems that you wish to assert that individuals of Person who have an hasAgent role should also be individuals of Person? That does not seem to give you any extra information. However, there are a number of ways to save an ontology as a separate file, many of which are shown in the OWLAPI documents (http://owlapi.sourceforge.net/documen...). As for just pulling out the ABox, some of this can be done with the InferredOntologyGenerator, as below if you use the default axiom generators: InferredOntologyGenerator generator = new InferredOntologyGenerator( getReasoner() ); inferredInstanceOntology = getManager().createOntology( URI.create( getOutputLogicalUri() ) ); generator.fillOntology( getManager(), inferredInstanceOntology ); getManager().saveOntology( inferredInstanceOntology, new RDFXMLOntologyFormat(),URI.create( getOutputPhysicalUri() ) ); Or, you can replace the first line above with the following...
- Allyson Lister
Pandora, a PAthway and Network DiscOveRy Approach based on common biological evidence. - http://www.citeulike.org/user...
Bioinformatics (Oxford, England) (22 December 2009) MOTIVATION: Many biological phenomena involve extensive interactions between many of the biological pathways present in cells. However, extraction of all the inherent biological pathways remains a major challenge in systems biology. With the advent of high-throughput functional genomic techniques, it is now possible to infer biological pathways and pathway organization in a systematic way by integrating disparate biological information. RESULTS: Here, we propose a novel integrated approach that uses network topology to predict biological pathways. We integrated four types of biological evidence (protein-protein interaction, genetic interaction, domain-domain interaction, and semantic similarity of GO terms) to generate a functionally associated network. This network was then used to develop a new pathway finding algorithm to predict biological pathways in yeast. Our approach discovered 195 biological pathways and 31 functionally...
- Allyson Lister
Comment on Short Tutorial on using Pellet + OWLAPI + SWRL Rules by themindwobbles - http://themindwobbles.wordpress.com/2009...
For the OWLAPI I would look at the documentation page for it here: http://owlapi.sourceforge.net/documen... . All of that seems up to date. Also, looking at the source code, which can be checked out with Subversion (http://owlapi.sourceforge.net/source...), is useful. For Pellet, the mailing list, javadoc, and FAQs available from their website are useful: http://clarkparsia.com/pellet... . Good luck!
- Allyson Lister
Comment on Short Tutorial on using Pellet + OWLAPI + SWRL Rules by rodo2024 - http://themindwobbles.wordpress.com/2009...
hi, i am new to pellet and owlapi and i am trying to get to know the latest versions of them. Could you tell me where can i get a good and updated tutorial (like yours but with more topics), because everything i have found until now seems old.
- Allyson Lister
Fwd: Should you be tweeting? - http://www.hubmed.org/display... (via http://friendfeed.com/ff-for-...)
Hope Leman, Sandeep Gautam, rowlikeagirl and 20 other people liked this
No mention of friendfeed, so what about writing a correspondence piece on this? It could be based on http://ff4s-paper.wikidot.com/start and perhaps also put the recent NIH grant for a "Facebook for Scientists" ( http://ff.im/beKk7 ) in perspective by providing an overview over existing tools along these lines and why they are not widely used.
- Daniel Mietchen
http://www.cell.com/authors... / Correspondence: "The Correspondence format provides our readers with the opportunity to respond to an article in Cell—either a research article or Leading Edge article—that has been published within the last 2 months. Correspondence should be no more than 900 words in length with up to five references and should be of interest to the broad...
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- Daniel Mietchen
Now that sounds like a good idea! I'm all for it - especially mention the gazillion "facbook for scientists" already out there.
- Björn Brembs
I gave it a start at http://etherpad.com/Microbl... - feel free to join in!
- Daniel Mietchen
Added some stuff...
- Björn Brembs
333 words so far, and once the generic FF description and some highlights from the spreadsheet are in, we will be near the limit. So probably no time to dwell on fb4sci, though I would still like to mention the NIH grant in the hope that those people will build on the ideas we lay out.
- Daniel Mietchen
Maybe steer away from a "but we want to talk about friendfeed" towards more "there is a much richer set of tools out there...and here is a good example..."? Might mean the Fb4Sci stuff can get squeezed in?
- Cameron Neylon
I would actually prefer the Fb4Sci stuff in there, and the article would be more balanced if we were to name a few more services that offer microblogging (I listed some in the Organization part of the document). FF can then be described in two sentences as a particularly useful example because it provides hierarchies of threaded conversations in which the most current and the most popular entries compete for the top of attention.
- Daniel Mietchen
Correspondence has to be submitted within two months, so we got four weeks to go if we are to submit something on the matter. Perhaps we can indeed expand this into a general overview on the potential of web 2.0 stuff for science. To this end, I just started a vote on the "open science breakthrough of the year" at http://ff.im/cidKG .
- Daniel Mietchen
thanks guys - a very interesting read (the paper, these responses, the etherpad document). I've added a couple of possibly-relevant points to the etherpad doc. :)
- Allyson Lister
...bumping to remind me to try and do something about this before deadline...
- Cameron Neylon
To those coordinating this: let me know if you need any extra help with anything...
- Allyson Lister
Allyson, help with shortening the FF part and with adding in something on the non-FF alternatives would certainly do something good to push things forward at this stage. Thanks!
