I'm going to annotate a bunch of PubMed Central full-text papers for a specific purpose. Would like the results to be easy for random others to quickly skim. Suggestions for best practice approach?
might honestly go with Zotero in this case -- their HTML (repeat: HTML) annotation is still my favourite for sharing, though I don't think that particular feature has been degrafted from Firefox yet if that's a concern.
- Alex
I've used Google Notebook for this in the past. Not bad, but guessing there might be a better option. Note PMC full text is free to view but not download in its entirety. Looking for something lightweight and straight forward. Thanks for your ideas!
- Heather Piwowar
My first instinct was also Zotero - not sure if you and random others all have EndNote web, so a freely available tool like Zotero might be your best choice.
- Rachel Walden
The OA subset of PMC is free to be downloaded in its entirety. And it comes with XML.
- Daniel Mietchen
Daniel, thanks. Yes, too true, I have used the OA subset for all sorts of lovely purposes because of that XML. I'm living outside the OA zone for this one though. Rachel and Alex, will look into Zotero for this, thanks for the recc.
- Heather Piwowar
if these are really html texts, then Diigo is a good, free tool for this, too. Mendeley also offers an annotation tool that is pretty neat.
- Mickey Schafer
Heather raises a good question--and, Bill, neither of those posts seems to object to CC-BY. Assuming that remixes included credits for sources of data, why would CC-BY be objectionable? (If you interpret it, for data, not to require a credit for each and every item when used.) Then again: In the U.S., at least, true "data"--facts--are not copyrightable.
- Walt Crawford
No time to find at moment but there is a john wilbanks piece at nature precedings which is my main touchstone piece. I should probably write something on this
- Cameron Neylon
from Android
Walt, that's true -- the main point of the posts I linked is license incompatibility, which is a reason to avoid CC-BY for data, but not the main one.
- Bill Hooker
I guess the only reason I can think of is that a strict interpretation of "BY" might make it impossible to reuse the data properly. Otherwise, is there a reason a researcher wouldn't credit sources? (Not trying to be argumentative here. In fact, if I had useful data sets as such, they'd have CC0, I think.)
- Walt Crawford
Perhaps more important than license incompatibility is the "attribution thicket" effect, cf. patent thickets -- when you pull together multiple sources of data, it can become virtually impossible to attribute them all, especially since each owner gets to define *how* attribution should be effected (that last is, imo, a much overlooked fly in the CC-BY ointment).
- Bill Hooker
And that may be reason enough--that attribution is too difficult. Thanks. So: Source of data: The World?
- Walt Crawford
re: source, I am sure that I got the idea from David Wiley.
- Bill Hooker
The main arguments are: objects created from data may not be appropriate to a copyright based licence (why share-alike is not ideal). Massive re-use of data could lead to attribution stacking problems (what is the appropriate form of attribution). Other requirements on data (privacy, ethics) may trump licence provisions, effectively ruling out data use in specific areas. And finally....
more...
- Cameron Neylon
Very helpful points, Bill, Walt, and Cameron. Thank you.
- Heather Piwowar
not to make this shameless self promotion, but this is the follow on from the 4 hour tutorial i did with tom and leigh from talis on the issue, laying out the science commons position and implications of the license toggles: http://blogs.talis.com/nodalit...
- Kaitlin Thaney
"The Open Citations Project is global in scope, designed to change the face of scientific publishing. It aims to make bibliographic citation links as easy to use as Web links. Its goals are three-fold: To establish OpenCitations.net, a public RDF triplestore for biomedical literature citations. (Note: In this context, a bibliographic citation is a reference within a particular citing work to another publication termed the cited work. This use of the word ‘citation’ should be clearly distinguished from the common related use of this word to indicate the cited work itself. Within this application, ‘cite’ and ‘citation’ denote the performative act of citation itself, not the target document of that citation.) To harvest the reference lists from many current and recent open access journal articles, and to convert these datasets into RDF, starting with those in UK Pubmed Central, those published by the Public Library of Science and Biomed Central, those from other publishers willing for...
more...
