[query] good venue for publishing a dataset?

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[query] good venue for publishing a dataset?

William Ray

Oddball question for the list, but I figure people here probably
have the best ideas of useful venues for publishing volume
datasets.

Specifically I'm looking for an appropriate place to
publish/disseminate a volume dataset we acquired this past
summer.  It's a rather high-resolution visible-light photo
set, taken from a de-fleshed Chinchilla skull.

Fine bone (and some cartilage) detail is visible in the nasal
passsages, (which was the point of doing the dataset), and we
have a partially segmented version, segmenting for bone, that's
probably 98% right, but still needs some minor corrections.

The raw dataset volume is on the order of 1024x1024x512, but
we've done most of our work with a 1/4 planar resolution (512x512x512)
downsampling.


At this point, the project that was driving the creation of the
dataset is pretty much finished with it, and probably won't take
it much further in terms of model refinement, etc.  So I'm
interested in turning it loose, if there's a useful venue for
publishing it.


I'm aware of the online Insight Journal, but from visiting the
web page it's not clear to me that there's much life there, and
due to the amount of effort that went into capturing this dataset,
I'd rather not relegate it to a throw-away publication (of course,
my perception of the I.J. might be completely wrong, and you're
welcome to tell me that as well).


Many thanks for any suggestions,

Will Ray
The Ohio State University Biophysics Department
Columbus Children's Research Institute.

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Re: [query] good venue for publishing a dataset?

Mathieu Malaterre-2

> I'm aware of the online Insight Journal, but from visiting the
> web page it's not clear to me that there's much life there, and
> due to the amount of effort that went into capturing this dataset,
> I'd rather not relegate it to a throw-away publication (of course,
> my perception of the I.J. might be completely wrong, and you're
> welcome to tell me that as well).

Ok I think before hurting people feeling we need more info, Where
exactly did you go ? I am looking at:
http://www.insight-journal.org/


And here are the latest publications:

Image projections along an axe (Lehmann, Gaetan) [revision #2]
February 7, 2006

N-D $C^k$ B-Spline Scattered Data Approximation (Tustison, Nicholas J.)
[revision #2]
February 7, 2006

Binary morphological closing and opening image filters (Lehmann, Gaetan)
[revision #2]
February 6, 2006

JPEG 2000 in Medical Applications (Malaterre, Mathieu)
February 3, 2006

An ITK Filter for Bayesian Segmentation:
itkBayesianClassifierImageFilter (Melonakos, John) [revision #3]
February 3, 2006


So either we don't have the same definition of 'much life' or I am
missing something, but seriously the last 5 publications are from this
month.

Mathieu
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Re: [query] good venue for publishing a dataset?

Luis Ibanez
In reply to this post by William Ray


Hi Will,

We are very happy to hear about your willingness
to disseminate the data that you acquired in your
research project.

The world will be a better place if more researchers
shared your attitude and support for Open Access to
scientific information, whether it is in the form of
data, source code, parameters or papers.

The first thing that you should consider when releasing
data is the licensing that you want to use for it. Note
that you or your institution are the copyright holders
of the data. In order to make your data sharable (at least
under US copyright laws), you should choose one of the two
following options:



1) Release it on the "public domain" and renounce
    to your copyright.

    or


2) Retain your copyright and release the data with a
    license for a specific set of uses.


Option (1) is certainly the simplest way to go, but it may
imply that you will not even get credits for giving your
data away. Note that the term "public domain" has a specific
legal meaning.


Option (2) is the most commonly used, and then the question
is:

            What license to use  ?


One of the widespread licenses for data is the

        "Creative Commons Attribution License"
     http://creativecommons.org/licenses/by/2.5/


This license states that you (or your institution) retain
the copyright of the data, but you give permission to anybody
to copy your data, and to create derivative work from it.
(e.g. segment the data and distribute the segmentation), for
free (gratis). With the only condition that they will give
credit to you (or your institution).

This license is the one used by most of the Open Access Journals,
including the prestigious Public Library of Science (PLoS) and
BiomedCentral.


Once you have selected a license, you can distribute your data
in different databases. Note that the great advantage of the
Creative Commons Attribution License is that you retain the
copyright of your data. Therefore you are still the ultimate
authority deciding what can and what cannot be done with the
data. For example, you can submit your data to multiple databases.


This is in contrast with the voracious practice of most publishers,
that require you to "transfer" your copyright to them, and therefore
renounce to any rights on deciding what can be done with the data.




The Insight Journal uses the same Creative Commons Attribution license.
You are welcome to submit your dataset to the Journal, along with a
paper (in the format of a technical report) describing the value of the
data and its potential use.  A template for the submissions to the
Insight Journal is available at:

http://www.insightsoftwareconsortium.org/wiki/index.php/IJ-Article-Template


It is true that the level of activity in the Insight Journal is not
yet what we want to see in our community. However, you should put in
perspective that we are talking about a journal that has 8 months of
life, and in that period already was used for hosting the papers of the
MICCAI Open Source Workshop 2005.