- Daniel Mietchen
Edited a bit and tried to merge the new contributions into the draft. The word count for the FF part now stands at ~570 excluding FF real science examples. I still don't see how we can give an overview of more than one of these services and accomplish anything better than a boring enumeration without spirit. On the contrary, people will just get the impression that scientists can't make...
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- Björn Brembs
Correction: 660 words... :-)
- Björn Brembs
See also Jean-Claude's stylesheet about FriendFeed + Science ? FFscience: https://spreadsheets.google.com/ccc...
- Pierre Lindenbaum
Thanks, Pierre, was already mentioned. Just added some examples from this spreadsheet. Word count is now at 760. Tasks remaining (if you agree on the general structure): polishing and final, concluding paragraph. Tasks remaining if you don't agree: re-write :-)
- Björn Brembs
have removed a few words, tightened things up. will do more as time permits
- Allyson Lister
Getting there ... >800 words.
- Björn Brembs
953, so some trimming needed. Mentioned the NIH grant in the roundup section. Which references to take?
- Daniel Mietchen
Good job, Daniel! I think the references are fairly clear, most of them are in the text already (i.e., papers from FF). We have until December 30 to get it all finalized, so we have some time, but I'd rather get it there sooner than later. I think a few more runs of polishing and honing and we should get the final author list together and submit. I suggest everybody who wants to be an author leave the URL to their FFfeed at the end, that way readers get an idea of what FF looks like.
- Björn Brembs
What about signing with a group pseudonym (something like D H J Polymath; http://arxiv.org/find... ) and a link to this thread or the etherpad?
- Daniel Mietchen
I have inquired with them whether links count as references.
- Daniel Mietchen
@Daniel as a pseudonym, I suggest to use what Deepak calls the "BioGang" http://openwetware.org/wiki... http://www.linkedin.com/groups...
- Pierre Lindenbaum
What about the title? "Should you be sharing science online?" would be my favourite but it is not reflective of the current emphasis. Any suggestions?
- Daniel Mietchen
Pierre - good one. Perhaps add FF as initials?
- Daniel Mietchen
BTW, the doi does not resolve - anybody has the correct one?
- Björn Brembs
895 words...
- Björn Brembs
I like Clay's idea for a title: "It's not information overflow, it's filter failure " :)
- Allyson Lister
884 words, and a few more slight tweaks. This means we could probably fit an entire sentence about other approaches' existence, if we wanted :)
- Allyson Lister
Björn - http://dx.doi.org/10... .
- Daniel Mietchen
@Allyson: awesome! @daniel, sorry, meant this one: http://dx.doi.org/10...)
- Björn Brembs
Added ref 4: the NAR paper ( http://tinyurl.com/mr5kvm )
- Pierre Lindenbaum
Right now this sentence is a mixture of DOIs & links: which to use? : "Such conference coverage has even received direct (e.g. ISMB09 http://www.iscb.org/ismbecc..., BioSysBio09 http://dx.doi.org/10...) or indirect (e.g. ISMB08) support from the conference organizers, see e.g. http://friendfeed.com/ismbecc... ." We can convert them all to links, & save some of the 5 publications, but all three examples here have papers associated with them (well, ISMB09 paper is accepted)
- Allyson Lister
Ah - actually it looks like the ref we would use for ISMB08 is actually ref 1 - am I correct? There isn't much detail in ref 1 yet. That could solve part of the problem
- Allyson Lister
I'd also like to find that out, but the DOI does not resolve (for me?). Haven't looked at ref1 yet, to determine if it's redundant.
- Björn Brembs
The DOI, if intact, should point to http://genomebiology.com/2009... , which is behind the paywall for me but perhaps Allyson can give us a hint ;-)
- Daniel Mietchen
Sorry - yes, @Daniel, the DOI seems broken, but the genomebiology link is the correct one. If we're limited for references, we could just link to the FF room, which is http://friendfeed.com/biosysb...
- Allyson Lister
We have 5 references and thus I added Allyson's to make it 5 :-)
- Björn Brembs
Question as to whether its advisable to include reference to the RW room. I think someone raised this somewhere but I can't see the discussion now.
- Cameron Neylon
Otherwise made a few very minor changes
- Cameron Neylon
I'm about adding a ref to O'Reilly/"Beautiful Data". The collaboration for this book started here: http://friendfeed.com/fgibson...
- Pierre Lindenbaum
@Cameron - yep, a few of us have brought up that point (me and michael and some others I think in the etherpad doc). I'm happy to go with whatever the owners of the room, or the general consensus, wants :)
- Allyson Lister
Cameron, do you have a reference for the second grant? I am only aware of http://www.labgrab.com/users... .
- Daniel Mietchen
Added mention of polymath project.
- Daniel Mietchen
Found reference mentioning both grants: http://www.nih.gov/news... .
- Daniel Mietchen
RW room discussion is in the header of the document. IMHO there are several crucial reasons for finally going public: it's a grey area probably still fair use; more subscribers mean more access; readers will see the usefulness of this room, even if they don't get any of the other features; the kinds of hoops we have to jump through to get access need to be made public and the room has a significant record now.
