[open-science] Open data in life sciences use cases?

Graham Steel steelgraham at hotmail.com
Sat Jan 7 14:20:04 UTC 2012 


Iain,

On the subject of lack of data in this regard, have just spotted this post:- http://www.forbes.com/sites/larryhusten/2012/01/04/missing-data-the-elephant-thats-not-in-the-room-guest-post/

Graham

  
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> From: open-science-request at lists.okfn.org
> Subject: open-science Digest, Vol 39, Issue 3
> To: open-science at lists.okfn.org
> Date: Fri, 6 Jan 2012 12:00:07 +0000
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> Today's Topics:
> 
>    1. Re: response to the White House RFI on OA to publicly funded
>       research (Marcus D. Hanwell)
>    2. Re: Open data in life sciences use cases? (Daniel Mietchen)
> 
> 
> ----------------------------------------------------------------------
> 
> Message: 1
> Date: Thu, 5 Jan 2012 09:44:57 -0500
> From: "Marcus D. Hanwell" <marcus.hanwell at kitware.com>
> Subject: Re: [open-science] response to the White House RFI on OA to
> 	publicly funded research
> To: Raphael Ritz <raphael.ritz at incf.org>
> Cc: open-science at lists.okfn.org, Luis Ibanez <luis.ibanez at kitware.com>
> Message-ID:
> 	<CAMkPkZVGnyjAxAhu7-+qhrA2Y9b6zuDnLzGvy5ZNjRt2xW--Bg at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
> 
> On Thu, Jan 5, 2012 at 4:02 AM, Raphael Ritz <raphael.ritz at incf.org> wrote:
> > On 1/4/12 12:00 PM, Daniel Mietchen wrote:
> >
> > Dear all,
> >
> > I am sitting over this right now (though mostly offline, reading
> > through responses prepared by others) and shall post some rough draft
> > text today at
> >
> > http://meta.wikimedia.org/wiki/Research:Committee/Areas_of_interest/Open-access_policy/Request_for_Information_on_Public_Access_to_Peer-Reviewed_Scholarly_Publications_Resulting_From_Federally_Funded_Research
> >
> > and
> >
> > http://meta.wikimedia.org/wiki/Research:Committee/Areas_of_interest/Open-access_policy/Request_for_Information_on_Public_Access_to_Digital_Data_Resulting_From_Federally_Funded_Scientific_Research
> >
> > Any hint/ suggestion is very welcome.
> >
> >
> > Obviously several groups are on this right now.
> > Kitware is also drafting an open letter in response to this
> > and I'd like to point out that they welcome anyone contributing
> > in any way.
> >
> > Here is what I received from Luis Ibanez lately:
> >
> I think Luis and I are also on the list, and would certainly welcome
> comments and support in drafting a response. We had an interesting
> discussion yesterday about some related issues, which should hopefully
> be put out today as a podcast.
> 
> Marcus
> 
> 
> 
> ------------------------------
> 
> Message: 2
> Date: Fri, 6 Jan 2012 03:53:37 +0100
> From: Daniel Mietchen <daniel.mietchen at googlemail.com>
> Subject: Re: [open-science] Open data in life sciences use cases?
> To: Iain Hrynaszkiewicz <Iain.Hrynaszkiewicz at biomedcentral.com>
> Cc: open-science <open-science at lists.okfn.org>
> Message-ID:
> 	<CAN6n2b1shmbOBGVYLkO67tQfh2_kdH1MURZaKYSBzF9G34aYqA at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
> 
> Dear Iain,
> 
> one area where lack of open data has been problematic is the one that
> I had envisaged to specialize in before I found out that the
> conservatism and categorizationism of classical non-public grant peer
> review are an even more effective blocker in this regard than the lack
> of data sharing.
> 
> I am talking about applications of Magnetic Resonance techniques
> (mainly imaging, but with some spectroscopic components) to
> cross-species comparative studies (preferably in vivo) with the
> ultimate goal to better understand the evolution of specific traits. I
> am calling this EvoMRI, and that's the handle I commonly go under on
> the web if my real name is too long or otherwise does not fit.
> 
> For example, take a study on comparative MR-based brain morphometry in
> primates: Brain scans are regularly performed on a number of primate
> species, often even in large numbers per species, but typically just
> one or two species per study. This is understandable by considering
> that housing primates is an endeavour that requires a lot of effort
> and resources, and so is the operation of MR scanners capable of
> imaging living adult primates. So there are very few places in the
> world where multiple species of primates are located nearby a MRI
> center that is both equipped and licensed for non-human scans (as an
> aside, there is no MR center in the world that is dedicated to
> cross-species studies, and given the costs involved, none is on the
> horizon), and ethical considerations prevent transporting (non-human)
> primates long distances just to get them an MRI scan (mobile scanners
> exist and become better all the time, but so far, they are useless for
> the purposes of brain morphometry).
> 
> There is only one publicly available dataset that has brains from
> multiple primate species scanned according to a common protocol (even
> broadening the search to include post-mortem studies does not give
> further results), and these scans (of 11 species) have been recorded
> (in vivo) well over a decade ago, so do not meet the quality criteria
> that underpin more recent brain morphometric algorithms of the kind
> required for cross-species studies of brain structure.
> 
> Luckily, large multi-centre brain imaging studies (including ADNI that
> has repeatedly popped up in data sharing discussions) in humans have
> shown that some scanning protocols can be implemented in a way that
> cross-scanner variability does not interfere with clinical diagnoses.
> If pooling data from multiple scanners is indeed a valid option within
> a species, it certainly makes sense for cross-species studies too, and
> here's where the sharing of data (and code, btw) come in.
> 
> A review ( http://dx.doi.org/10.3389/neuro.11.025.2009 ) thus makes
> the point that
