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

Lance McKee lmckee at opengeospatial.org
Fri Apr 15 13:40:16 UTC 2011


re:
> 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.

PDF, no. HTML, no.

XML, yes.

Every domain needs a metadata council. Ultimately, it's about profiles  
of the ISO metadata standards and web service interfaces for catalogs  
that enable the xml-encoded ISO standard metadata -- and links to the  
data (and data processing services) -- to be published, discovered,  
assessed, accessed and used. See, for example, the Marine Metadata  
Interoperability Project (http://marinemetadata.org/). Ultimately,  
this approach enables chaining of web services in models that draw on  
multiple remote resources.

Lance

Lance McKee
Senior Staff Writer
Open Geospatial Consortium (OGC)
+1 508-752-0108
lmckee at opengeospatial.org

http://www.opengeospatial.org/contact


On Apr 15, 2011, at 9:11 AM, Peter Murray-Rust wrote:

>
>
> 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://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
> >
> -------------- next part --------------
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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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>
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>
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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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> open-science at lists.okfn.org
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