The summary of this event can be seen at:
http://www.na-mic.org/Wiki/index.php/Dissemination:MICCAI_Workshop_2005

     * 37 papers were submitted
     * 90 reviews for those papers were posted
     * 31 reviewers contributed to open and public reviews
     * 0 anonymous reviews
     * 261 subscribers to the Insight Journal


Note also that the Insight Journal is not intended to be the typical
vanity-science journal where people publish just to met their annual
quota of papers required to account for their "productivity". That
empty practice is void of any scientific value and only demonstrate
how the principles of scientific research can be degraded when they
are evaluated by bureaucrats who simply "count" the number of papers
in your CV and your annual reports, but never read those papers, and
probably can not discern their implications.


The Insight Journal is after the important goal of recovering honesty
in the scientific endeavor by enforcing REPRODUCIBILITY.  Papers sent
to the Insight Journal are expected to be in the format of a technical
report that makes possible for *any* reader to replicate the results
described in a paper.


Papers submitted to the Insight Journal are published in a matter of
hours and are available in Open Access (gratis) to anybody in the world.


Any reader is empowered for posting reviews of a paper (non-anonymous),
and authors are able to reply to those comments. The reviewer's comments
are public and give an extra value to the readers.



When you are joining a revolution based on principles,
you should not ask

                "How many have already joined?",

instead,
you should be proud to be among the first ones to join.



         Welcome to the Open Access Revolution !!



   Regards,



        Luis




Is anybody still listening to music in tapes ?
Is anybody still using 5.25" floppies ?
Is anybody still reading papers published in closed access journals ?


-------------------------------
Will Ray wrote:

> Oddball question for the list, but I figure people here probably
> have the best ideas of useful venues for publishing volume
> datasets.
>
> Specifically I'm looking for an appropriate place to
> publish/disseminate a volume dataset we acquired this past
> summer.  It's a rather high-resolution visible-light photo
> set, taken from a de-fleshed Chinchilla skull.
>
> Fine bone (and some cartilage) detail is visible in the nasal
> passsages, (which was the point of doing the dataset), and we
> have a partially segmented version, segmenting for bone, that's
> probably 98% right, but still needs some minor corrections.
>
> The raw dataset volume is on the order of 1024x1024x512, but
> we've done most of our work with a 1/4 planar resolution (512x512x512)
> downsampling.
>
>
> At this point, the project that was driving the creation of the
> dataset is pretty much finished with it, and probably won't take
> it much further in terms of model refinement, etc.  So I'm
> interested in turning it loose, if there's a useful venue for
> publishing it.
>
>
> I'm aware of the online Insight Journal, but from visiting the
> web page it's not clear to me that there's much life there, and
> due to the amount of effort that went into capturing this dataset,
> I'd rather not relegate it to a throw-away publication (of course,
> my perception of the I.J. might be completely wrong, and you're
> welcome to tell me that as well).
>
>
> Many thanks for any suggestions,
>
> Will Ray
> The Ohio State University Biophysics Department
> Columbus Children's Research Institute.
>
> _______________________________________________
> This is the private VTK discussion list.
> Please keep messages on-topic. Check the FAQ at: http://www.vtk.org/Wiki/VTK_FAQ
> Follow this link to subscribe/unsubscribe:
> http://www.vtk.org/mailman/listinfo/vtkusers
>
>

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Re: [query] good venue for publishing a dataset?

William Ray
In response to my query, Mathieu Malaterre and Luis Ibanez wrote:


> Ok I think before hurting people feeling we need more info, Where
> exactly did you go ? I am looking at:
> http://www.insight-journal.org/
>
>
> And here are the latest publications...

I'm going to answer you and Luis here, not because I want to start
a political argument, but because I really /want/ your proposed
publishing model to survive and gain credibility, and I can't be
the only one with these concerns, or who lives in an environment where
they are concerns.  

My point, before I start, is /not/ to hurt feelings.  I'd love to see
this model become the standard for publication and data sharing.  I've
personally always tried to operate as though it is (often much to my
employer's chagrin), and I've always insisted on making the code, data
and methods openly available for anything I've ever published anywhere.

Partly this is because I've been living in the bio/life-sciences world
for a while, where it's just gauche to not publish necessary and
sufficient data and code, and partly this is because growing up in the
era of Richard Stallman, one develops the sense that this is just the
right thing to do.

Still, it's not much use to anyone, to publish good data in venues where
it simply will not be seen, good intentions on the part of the venue, or
not.

(and as an aside, I don't see volume dataset publications in the
existing TIJ articles lists, so partly my question is whether this
is an appropriate venue for such a publication anyway)

You're free to convince me that TIJ has greater penetration than it
looks from the web page - once you do, put that convincing argument in
great big letters on the front page, because I guarantee that there are
other people with data and methods who would be willing to publish in your
venue, if they weren't worried that the statistics didn't add up to
much readership.