- Björn Brembs
I think we need to drop ref 6 since we only have 5 and it's not a journal article, correct?
- Björn Brembs
With Etherpad deleting everything by March 31, we should think of ways to archive existing pads - particularly relevant for this one, as it was meant to be citable. As far as I can tell, none of the currently available options preserves the version history, so if we want to have that, we should do a screencast.
- Daniel Mietchen
Indeed, we need to think of something!
- Björn Brembs
Incidentally, the threat of such services disappearing certainly contributes to the hesitation of people to adopt social networks, and the best ways I see to cope with that problem is to have either open standards on data portability, or - better still - social networks (or at least one of the most suitable ones) that are built entirely open source platforms, with open configuration (and of course data portability too). Any suggestions on whether and how this could fit into the concluding paragraph?
- Daniel Mietchen
Isn't it already in there, sort of? Where we write that these tools are in development and NIH funded?
- Björn Brembs
from iPhone
Haven't seen mention of open source and open standards in the news on these NIH grants, so it may be worth making more clear that this is needed.
- Daniel Mietchen
Interesting turn: Etherpad will remain operative until at least when they release their source code. http://etherpad.com/ep... .
- Daniel Mietchen
Upon feedback from Graham, I took the RW reference out. Still think some mention of Open Source would be good. http://www.nih.gov/news... does not mention it. 816 words.
- Daniel Mietchen
Can we be part of that feedback, please? I find the RW functionality so convincing for non-social web users that I fear the whole article might be wasted, i.e, preaching to the converted, without this component.
- Björn Brembs
It was in a DM that I just forwarded to you (dunno whether that works), and I asked him to comment here too.
- Daniel Mietchen
Did anyone manage to do a screencast? I could try and do that today if its useful? But maybe better to wait until you feel is finished?
- Cameron Neylon
I think we should wait until it's basically submitted.
- Björn Brembs
@Daniel: DM was blocked (private).
- Björn Brembs
Nothing wrong in testing, otherwise I'd also wait till it's submitted. @Björn - sent you screenshot.
- Daniel Mietchen
I'll comment once I get back form work (only have internet access here during lunch hour).
- Graham Steel
Right. 1) Having consulted with Bill, we have (the same) mixed views vis a vis raising the visibility of the RW room. 2) We don't feel that we "own" the room though, it belongs to everyone who uses it. 3) We agree that a poll should be set up for subscribers of the RW room to vote on the issue of whether or not they feel it appropriate to raise visilbility of the room outwith FF. 4) The poll is http://www.micropoll.com/akira... and I'll post a link to it in the RW room shortly.
- Graham Steel
Apart from inclusion of the RW room, the title has not been decided yet. Two suggestions are in there now (I threw away my older one).
- Daniel Mietchen
Also, what about the "like=bookmark" discussion? I would like to see that paragraph go back in.
- Daniel Mietchen
I thought that like=bookmark was clear from the context? If not, then it should be easy to add a sentence to make it explicit.
- Björn Brembs
Björn - see chat bar - Michael was not comfortable with the notion. Any other opinions? Also turned Shirky quote from title to quote and set the title to "Social filtering of scientific information - a view beyond Twitter".
- Daniel Mietchen
Besides, FF search has now been unusably slow for weeks, so I wonder whether we should take this formerly excellent feature off the draft. See also http://ff.im/cO3Jw .
- Daniel Mietchen
Two weeks left to submit. I plan to do it on Sat (Dec 19) around noon UTC. Still to address: RW room and perhaps ephemerality of non-Open Source services like FF. I think I saw somewhere that FF have released (part of) their source code, or plan to do so. Anyone know details?
- Daniel Mietchen
Added "the permanence of services whose source code is not public" as an unresolved issue. brushing welcome. What about the RW room?
- Daniel Mietchen
Also, authors need to identify themselves in the document, or they will be missed. Academic affiliations and FF feeds, please!
- Björn Brembs
Like the current version a lot! Also the source code permanence point was important! We should get it ready, clear authorship and author order. My suggestion is Daniel in front, me in the back and whoever feels should have a place in the middle, but I'm flexible (or does author order matter here at all?). From Bill's argument, we should leave the reference to the RW room in, but I'm also flexible there. If there are no storms of protest now, let's keep it the way it is.
- Björn Brembs
I did some more brushing - 899 words now without the title (spot landing). As for authoring, I would really like to go for a group pseudonym (as explained above), but the submission process will probably ask for the usual contact information (incl. email) anyway. Order does not matter to me. Will check back in about 36h, with the intention to submit.
- Daniel Mietchen
I was only pointing out that if you mention the RW room at all, you might as well name it. The poll stands at 41 votes (~25% representation, but it seems to me that there aren't many more than 41 really active contributors/users). The tally is No - 56%; Yes - 32%; Unsure - 12%. I don't think the piece loses much by deleting the mention of the RW room, and it seems to me that the users prefer to continue to keep quiet for now.
- Bill Hooker
I tend to agree with Bill. It seems to me that mentioning (and in doing so effectively naming) the RW room is not what users (that cared to vote) want FULL STOP
- Jan Wessnitzer
from iPod
(1) The point of the letter is to attract scientists who are not using social media for their work to FF. As far as I can tell, the one single thing that everybody can profit from that doesn't already exist in mailinglists etc. is the sharing of papers. Moreover, this is also the one single aspect that touches every single reader, as nobody has access to all the literature. So while it...