- Mike Chelen
from Bookmarklet
"Personal genome information application: view the specific genes and SNPs (location of potential genetic mutations or "typos") that research has linked to different conditions. Three views are available: health condition risk (Alzheimer's disease, diabetes, cancers, etc.), drug response for over 200 drugs (statins, warfarin, clopidogrel, viagra, caffeine, alcohol, etc.), and athletic performance (endurance, strength, recovery, tendon strength, etc.). Bonus: upload your 23andMe personal genome data to check your specific profile for the different conditions. (Email your 23andMe zip file to the mobile; click on the attachment in email or in downloads manager and an option to import it into DIYgenomics will appear. Delete private data later if desired from the DIYgenomics app menu.) Developers: v 3.0 Michael Kolb, Melanie Swan; v 1.0 Michael Kolb, Lawrence S. Wong, Melanie Swan. The software is open-source: https://github.com/lablogg... DIYgenomics is a non-profit...
more...
- Mike Chelen
from Bookmarklet
Anyone up for doing a few minutes of questionnaire hammering today, to scout for typos and bugs? Topic: impact of journal data sharing policies on corresponding author attitudes and experiences. Will post link when ready. If you don't mind an email, would like to test invite too. DM or email address to hpiwowar@gmail.com. thnx!
"To allow a maximal re-use of the information collected by this survey, the data are hereby released under a CC0 waiver, so to allow libraries, publishers, funding agencies and academics to further analyse risks and opportunities, drivers and barriers, in the transition to open access publishing."
- Bill Hooker
from Bookmarklet
I'm looking for some references which show evidence that some basic research is unnecessarily repeated due to a lack of openness or access to data - or is this not true? There are plenty of papers which say secrecy in science makes it difficult to accurately repeat research when necessary, but is there also unnecessary repetition?
I'm not sure it's that easy to distinguish between lack of openness and literature search failure
- Pawel Szczesny
from iPhone
In the argument around peer review this came up. I think it might be very difficult to quantify. I can give you a couple of anecdotes but given I've spent the last several days whining about anecdotal evidence... :-)
- Cameron Neylon
Back in the late 80s there was some research in the engineering technological gatekeepers literature showing that researchers would not walk 400 feet to the library to find an answer to a question, but would instead repeat the study. This was part of a body of literature examining preferred information sources for different specialties, with similar findings for all professions studied. I used the cite in a paper I wrote, but I no longer have electronic access to the original. If I can find it ... ?
- Patricia F. Anderson
Re: where is <vague behavior> in the brain? "The question presumes that a complex behavior or emotion can be localized to a brain region or regions. There are several philosophical pitfalls packaged into the answer, such as the ontological commitment to the narrative of cognitive neuroscience and the cerebral localization of function. [Ask instead], "can a person who has a lesion to that brain region not experience that emotion or do that behavior anymore?" If the person still can, then that is not where that behavior is located in the brain. And, in all likelihood, that function can't be localized to any one region at all."
- Adriano
from Bookmarklet
This is the kind of thing that makes sense of the current mess we're in. Go to the patients get them involved, get real data, make decisions. Numbers might be small here but enough to decide whether to focus on something more or leave it one side for more promising opportunities.
- Cameron Neylon
+1 Cameron. I've been asked to give a talk at an event in Cambridge re. 'health information in the digital world'. I'll definately be mentioning PLM and will most probably cite this blog post.
- Graham Steel
Impulse for widespread data sharing will come from such communities not scientists. Healthcare seems to be the only place where data really matter (on the other side of the spectrum you have gov data). Great story, BTW.
- Pawel Szczesny
from iPhone
"I've heard a few conversations in the last week treating open source interchangeably with crowdsourcing. Despite sounding the same they are very different, and the key difference is the ownership of the outcome." I've been at pains to points out this point in the talks I've given recently. There's data sharing, then there's crowdsourcing, and then there's open source. Open source is a process, distinct from the others.