> "the major barrier to cross-species MR-based brain morphometry is not
> the lack of data nor analytical tools but barriers preventing to
> combine them. "
> 
> Similarly, a poster ( http://dx.doi.org/10.1038/npre.2010.4511.2 )
> concludes by stating
> "In order to succeed, however, computational efforts on comparative
> morphometry depend on high-quality imaging data from multiple species
> being more widely available."
> 
> Yet there is no culture of making such datasets public, and while many
> researchers in the area (especially those personally known to each
> other) will happily share their data non-publicly, their individual
> terms (e.g. requests for co-authorship or for other datasets or tools
> or services in return) are not necessarily compatible with each other,
> and in general, they also make the sharing of any derivative works
> impossible.
> 
> In addition to that, some of the major software tools in the area are
> free but not open and thus cannot be adapted from their human-centric
> focus to cross-species applications. They took multiple person years
> to write, so starting from scratch is not necessarily an option.
> 
> Beyond primates, I remember a paper that described MRI of seals, but
> when I contacted the authors about getting the data, I got an outright
> refusal rather than the request simply being ignored, which is more
> common.
> 
> To sum up, cross-species studies going beyond the typical lab animals
> or typical toolkit of evolutionary depend on data and code sharing, so
> the lack of that blocks such fields from developing. As mentioned in
> the introduction, however, funding is an even more severe blocker.
> 
> First, most funding programs are dedicated to a certain topic. For
> things like comparative primate brain morphometry that can variously
> be tagged into and out of biology, physics, computer science,
> neuroscience, imaging and so on, the fit to basically any funding call
> (or scope-limited journal, for that matter) will always be
> sub-optimal, thus providing such projects with a bad starting
> position.
> 
> Second, the topic of the funding scheme defines the set of reviewers
> and panelists that are to judge such proposals, and they will
> invariably cover only part of the scope of such hard-to-categorize
> projects, especially those with a methodological focus. The only way
> to mitigate these problems, in my view, is to allow interaction
> between applicants and reviewers and to make those exchanges public by
> default.
> 
> Third, even in those lucky cases when such projects do get funded,
> they are normally impeded in ways that follow from the themes of the
> funding line - if the project sailed through under "primatology", you
> won't easily get expenses for number crunching equipment approved, or
> if it came in under "computational neuroscience", the budget for
> feeding the animals (nut crunching, perhaps?) will likely approach
> zero.
> 
> Fourth, the normal funding schemes think in terms of hiring a postdoc
> or so for about three years, but certain types of problems - the
> Polymath project perhaps being the most well-known example,
> comparative brain morphometry probably another - do not necessarily
> lend themselves to being solved this way, as they typically require
> sets of skills that are unlikely to be adequately represented in the
> set of people whose participation can be funded by such classical
> hiring schemes, especially if working remotely is not an option. Plus,
> some of the skills will be needed for a very small part of the
> project, and much of the skill set is hard to predict in the funding
> proposal anyway.
> 
> Sorry for the long post, but you hit one of my major resonances, and
> much of my motivation to deal with matters of open data, open source,
> public peer review or open science more generally derives from the
> issues outlined above.
> 
> Daniel
> 
> On Wed, Jan 4, 2012 at 4:00 PM, Iain Hrynaszkiewicz
> <Iain.Hrynaszkiewicz at biomedcentral.com> wrote:
> > Dear all,
> >
> >
> >
> > I?m interested in further developing some specific use cases where open data
> > (i.e. available under CC0 or equivalent terms) in journal publications would
> > be useful or lack of open data has been problematic ? to individual
> > scientists/research groups, and perhaps even the original data publishers.
> > I?m aware of reasonable evidence of societal/economic benefits for open data
> > (e.g. within :
> > http://ie-repository.jisc.ac.uk/279/2/JISC_data_sharing_finalreport.pdf;
> > http://www.jisc.ac.uk/media/documents/publications/keepingresearchdatasafe0408.pdf)
> > but more evidence (aside from more citations, in microarray research), or
> > anecdotes/cases studies in its absence, of benefits to individuals/groups
> > would be good.
> >
> >
> >
> > E.g. ?I am scientist doing X kind of experiment and being able to reuse or
> > harvest all types of Y data from Z journal (or publisher) would be excellent
> > because??
> >
> >
> >
> > And ideally?
> >
> >
> >
> > ?here?s why ?the current model prohibits or makes this difficult; or here?s
> > an example of where such an approach has been beneficial previously?.
> >
> >
> >
> > I?d like to include some of these use cases as part of a white paper,
> > currently well under way, on implementation of a variable license agreement
> > for open access publications enabling CC0 for data (as agreed at
> > http://blogs.openaccesscentral.com/blogs/bmcblog/entry/report_from_the_publishing_open).
> >
> >
> >
> > If anyone has any suggestions they would be much appreciated ? and of course
> > acknowledged.
> >
> >
> >
> > Best regards,
> >
> >
> >
> > Iain
> >
> > Iain Hrynaszkiewicz
> > Journal Publisher
> >
> > BioMed Central
> > 236 Gray's Inn Road
> > London, WC1X 8HB
> >
> > T: +44 (0)20 3192 2175
> > F: +44 (0)20 3192 2011
> > M: +44 (0)782 594 0538
> > W: www.biomedcentral.com
> > Skype: iainh_z
> >
> >
> >
> >
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