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- Björn Brembs
(2) This has been mentioned before, but I see no reason why one would have any interest other than supporting closed access, in keeping quiet. The purpose of the room clearly is to 'document', so nobody in his/her right mind would think that their actions remain anonymous. This means that everybody participating must have been well aware that one day this documentation will be...
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- Björn Brembs
(3) I have now voted often enough to skew the results to more than 50% 'yes'. Who can verify that this has not occurred before, on the 'no' side?
- Björn Brembs
Bjoern, I do agree with your arguments. W.r.t. (3), I was merely trying to argue that the vote should be respected (if it were representative). Allowing multiple votes clearly screwed that up beyond repair! ;)
- Jan Wessnitzer
BTW, I voted 'yes' and maybe the only way to do this now is to vote openly here in the Forum!
- Jan Wessnitzer
@Bjoern: "I see no reason why one would have any interest other than supporting closed access, in keeping quiet" -- are you going to pay my legal bills for me, if I get sued? That's a completely serious question. I'm one of the heaviest suppliers of papers in the room -- if anyone is targeted, I certainly will be. I have said many times that I don't think I am doing anything wrong OR...
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- Bill Hooker
@Bjoern, cont'd: I see no reason to think that (before you fucked it up :-) ) the vote was not representative, which means that most of the RW room users were less willing than you to take up arms against their closed-access oppressors. Judge that as you will, my friend, but some of us have limited resources. If even one publisher sends even one cease-and-desist letter to FriendFeed we...
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- Bill Hooker
@Bjoern, cont'd: I fucking HATE that I have to make this calculation. I would rather publish and be damned -- if the publishers do send lawyers, mount an international campaign in defense of the room and its users and bring their shitty empire crashing down around their beancounting ears. But I have my newly acquired all-American cowardice to consider: I have no health insurance and my...
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- Bill Hooker
P.S. I do not really think I can be accused of "supporting closed access"... merely of refusing to fight it to -- not my, but my family's -- last drop of cash...
- Bill Hooker
Bjoern, I will add that any librarians in this room (and I am not the only one) may have a professional interest in keeping mum. We are pathologically helpful folk, so it's hard to resist sending papers -- but we also belong to a profession that looks incredibly askance at even a HINT of copyright-related impropriety. Are you willing to lose me my job over this? Like Bill's, completely serious question. Remember also that my job is intimately OA-related.
- D0r0th34
I cannot sit here and say nothing in light of recent input. I'll be brief simply by saying, 'as Bill and D0r0th34 say(s)'. I too am not willing to put my livelyhood on the line over this (single) issue. All my (OA) eggs in one basket re. this one? I think not.
- Graham Steel
Just a couple of points. (1) I'd assumed that most or all contributors voted in good faith, i.e. once, on this issue. (2) Having read through the draft at etherpad, I think it reads as a good summary of the utility of FF, with or without the mention of RW room (which is only one small paragraph). Is this one aspect really so important, really such a major component of the FF science experience? I think our interactions and discussions are much more important and interesting.
- Neil Saunders
IMHO, the 'no' voters here are blowing the matter way out of proportion. I'll try and put it back into proportion, which may or may not work :-)
- Björn Brembs
@Neil: Good point. I think it may not be all that much of FF for us, but for people not using social media for their work, it may well be *the only* useful thing they can see in this article. That's one of the reasons I'm fighting for it to remain in the letter. I agree, for anybody who is already using this technology, the RW room may only be a minor benefit, compared to the rest of the features.
- Björn Brembs
To all those who "are not willing to put their livelihoods on the line": what part of "document" did you not understand when you signed up? Bill used the right description for this kind of behavior: cowardice. But if you really think our little room of 40 scientists with inadequate access to scientific literature will wake a sleeping giant, I have several additional accurate descriptions.
- Björn Brembs
(1) Delusion. If you really think someone like Elsevier is risking their 800 millions annual profit in tax payer money by going after people who can barely support themselves, you must be deluded. The music industry doesn't have any profits left to lose, but publishers do. They wouldn't be making record profits during the worst financial crisis in 80 years if they really were so stupid to go after us.
- Björn Brembs
(2) Stockholm syndrome. How many salaries and healthcare plans could you pay from 800 million each year from Elsevier alone? Basically, these guys take your salary and your healthcare and then hold you ransom to shut up and keep your head down - and in response you have nothing better to do than to defend that behavior and cozy up with your captors? You must be the only ones who can see any shred of sanity in such behavior.
- Björn Brembs
(3) Hypocrisy. Isn't it hypocritical to oppose a regime on the surface but then support it when real action needs to be taken? Isn't it ironic that a German is arguing for and volunteering to putting your actions where your mouth is and Americans are arguing in favor of personal safety long before any hint of a serious threat is even perceivable?
- Björn Brembs
(4) Paranoia. There is no precedence of any publisher going after individuals. Publishers have much more to lose than we. Thus, the only potential threat is purely in your minds. There isn't even the slightest hint of any hazard for any one of us on the horizon, yet you defend yourselves against imaginary future actions of your oppressors. More than any of the above, this paranoia...