> So either we don't have the same definition of 'much life' or I am
> missing something, but seriously the last 5 publications are from this
> month.


From the same page, you'll see that TIJ sports 16 articles from the
August-December issue, and that your 5 articles from this month, are
five of six total, between this month and last month.

So, no, we don't have the same definition of "much life".  My typical venues
are Nucleic Acids Research, and Bioinformatics, where I spend $1500 to
$2500 per article, so that I can get them into their "open access"
(equals instantly online, no subscription required, in their model) section.

30-50 original (not revision - or rather, only a single version, revision
or not, is ever published) peer-reviewed articles per month are about par.
Not that that's a necessity for "life", but the reality is that high and
lofty goals aside (good though they may be), it's difficult to risk putting
a year's work into a venue where one can't tell if anyone's ever going to
see it.

Young journal or not, you might want to put some statistics on the TIJ
web-page that indicate how many views/downloads the articles are getting,
etc - something to inspire some confidence that things are going well.

> Is anybody still reading papers published in closed access journals ?

It's a nice quote, but... What does CiteSeer have to say about this?
I know the statistics suggest that web-access articles are cited more
frequently than dead-tree-access.  How are comparable articles in
"closed" publications doing compared to articles in TIJ in terms of
actually being used by other people to develop and further their own
research?  I know the model sounds like a good idea.  The tools exist
to generate a convincing statistical argument that it /is/ a good idea,
if the statistics bear out that assertion.

Again, if they _do_ show that TIJ's impact exceeds other start-up
journals with a closed model and traditional reviews, you /really/
need to publish this on your web page - leaving it out, almost implies
that the statistics disagree with the supposed benefits.

> Papers submitted to the Insight Journal are published in a matter of
> hours and are available in Open Access (gratis) to anybody in the world.

That is part of the problem, rather than the solution...  Whether
you like it or not, the lack of a peer-review mechanism that can prevent
a bad publication from ever seeing the light of day, devaluates
publications in TIJ considerably.   The fact that a bad article can be
clobbered with publicly visible bad reviews, doesn't change the fact that
few people will risk publishing their work in a venue where it might appear
beside something that's utter bunk.  It also doesn't change the fact that
research published in such an "un-reviewed" format is all but valueless
when it comes to supporting grant applications, etc.

As far as NIH reviewers are concerned, for example, you'd be better
off not admitting to having done preliminary experiments, as compared
to publishing your results in a non-reviewed journal.

I'd love to see TIJ demonstrate that these articles have significant
impact, and that the open review process works.  Right now, I don't
see it - I see arguments that it _should_ work, not facts that
it _does_.

> Note also that the Insight Journal is not intended to be the typical
> vanity-science journal where people publish just to met their annual
> quota of papers required to account for their "productivity". That
> empty practice is void of any scientific value and only demonstrate
> how the principles of scientific research can be degraded when they
> are evaluated by bureaucrats who simply "count" the number of papers
> in your CV and your annual reports, but never read those papers, and
> probably can not discern their implications.
>
> The Insight Journal is after the important goal of recovering honesty
> in the scientific endeavor by enforcing REPRODUCIBILITY.  Papers sent
> to the Insight Journal are expected to be in the format of a technical
> report that makes possible for *any* reader to replicate the results
> described in a paper.

Again, believe me, you're preaching to someone who already drinks
the kool-aid.  Wearing one of my other hats, I could have written
almost exactly the same thing you did above.  (I wrote down a total
of three notes from SIGGRAPH this year, one of those is to check out TIJ,
based on Terry Yoo's talk).

("vanity journals" however is kind of a red herring - there are
plenty of CV-padding vanity journals out there.  ISI top-10 journals,
etc, are not part of this list (despite success in getting an article
into them, being worth a bit of vanity). Even bureaucrats are
clever enough to have scoring schemes that de-weight vanity journals
significantly, and up-weight publications that actually contribute to
other people's research and productivity.  My biggest concern is that
TIJ is currently _exactly_ what it's claiming to fight against - a
CV-padding venue that doesn't actually measurably impact anyone's
productivity.  I'd love to be proven wrong.)

However...  The reality of the academic world is that
one lives or dies, depending on whether one's research is seen, and
found to be valuable by one's peers.  The only measure that's applied
to that "found to be valuable" statistic, is re-citation by other
researchers.

I don't like the model.  I don't like having to work
under it.  I don't like the fact that there's a huge amount of social
inerta that keeps the machine working this way.

I am however, pragmatic enough to be worried about putting the results
of a year's worth of an institution's support funds, into a venue that
they may see as valueless.  Give me the ammunition to prove that they're
wrong, and I'll happily make the effort to try to prove it to them.
Then put that ammunition up on your web-page, because I guarantee there
are others with the same concerns that I have.


> When you are joining a revolution based on principles,
> you should not ask
>
>                 "How many have already joined?",
>
> instead,
> you should be proud to be among the first ones to join.

Been there.  Done that.  Since 1989 or so.




Will Ray
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