[open-science] (Lack of) data sharing for fossil data

Fri Apr 15 13:11:50 UTC 2011

On Fri, Apr 15, 2011 at 1:54 PM, Ross Mounce <ross.mounce at gmail.com> wrote:

> Hi all,
>
> I've been quietly lurking on this list for a few weeks now. Seems like an
> excuse to say "hi"
>
> The motivator for the Nature piece was a long thread on the PaleoNet
> mailing list discussing an Open Letter
> http://supportpalaeodataarchiving.co.uk I co-organised to demonstrate
> support from *within* the paleo-community for better data archiving. Ewen
> picked up the story from there and decided to spin a story out of it -
> great! You might be interested to know that we drafted and organised the
> Open Letter on an EtherPad - an idea I entirely 'stole' from OKFN pads i'd
> seen ;)
>
> I agree - I have been cloning them for virtuous projects

> I'm particularly pissed off that when data is published [sic] in
> supplementary materials it's regularly corrupt / unusable / obfuscated /
> near useless... etc and one has to then run the gauntlet of contacting the
> original authors, which I hope we all know has decidedly mixed success rates
> (e.g. Wicherts et al, 2006), not to mention the additional hassle for both
> parties.
>

I am trying to fight this. There are some publishers who are good (IUCr,
BMC, EGU/ACP, etc.), some who do not check the quality of the material and
so it's up to the authors, some who do not check but copyright it (ACS) and
some who refuse to publish any suppdata (J. Neurosci).

It's a human problem, not technical in most cases. It requires the corporate
will of the publishers and senior editors. In some areas such as Proteomics
the editors have prevailed and force data to be deposited. It's very
domain-variable.

>
> This is what I'm aiming to change in particular - the way in which
> underlying data that supports a research article is made available, in the
> systematics [~phylogenetics] and palaeontological communities.
> My first attempt at pitching this idea to the systematics community was
> very well received:
>
> http://prezi.com/1s0lkatmc30t/the-continued-growth-of-phylogenetic-information/
> However it was given at a small conference (Young Systematists' Forum) so
> it hasn't had anything like the impact of the paleo-focused Open Letter.
>

You are certainly doing the right thing by working with OKFN. At the least
you will find people who share your views. When you are losing heart and
wonder what is wrong there are others who share the same burden. Yes, it's a
burden, and a partial lifestyle. But we believe in the simple idea that if
work is publicly funded then the results should be public.

The semantic problems you allude to are harder. PDF is an abomination in
science - it has no role. We're trying to develop scholarly HTML as the
right way to communicate science. It will need critical mass but we are as
always optimistic.

This is an n^2 effect (or even higher power). Everyone like you enhances
*our* power and determination. The dam is starting to crack but it needs
constant work on our part. Probably at this stage it's worth sticking to a
fairly clear message - don't try and solve everything at once.

We are writing Panton papers on some of these areas and it may well be that
Panton Prezis would be a great addition!

>
> The Open Dino project people are awesome, and there are actually many many,
> other people as I've recently discovered, in the paleo-community that want
> more Openness of research data.
>
> Just one further note - I'm going to be at the Linked Open Data EBI
> short-course in May soon.
> http://www.ebi.ac.uk/Rebholz-srv/semantics_WS_May2011.html
> Do let me know if you're around then in the evening - I would really like
> to integrate / meet a bit more of the open science community, and I know a
> fair few of you are Cambridge-based... just a thought ;)
>
> I shall be at the EBI at the course.