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- Björn Brembs
(5) Documentation. This thread, more than any number of exchanged papers documents how bad corporate publishers are for the scientific community. Their stranglehold on the community stifles freedom and liberty, intimidates all community members to the point that they delude themselves, develop paranoia and act hypocritically. I think this thread documents more than anything else in this...
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- Björn Brembs
(6) Anticipatory obedience. It is a well-known consequence of dictatorships around the world that individuals in these dictatorships support the dictator even if there is no explicit force, merely because they imagine some bad consequence for themselves or their family if they wouldn't support the dictator. In Germany, every child is raised with what the term 'anticipatory obedience' means. We are being taught how it works to stop all potential threats to democracy at the roots.
- Björn Brembs
1) Elsevier has lawyers on retainer, sending a take down letter costs them very little and makes a point - compare to RIAA - how many college students did they take to court? they are actually legally in their right so you would lose without even a trial 4) it's not paranoia if they really are after you. There is a precedence - in the OSTP letters someone complained about ACM going after a Taiwanese grad student
- Christina Pikas
Björn, don't take this for more than the friendly advice that it is: I don't think it will win over many people in a debate (or win you many friends) to accuse those who are not willing to publicly encourage illegal activities of suffering from delusions, Stockholm syndrome, hypocrisy, and paranoia.
- Lars Juhl Jensen
Bjorn, you have lost my respect. I am blocking you and leaving this room. My email is findable if you care to apologize.
- D0r0th34
Re-reading my posts from this morning, it seems indeed I may have over-exaggerated my points a bit too far. It was and still is my purpose to rouse people and ruffle some feathers on a topic which to me is the worst side of my job. In my frustration that even people who I thought were on my side don't dare to leave their comfort zone for something I find so important, I may have gone a...
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- Björn Brembs
Hadn't voted earlier, but vote now for the references to RW to be included in the article. (nice commentary/response BTW) . RW room is one great thing that you guys are doing and should be proud of. People like me who have no access to any scientific literature (that OA or PNAS or some other because of my country of origination (india) ) are able to do science because of that support;...
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- Sandeep Gautam
I am basically offline now and thus postpone submission until Dec 22. Hope to be able to comment in more detail tomorrow night.
- Daniel Mietchen
@Bjoern: I do understand your position, and I cannot disagree with a lot of what you say. But this is my point of view when I step back a little. 1) the number of subscribers to the room cannot claim to represent the sceintific community (they may or may not be representative, but the claim cannot be made based on the numbers). Nor do I think it can claim to represent the scientific...
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- Kubke
@Kubke: Indeed, very measured words. Last night I've also come to the conclusion that apparently, the situation is not bad enough, yet, for people to seriously push for change. It first has to become a lot worse, before it will get better, I totally agree.
- Björn Brembs
I just rephrased the critical section (lines 45-47). further brushing welcome.
- Daniel Mietchen
That letter looks great! Kudos to all of you!
- Kubke
Sorry, won't make it today. Next online time scheduled for 27, just in time.
- Daniel Mietchen
Just submitted. Latest version: http://etherpad.com/ep... .
- Daniel Mietchen
@Daniel - thanks for submitting, and for including me :)
- Allyson Lister
Just caught up on the thread as I was on vacation for the past week or so. I'll just say that although I am not a member of the room in question, I am in agreement with those who did not wish its inclusion.
- Allyson Lister
Got mail from Cell: "Dear Dr. Mietchen, Thank you for your proposal to write a Correspondence for Cell in response to the article on tweeting by Laura Bonetta published in the October 30th 2009 issue of Cell. Your proposal has now been discussed by the Cell editorial team. We think that your proposal would work well as a 500-word online comment. Our new online comments feature enables...
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- Daniel Mietchen
I hadn't even noticed the comment feature before but here are three previous comments on the Bonetta article: http://www.cell.com/comment... . The first one by Jo Badge ( http://friendfeed.com/jobadge ) already tells much of our story, and we could simply build on it. An easy way to comply with the 500-word limit (which is stated as 8000 characters in the guidelines for posting comments) would be to just split it in two.
- Daniel Mietchen
Found out why I hadn't seen the comment feature before: The comments are only visible if you access the article directly via cell.com (I usually go there via sciencedirect.com).
- Daniel Mietchen
It seems the comments are not indexed by Google - taking the first sentence of Jo's comment as a search string does not yield any results: http://www.google.de/search... . In other...
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- Daniel Mietchen
Asked Cell Press via Twitter: http://ff.im/dC7Na .
- Daniel Mietchen
Comment on Google Wave: Just another ripple or science communication tsunami? (Science Online London 2009) by CameronNeylon.Net » Blog Archive » Reflecting on a Wave: The Demo at Science Online London 2009 - http://themindwobbles.wordpress.com/2009...
[...] Lister blogged the session, there was a FriendFeed discussion, and there should be video available at some [...]
- Allyson Lister
Comment on Short Tutorial on using Pellet + OWLAPI + SWRL Rules by alswamy - http://themindwobbles.wordpress.com/2009...