- Matthew Todd
from Bookmarklet
Number of times my smoke detector has gone off because there is a fire = 0. Number of times my smoke detector has gone off because I am cooking something delicious = eleventy billion.
Does a furnace burning out in the middle of the night setting it off count?
- Bluesun 2600
I think it's just hungry, and mad because you won't share.
- chrisofspades
When I'm cooking something delicious I generally turn the fan on and also close the kitchen door so the smoke detector doesn't get wind of it. It just saves time.
- Deborah Fitchett
This happens all the time at our house because of how sensitive the smoke detector is and where it's placed upstairs. I've learned to open all the doors and not just my windows.
- Kisha
from FreshFeed
Mine is eleventy billion to 1. I notice that some smoke alarms are now available with wireless remotes to shut them off for a minute after they alarm to lessen the frustration with the inevitable false alarm.
- Brian Sullivan
Deborah, no fan and no kitchen door. :/ One-bedroom apartment with the smoke detector some twenty feet from the stove.
- Jandy
Oh, ouch. I guess you'll just have to give up every cooking method except boiling and microwaving. :-P
- Deborah Fitchett
New Post: Kids With Dyslexia: Predicting Their Reading Skills With MRI: An international team of researchers has... http://getbetterhealth.com/kids-wi...
Crikey! I just realized that I have accounts on Wordpress, Blogger, Tumblr and Posterous. I don't have enough to say for ONE blog. How did I end up with so many? I guess I need to check them all out and decide on just one. Posterous seems to be my speed. Or is it just the blog of the moment for me?
Well, I hadn't used the Blogger blog since 2007 so that was easy to dump. I barely used the Tumblr so no sad feelings for dropping it. I think I'll keep my Posterous for short posts and easy distribution. I kept the Wordpress since I like the format and how it worked. Whenever I'm feeling wordy, I'll drop it there. :)
- Curtis (a) Jackson
When I make realisations like this, I simply blame Louis and carry on. Sounds like you've got it sorted :)
- WoH: Professor MOTHRA
I love the concept of social media and sharing information. It's the how that always trips me up. :D
- Curtis (a) Jackson
I have blogs on all of those, plus livejournal and MBlog (a Moveable Type enterprise installation). But most languish now, and I only have 2 active on Wordpress and 4 on Posterous.
- Patricia F. Anderson
Talk basically finished; will leave for San Diego tonight. If you are attending online (there will be video), please post questions and comments on the Q & A page.
- Daniel Mietchen
from Bookmarklet
You're going? Thats fantastic. Was chatting to Martin and Paul Groth about their ideas, really wish I could have gone. Great job.
- science3point0
"A Florida airport recently had to close its main runway to repaint directional signs, due to the changing location of magnetic north. Over time, the location of magnetic north has shifted, with the magnetic north pole moving gradually towards Siberia. That shift made the airport signs, which reference a heading based on magnetic north, incorrect. But what causes the magnetic field, and why is it shifting? The planet has undergone several magnetic polar reversals in its past, with north becoming south and vice versa. Are we due for another shift? We'll talk about the planet's magnetic field."
- Jenny H
from Bookmarklet
Can we figure out a way to blame this on humans?
- Andy Bakun
"life has a kind of built-in randomness generator which allows it to hedge its bets. (...) No one now doubts that environmental factors can produce changes in the offspring of animals even when there is no change in DNA. Many different epigenetic mechanisms have been discovered, from the addition of temporary “tags” to DNA or the proteins around which DNA is wrapped, to the presence of certain molecules in sperm or eggs. (...) Rather than being another way to code for specific characteristics, as biologists like Jablonka believe, Feinberg’s “new way of looking at evolution” sees epigenetic marks as introducing a degree of randomness into patterns of gene expression. (...) There is evidence that epigenetic changes, as opposed to genetic mutations or environmental factors, are responsible for a lot of variation in the characteristics of organisms. The marbled crayfish, for instance, shows a surprising variation in coloration, growth, lifespan, behaviour and other traits even when...
more...
- Amira
from Bookmarklet