>
> *waves hello*
>
> Ross
>
> --
> -/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-
> Ross Mounce
> PhD Student
> Fossils, Phylogeny and Macroevolution Research Group
> University of Bath
> 4 South Building, Lab 1.07
> http://twitter.com/rmounce <http://twitter.com/#%21/rmounce>
> http://bath.academia.edu/RossMounce
> -/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-
>
>
>
>
>
> On Fri, Apr 15, 2011 at 12:00 PM, <open-science-request at lists.okfn.org>wrote:
>
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>>
>> Today's Topics:
>>
>>   1. (Lack of) data sharing for fossil data (Rufus Pollock)
>>   2. Re: (Lack of) data sharing for fossil data (Matt Jones)
>>   3. Re: (Lack of) data sharing for fossil data
>>      (cameron.neylon at stfc.ac.uk)
>>
>>
>> ----------------------------------------------------------------------
>>
>> Message: 1
>> Date: Thu, 14 Apr 2011 15:23:23 +0100
>> From: Rufus Pollock <rufus.pollock at okfn.org>
>> Subject: [open-science] (Lack of) data sharing for fossil data
>> To: open-science <open-science at lists.okfn.org>
>> Message-ID: <BANLkTikHbWx9VsBg7SWq+qAqrECHKUcm7Q at mail.gmail.com>
>> Content-Type: text/plain; charset=UTF-8
>>
>>
>> Interesting article on data sharing in Palaeontology:
>> <http://www.nature.com/news/2011/110411/full/472150a.html>
>>
>> Made me think of the excellent Open Dinosaur project:
>>
>> <http://ckan.net/package/open-dino>
>> <http://opendino.wordpress.com/>
>>
>> Rufus
>>
>>
>>
>> ------------------------------
>>
>> Message: 2
>> Date: Thu, 14 Apr 2011 11:59:37 -0800
>> From: Matt Jones <jones at nceas.ucsb.edu>
>> Subject: Re: [open-science] (Lack of) data sharing for fossil data
>> To: rufus.pollock at okfn.org
>> Cc: open-science <open-science at lists.okfn.org>
>> Message-ID: <BANLkTin3eHQv2vtqx1HPx92EJfqJ46+qvw at mail.gmail.com>
>> Content-Type: text/plain; charset="iso-8859-1"
>>
>>
>> Definitely interesting.  The article also didn't mention PaleoDB (
>> http://paleodb.org/), one of the main international data sharing efforts
>> in
>> paleontology, crossing all taxa, with replica sites in Australia, Germany,
>> and two sites in the US.  Its a voluntary effort, so differs somewhat from
>> the journal mandated sharing described in the article, but still I would
>> think it deserved a mention.  Its quite a bit more targeted than MorphBank
>> for this topical area.
>>
>> Do you know if the Open Dinosaur project is contributing their specimen
>> measurements to the broader PaleoDB?
>>
>> Getting these types of data repository systems to interoperate, expose
>> data
>> to each other, and be able to provide persistence and replication services
>> to each other are some of the goals of the DataONE federation (see
>> http://dataone.org).  Dryad, mentioned in the article, is one of the
>> founding nodes in DataONE. If DataONE is successful, when researchers
>> choose
>> to use one repository for their data, they won't be contributing to a
>> single
>> repository, but rather to a federation that allows data to persist beyond
>> the lifetime of the individual repository project they choose.  Seems
>> pretty
>> compatible with OKFN goals to me.
>>
>> Matt
>>
>> On Thu, Apr 14, 2011 at 6:23 AM, Rufus Pollock <rufus.pollock at okfn.org
>> >wrote:
>>
>> > Interesting article on data sharing in Palaeontology:
>> > <http://www.nature.com/news/2011/110411/full/472150a.html>
>> >
>> > Made me think of the excellent Open Dinosaur project:
>> >
>> > <http://ckan.net/package/open-dino>
>> > <http://opendino.wordpress.com/>
>> >
>> > Rufus
>> >
>> > _______________________________________________
>> > open-science mailing list
>> > open-science at lists.okfn.org
>> > http://lists.okfn.org/mailman/listinfo/open-science
>> >
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>> ------------------------------
>>
>> Message: 3
>> Date: Fri, 15 Apr 2011 07:39:48 +0000
>> From: <cameron.neylon at stfc.ac.uk>
>> Subject: Re: [open-science] (Lack of) data sharing for fossil data
>> To: <jones at nceas.ucsb.edu>
>> Cc: open-science at lists.okfn.org
>> Message-ID: <484DF39D-994A-428E-AC85-EFFE4EE6E914 at stfc.ac.uk>
>> Content-Type: text/plain; charset="us-ascii"
>>
>>
>> I've had a couple of chats to Ross Mounce who was the instigator of the
>> open letter that tipped off this article. He's aware of (and involved with)
>> Dryad UK and I also pointed him in the general direction of OKFN. Given his
>> main focus at the moment was data to do with published articles Dryad (and
>> DataONE) seem like a good place to start for him. His main task really is
>> getting a bit more community backing behind the idea that _something_ needs
>> to be done and he seems to be doing a good job on that.
>>
>> Cheers
>>
>> Cameron
>>
>>
>> On 14 Apr 2011, at 20:59, Matt Jones wrote:
>>
>> > Definitely interesting.  The article also didn't mention PaleoDB (
>> http://paleodb.org/), one of the main international data sharing efforts
>> in paleontology, crossing all taxa, with replica sites in Australia,
>> Germany, and two sites in the US.  Its a voluntary effort, so differs
>> somewhat from the journal mandated sharing described in the article, but
>> still I would think it deserved a mention.  Its quite a bit more targeted
>> than MorphBank for this topical area.
>> >
>> > Do you know if the Open Dinosaur project is contributing their specimen
>> measurements to the broader PaleoDB?
>> >
>> > Getting these types of data repository systems to interoperate, expose
>> data to each other, and be able to provide persistence and replication
>> services to each other are some of the goals of the DataONE federation (see
>> http://dataone.org).  Dryad, mentioned in the article, is one of the
>> founding nodes in DataONE. If DataONE is successful, when researchers choose
>> to use one repository for their data, they won't be contributing to a single
>> repository, but rather to a federation that allows data to persist beyond
>> the lifetime of the individual repository project they choose.  Seems pretty
>> compatible with OKFN goals to me.
>> >
>> > Matt
>> >
>> > On Thu, Apr 14, 2011 at 6:23 AM, Rufus Pollock <rufus.pollock at okfn.org>
>> wrote:
>> > Interesting article on data sharing in Palaeontology:
>> > <http://www.nature.com/news/2011/110411/full/472150a.html>
>> >
>> > Made me think of the excellent Open Dinosaur project:
>> >
>> > <http://ckan.net/package/open-dino>
>> > <http://opendino.wordpress.com/>
>> >
>> > Rufus
>> >
>> > _______________________________________________
>> > open-science mailing list
>> > open-science at lists.okfn.org
>> > http://lists.okfn.org/mailman/listinfo/open-science
>> >
>> > _______________________________________________
>> > open-science mailing list
>> > open-science at lists.okfn.org
>> > http://lists.okfn.org/mailman/listinfo/open-science
>>
>> --
>> Scanned by iCritical.
>>
>>
>>
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-- 
Peter Murray-Rust
Reader in Molecular Informatics
Unilever Centre, Dep. Of Chemistry
University of Cambridge
CB2 1EW, UK
+44-1223-763069
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