Thank you for sharing useful info. I have rule like this below Rule( antecedent(Person(?p) hasAent(?p ?a)) consequent(Person(?p)) ) You mentioned above that "you could just iterate over the ABox and just save the new individuals to a file" I don't understand how do use that? can you please tell me bit detailed? Thanks a lot. alswamy@gmail.com
- Allyson Lister
Using the glossaries package in Latex and Linux, Kile - http://themindwobbles.wordpress.com/2009...
I was recently frustrated by the limitations of the acronym and glossary packages: I wanted to have something that joined the functionality of both together. Luckily, I found that with the glossaries package, which actually states that it is the replacement for the now-obsolete glossary package. In order to make this tutorial, I have used the [...]
- Allyson Lister
CTAN: directory: /tex-archive/macros/latex/contrib/glossaries - http://tug.ctan.org/tex-arc...
'Mummi' Thorisson liked this
The glossaries package for Latex. This obsoletes the glossary package. What's great about glossaries is that you can combine your acronyms and your glossary together in one file, and reference acronyms inside your glossary entries. Unfortunately not in texlive-latex-extra on ubuntu :( , which only has the old glossary package.
- Allyson Lister
How about trying to use Google Wave to cover a talk? - http://www.doodle.com/8zg76sy...
Mike Chelen, Lucas Brouwers, François Dongier and 6 other people liked this
I'm thinking of trying to simulate covering a talk by simultaneously watching the same video, e.g. this one by Gary Bader: http://www.youtube.com/watch... Follow link above to a Doodle date finding poll
- Michael Kuhn
from Bookmarklet
I've proposed the afternoon in Europe, so that people from the US can join in the morning
- Michael Kuhn
I've put in my availability. Should be interesting - we can compare (subjectively) the experience on that as compared with our known experiences on FF. Btw, if anyone wants a wave account, just let me know. We all have loads of invites now, it seems.
- Allyson Lister
I've also put in my availability.
- Graham Steel
thanks Allyson, Roland and Graham. I agree with Ally that we should compare Wave to FF, so I'd like to give priority to people who have covered ISMB. Also, I'm just curious to see how well Wave handles Ally's writing speed. :)
- Michael Kuhn
I'll be covering the Recomb Satellite via FF for now; given the limited number of people who have access to it so far that seems to be the only venue.
- Oliver Hofmann
I'm giving a talk on Wave in a few weeks - was thinking I might put the slides in as images, then work through them using the slideshow function - if I can stream audio out and people could leave comments on the slides as we go...but collaborative note taking with a relatively small number of people seems to work really well - if you can pull the video/slides in even better.
- Cameron Neylon
The talk is supposed to be 3:30 on Tuesday 15th but is late in the day so would probably be later. Will looking into what networks facilities are available...
- Cameron Neylon
@Michael, nothing can handle Ally's writing speed :D
- Benjamin Tseng
@Cameron, forgive me if this is a dumb question, but how would a talk like that work? would you interrupt it to answer comments/questions as they came in?
- Benjamin Tseng
@Michael, @Benjamin - you're really bigging me up there! :) FF seemed to be able to keep up, so hopefully so will Wave :)
- Allyson Lister
@Benjamin - thinking I would have the slides in a Wave, webcast video, people could comment next to the slides as appropriate (or inappropriate) and then at the end you have an annotated version of the talk as it happened. Could certainly answer questions - people often interrupt inside the room anyway - but there wouldn't be a simple mechanism to get speakers attention. Anyway I don't...
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- Cameron Neylon
looks like Wed, Dec 16 at 4 pm UT / 5 pm CET will be it. (Sorry Roland.) Any other nominations than for what to watch instead of Gary Bader: Predicting Protein Interaction from the Genome, http://www.youtube.com/watch... ?
- Michael Kuhn
@Cameron: I also think having slides and comments in the same Wave is a separate experiment, also streaming live can have its own problems. so let's keep this one simple :)
- Michael Kuhn
Yep, that's cool. I should be available on 16th as well anyway
- Cameron Neylon
Just saw this thread and plan to be there on 16th. My suggestions for videos to watch are at http://en.citizendium.org/wiki... . Alternatively, we could also go for 2-3 TED talks where the change of subject may provide for additional testing functionality.
- Daniel Mietchen
A further suggestion would be to go for Michael Nielsen's talk at http://www.youtube.com/watch... .
- Daniel Mietchen
*bump* I've created a Wave with those that entered their times on Doodle. Could you guys please check and vote for a talk?
- Michael Kuhn
We're creating an #OWL version of the #ChEBI ontology http://sourceforge.net/mailarc... If you have any comments or feedback, we'd like to hear from you.
Egon Willighagen liked this
Good idea putting this PDF up. It's my opinion that you should go for option B, as it will allow you to not only have the extra attributes (souce/value etc), but will allow you to later add new attributes of the Synonym class if you ever need it. I haven't worked much with annotation properties - can the reasoner see them in the same way as it can see the datatype and object properties?
- Allyson Lister
Have you looked at how OBI have done this? They have sources for definitions, but not for the multiple labels. The difference between the label you call name and the label you call synonyms is arbitrary, as in they are all lables for the same definition. I would probably avoid the word synonym altogether and just have <label:value><source:chebi>, <label:value><source:kegg>, as in option B.
- Frank
good point @Frank
- Allyson Lister
@Frank got any specific examples you can point to in OBI? I'm currently investigating the OWL 2 approach mentioned by Michel Dumontier, to use annotation axioms http://sourceforge.net/mailarc... which look like they'll be accessible to the reasoner
- Duncan Hull
Annoyingly I can find the minimum metadata spec but not the implementation. They are imported from the IAO. If you just look at OBI itself you should be able to see it. Do you know how to view it in Protege?
- Frank
However, taking the OWL2 approach would seem a lot more sensible than trying to import another ontology
- Frank
@Frank isn't IAO "work in progress" at the moment? Not quite finished yet and ready to use *now*
- Duncan Hull
@Duncan, that is certainly one synonym you could apply to it, I can think of many others.. :)
- Frank
Tips for Installing Glossaries in Latex - http://www.latex-community.org/forum...
Extra tips for installing the glossaries package.
- Allyson Lister
Modelling data across labs, genomes, space and time - http://www.citeulike.org/user...
Deepak Singh and 'Mummi' Thorisson liked this
Nature Cell Biology, Vol. 8, No. 11. (01 November 2006), pp. 1190-1194. Logical models and physical specifications provide the foundation for storage, management and analysis of complex sets of data, and describe the relationships between measured data elements and metadata — the contextual descriptors that define the primary data. Here, we use imaging applications to illustrate the purpose of the various implementations of data specifications and the requirement for open, standardized, data formats to facilitate the sharing of critical digital data and metadata. Jason Swedlow, Suzanna Lewis, Ilya Goldberg
- Allyson Lister
Integrating biological databases - http://www.citeulike.org/user...
Nature Reviews Genetics, Vol. 4, No. 5. (01 May 2003), pp. 337-345. Recent years have seen an explosion in the amount of available biological data. More and more genomes are being sequenced and annotated, and protein and gene interaction data are accumulating. Biological databases have been invaluable for managing these data and for making them accessible. Depending on the data that they contain, the databases fulfil different functions. But, although they are architecturally similar, so far their integration has proved problematic. Lincoln Stein
- Allyson Lister
GENETICS: Getting Closer to the Whole Picture - http://www.citeulike.org/user...
Science In Science, Vol. 316, No. 5824. (27 April 2007), pp. 550-551. 10.1126/science.1142502 Uwe Sauer, Matthias Heinemann, Nicola Zamboni
- Allyson Lister
Advancing translational research with the Semantic Web - http://www.citeulike.org/user...
BMC Bioinformatics, Vol. 8, No. Suppl 3. (2007), S2. BACKGROUND:A fundamental goal of the U.S. National Institute of Health (NIH) Roadmap is to strengthen Translational Research, defined as the movement of discoveries in basic research to application at the clinical level. A significant barrier to translational research is the lack of uniformly structured data across related biomedical domains. The Semantic Web is an extension of the current Web that enables navigation and meaningful use of digital resources by automatic processes. It is based on common formats that support aggregation and integration of data drawn from diverse sources. A variety of technologies have been built on this foundation that, together, support identifying, representing, and reasoning across a wide range of biomedical data. The Semantic Web Health Care and Life Sciences Interest Group (HCLSIG), set up within the framework of the World Wide Web Consortium, was launched to explore the application of these...
- Allyson Lister
The model organism as a system: integrating 'omics' data sets - http://www.citeulike.org/user...
Nature Reviews Molecular Cell Biology, Vol. 7, No. 3. (01 March 2006), pp. 198-210. Many genome-scale, or 'omics', data sets are becoming available for various model organisms. Although each of these data types is valuable on its own, further insights into whole systems can be gained through the integration of omics data sets. Andrew Joyce, Bernhard Palsson
- Allyson Lister
OWL 2 Web Ontology Language Structural Specification and Functional-Style Syntax - http://www.citeulike.org/user...
(11 June 2009) Conrad Bock, Achille Fokoue, Peter Haase, Rinke Hoekstra, Ian Horrocks, Alan Ruttenberg, Uli Sattler, Mike Smith
- Allyson Lister
Ontology - http://www.citeulike.org/user...
In Encyclopedia of Database Systems (2009) Definition of ontology written in neutral voice with historical and scientific context. Tom Gruber
- Allyson Lister
Re: [ontolog-forum] Just What Is an Ontology, Anyway? (archive of ontolog-forum mailing list) - http://www.citeulike.org/user...
(26 October 2009) Ed Barkmeyer, Leo Obrst
- Allyson Lister
Re: Help Required (Archive of public-owl-dev mailing list) - http://www.citeulike.org/user...
(29 July 2009) Bijan Parsia
- Allyson Lister
Re: [jena-dev] Definition of Ontology (archive of jena-dev mailing list) - http://www.citeulike.org/user...
(29 July 2009) (Definition as described by Adrian Walker) Edward Barkmeyer
- Allyson Lister
Started reading _Inequality By Design: Cracking the Bell Curve Myth_ http://www.amazon.com/gp...
Jimminy Fuller, Derek Mahar, Jenny Morman and Piaw Na liked this
I've been fortunate to be acquainted both with a number of highly intelligent people and a number of very wealthy people. It's clear to me that the rankings of intelligence and wealth don't correspond with each other. The most intelligent people are not the most wealthy, nor vice versa. Do all the people who buy into _The Bell Curve_ really not have the opportunity to notice this?
- Ruchira S. Datta
What do you mean, rigorously, by "don't correspond"? Do you mean the rankings aren't correlated? I'll bet you five bucks they are! (Whoever wins the bet will be both smarter and richer, proving my point on a micro scale.)
- Doug Beeferman
Doug, that's roughly what I mean: at the high end, the rankings are not consistent with each other. I would say that what I know of my acquaintances confirms the thesis of _Fooled By Randomness_ http://www.amazon.com/gp... I'm afraid I can't take the bet, though, for two reasons: 1)...
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- Ruchira S. Datta
It so happens that the very wealthy people I know are all quite intelligent, because I know them from Google. I suspect the correlation would be even less if I knew a more representative sample of very wealthy people.
- Ruchira S. Datta
To be concrete, my guess would be that Spearman's rank correlation coefficient would be much less than 1, though greater than 0. I don't have enough experience with this coefficient to name a number.
- Ruchira S. Datta
Yeah, my bet didn't make a whole lot of sense, I confess. I was trying to pose a bet that was logically impossible for me to lose. But I think I only managed to prove that I'm not among the most intelligent people. :-)
- Doug Beeferman
BTW, check out http://paul.kedrosky.com/archive... for a semi-convincing scatterplot that agrees with you (I'm unable to access the full article).
- Doug Beeferman
That appears to be Fig. 2 of http://www.eric.ed.gov:80/ERICWeb... From that article, "The Pearson correlation between IQ score and net worth is roughly half (0.156, p<0.01) the correlation between IQ score and income (0.297, p<0.01)." The number...
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- Ruchira S. Datta
BTW, both this article and _Inequality By Design_ use the same dataset analyzed in _The Bell Curve_
- Ruchira S. Datta
Thanks, @Ruchira - I recently read the Mismeasure of Man, by Stephen Jay Gould, and enjoyed it immensely. It covers unconscious bias, flaws in historical measuring of IQ (and why IQ is not a good measure of people) and much more. In fact, the second edition that I have deliberately addresses _The_Bell_Curve_. http://www.amazon.com/Mismeas...
- Allyson Lister
@Allyson, this blogpost http://www.gnxp.com/blog... says "My reading of the available evidence is that there is a significant shared environmental input to adult IQ, and that it is associated with socioeconomic status." In other words, to the degree that there is a correlation, some of it may be due to SES influencing IQ rather than the other way around.
- Ruchira S. Datta
Yep - in other words, asking immigrants to figure out what is missing in a drawing of a man playing baseball (e.g. his bat is missing) does not measure his intelligence, but his knowledge of baseball. (I believe that was one of the examples from one of the very early IQ tests discussed in Gould's book).
- Allyson Lister
Check this out: 8 weeks of playing games improves needy kids' processing speed and reasoning ability, equivalent to an IQ gain of 13 points! http://ff.im/cPUSY
- Ruchira S. Datta
Semantic Web Approach to Database Integration in the Life Sciences - http://www.citeulike.org/user...
Khader Shameer liked this
Semantic Web (2007), pp. 11-30. This chapter describes the challenges involved in the integration of databases storing diverse but related types of life sciences data. A major challenge in this regard is the syntactic and semantic heterogeneity of life sciences databases. There is a strong need for standardizing the syntactic and semantic data representations. We discuss how to address this by using the emerging Semantic Web technologies based on the Resource Description Framework (RDF) standard. This chapter presents two use cases, namely YeastHub and LinkHub, which demonstrate how to use the latest RDF database technology to build data warehouses that facilitate integration of genomic/proteomic data and identifiers. Kei-Hoi Cheung, Andrew Smith, Kevin Yip, Christopher Baker, Mark Gerstein
- Allyson Lister
From XML to RDF: how semantic web technologies will change the design of 'omic' standards - http://www.citeulike.org/user...
io2a, Khader Shameer, Egon Willighagen and Pierre Lindenbaum liked this
Nature Biotechnology, Vol. 23, No. 9. (07 September 2005), pp. 1099-1103. With the ongoing rapid increase in both volume and diversity of 'omic' data (genomics, transcriptomics, proteomics, and others), the development and adoption of data standards is of paramount importance to realize the promise of systems biology. A recent trend in data standard development has been to use extensible markup language (XML) as the preferred mechanism to define data representations. But as illustrated here with a few examples from proteomics data, the syntactic and document-centric XML cannot achieve the level of interoperability required by the highly dynamic and integrated bioinformatics applications. In the present article, we discuss why semantic web technologies, as recommended by the World Wide Web consortium (W3C), expand current data standard technology for biological data representation and management. Xiaoshu Wang, Robert Gorlitsky, Jonas Almeida
- Allyson Lister
opps, it's a paper from 2005...
- Pierre Lindenbaum
yep - quite old - have just spent an afternoon following interesting citation links through papers... :)
- Allyson Lister
Institute for Systems Biology: Why Systems Matter - http://www.citeulike.org/user...
(11 December 2009)
- Allyson Lister
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