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RESEARCH-DATAMAN  April 2014

RESEARCH-DATAMAN April 2014

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Subject:

assigning DOIs to tissue samples (2)

From:

[log in to unmask]

Reply-To:

Research Data Management discussion list <[log in to unmask]>

Date:

Mon, 7 Apr 2014 00:34:33 +0000

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (245 lines)

Forwarded on behalf of K. Lehnert.

-----Original Message-----
From: Kerstin Lehnert [mailto:[log in to unmask]] 
Sent: Monday, 7 April 2014 2:04 AM
To: Klump, Jens (CESRE, Kensington); [log in to unmask]
Subject: Re: assigning DOIs to tissue samples (2)

Hi Miriam,

Nice to hear from you again, as we met at the RDA BoF session on the Internet of Samples.

The requirements that have guided the design of the IGSN architecture, procedures, and syntax have been, among others:

- ensure that there will not be multiple registrations of the same sample (Only the owner of the physical object should register it, not the owner of the digital data. The primary purpose of the ID is that disparate data generated in different labs and over longer periods of time can be unambiguously linked.)
- The identifier should easily fit on sample labels and into data tables.
- Users should be able to generate their own identifiers while in the field (work within their name space).
- The identifier should not replace "local" sample names (Many investigators and repositories have their own naming protocols that they will want to retain. Those naming protocols may not generate globally unique names. We have recently started to relax the IGSN syntax rules, which now allows some organizations to register their local identifiers as IGSNs.)
- Relationships between samples (e.g., subsamples and samples) need to be recorded in the metadata schema.

Citation of samples:
In the geosciences, samples are often listed in data tables together with the data. We recommend to authors to include a column with the IGSNs of the samples. The IGSNs should be tagged so that they resolve to the metadata record in the sample registry (see
http://www.elsevier.com/journals/earth-and-planetary-science-letters/0012-821X/guide-for-authors#88110). In order to establish a link with the article DOI, we would like the IGSNs can be included in the DataCite metadata record as "related_identifier" of "related_identifier_type" = IGSN. I talked to Jan Brase about including IGSN as a related identifier type in the DataCite metadata.

I hope we can set up the RDA IG for samples and continues our discussions within this IG.

Best wishes,
Kerstin



Dr. Kerstin Lehnert
Director, Integrated Earth Data Applications Director, EarthChem President, IGSN e.V.

Lamont-Doherty Earth Observatory
Columbia University
Palisades, NY, 10964
(845) 365-8506
http://www.iedadata.org
http://www.earthchem.org
http://www.igsn.org








On 4/3/14 21:22 PM, "[log in to unmask]" <[log in to unmask]> wrote:

>Hi Miriam,
>
>In geology samples play a very big role and it is crucial to be able to 
>link samples, data derived from samples, and literature interpreting 
>the results. In a project funded by the US National Science Foundation 
>Lamont-Doherty Earth Observatory of Columbia University explored 
>assigning persistent identifiers to samples and built prototype web 
>services <http://www.geosamples.org>. This was later expanded to other 
>institutions and made into an international organisation as the 
>International Geo Sample Number (IGSN). <http://www.igsn.org> A more 
>detailed description of organisational and technical aspects of the 
>IGSN can be found here:
><http://dokuwiki.gfz-potsdam.de/datawiki/doku.php?id=igsn:start>.
>
>The IGSN is based on the handle system and was developed as an internet 
>of things analogy to DataCite, taking into account the requirements 
>specific to geological samples. These can be individual samples from 
>the field or large collections from scientific drilling, museum 
>collections or government geological survey collections. IGSN works in 
>close cooperation with scientists, geological survey organisations, 
>publishers and research infrastructure providers.
>
>As you said, being able to identify physical objects on the web is a 
>growing concern and it will be interesting to see future developments.
>Please feel free to contact Kerstin Lehnert 
><mailto:[log in to unmask]> or me <[log in to unmask]> for more 
>information.
>
>Regards,
>
>Jens Klump
>
>
>
>--
>Dr Jens Klump
>OCE Science Leader Earth Science Informatics Earth Science and Resource 
>Engineering CSIRO
>
>E [log in to unmask] T +61 8 6436 8828 CSIRO ARRC, 26 Dick Perry 
>Avenue, Kensington, WA 6151 www.csiro.au
>
>
>
>-----Original Message-----
>From: Research Data Management discussion list 
>[mailto:[log in to unmask]] On Behalf Of RESEARCH-DATAMAN 
>automatic digest system
>Sent: Friday, 4 April 2014 7:03 AM
>To: [log in to unmask]
>Subject: RESEARCH-DATAMAN Digest - 2 Apr 2014 to 3 Apr 2014 (#2014-50)
>
>There are 12 messages totaling 3048 lines in this issue.
>
>Topics of the day:
>
>  1. The Value & Impact of Data Sharing & Curation (7)  2. JISC Storage 
> Workshop v 2-SDH (3)  3. assigning DOIs to tissue samples (2)
>
>----------------------------------------------------------------------
>
>
>------------------------------
>
>Date:    Thu, 3 Apr 2014 08:22:51 +0000
>From:    "M. Casula" <[log in to unmask]>
>Subject: assigning DOIs to tissue samples
>
>Dear all,
>
>Some months ago I posted a question about assigning DOIs to samples and 
>got some useful feedback. Having participated at the 'Internet of 
>samples' session at the recent RDA plenary,  it is clear that this 
>topic is of general interest with representatives from the earth, 
>agricultural sciences, life sciences and engineering sciences 
>participating at this session. Having now set up a prototype for the 
>DOI enabled site for tissue samples, I have now run in another 
>conundrum on which I would be grateful for advice. Having discussed the 
>assignment of DOIs to tissue samples with colleagues, they have raised 
>a very valid issue in the circumstance of the results form several 
>hundred tissues samples being reported in the same article. If current 
>recommendations are followed such as those of DataCite, then the 
>citation format for datasets is very similar for that of conventional 
>written publications, in which case the reference section would extend 
>to several pages. While I am aware that DOIs can be assigned to data 
>collections and that supplements to articles are also becoming common, 
>neither of these solutions are particularly appropriate. In the first 
>case it would mean having to define a collection for every article 
>which is not practicable and in the second instance the data are 
>becoming dissociated from the written article which is basically 
>counter to the purpose of data citation. As this is surely a potential 
>issue in any discipline, if anyone is aware of an alternative solution I would be grateful for further information.
>
>Kind regards,
>Miriam Casula
>________________________________
>
>------------------------------
>
>Date:    Thu, 3 Apr 2014 12:25:54 +0100
>From:    Andy Turner <[log in to unmask]>
>Subject: Re: assigning DOIs to tissue samples
>
>Hi,
>
>At the University of Leeds we've been giving this some thought. There 
>are a lot of scenarios to deal with, so the right solution as nearly 
>always depends. Let me outline one of our cases briefly and give you my 
>reckoning which is not necessarily that of my institution or my other 
>colleagues working on this.
>
>ForestPlots.net have amongst other things soil sample physical stores.
>Some physical samples have not been catalogues yet, but most have. Most 
>physical samples have been analysed in some way in a laboratory. This 
>generates digital metadata for them and a digital profile for the 
>physical samples is created. These are stored collectively in a form of 
>database.
>
>Assigning DOIs for individual samples (bags of dried soil) does not 
>scale in the Forestplots.net example. Some of the samples we deal with 
>are collections from specific surveys. These surveys may be for area 
>that are resurveyed or from a transect that is not planned to be 
>resurveyed necessarily. Some 'plots' are monitored in an on-going long 
>terms fashion. In general for ForestPlots.net it makes sense to assign 
>DOIs for each survey and for each plot and for collections of plots. At 
>the moment, a single DOI has not been assigned for all the 
>ForestPlots.net data, but as a pilot ForestPlots.net has its own DOI prefix.
>
>The appropriate granularity of DOI assignment all depends.
>
>The issue of having large author lists on journal articles is similar 
>to the problem of having lengthy reference lists. We have debated the 
>creation of DOIs to represent all the ForestPlots.net data that is used 
>for the results reported in a particular journal article. If the 
>article uses more than just these data, then it can refer to other data 
>in the same way. One of our team was keen to avoid the creation of a 
>single DOIs unique to each journal article which refers to all the data 
>used for that. I think though that in some cases this might be the way 
>forward to mitigate the problems caused by having too long a list of references.
>
>We debated using the suffix of a DOI to represent a hierarchical 
>structure of the data, but I think for the time being, the DOIs are 
>simply numerical and the detail of what the DOI refers to is metadata 
>to be found via the DOI landing page.
>
>I hope that is a useful and accurate summary and helps moves the 
>discussion forward. Apologies in advance if I've got anything wrong.
>
>Best wishes,
>
>Andy
>
>-----Original Message-----
>From: Research Data Management discussion list 
>[mailto:[log in to unmask]] On Behalf Of M. Casula
>Sent: 03 April 2014 09:23
>To: [log in to unmask]
>Subject: assigning DOIs to tissue samples
>
>Dear all,
>
>Some months ago I posted a question about assigning DOIs to samples and 
>got some useful feedback. Having participated at the 'Internet of 
>samples' session at the recent RDA plenary,  it is clear that this 
>topic is of general interest with representatives from the earth, 
>agricultural sciences, life sciences and engineering sciences 
>participating at this session. Having now set up a prototype for the 
>DOI enabled site for tissue samples, I have now run in another 
>conundrum on which I would be grateful for advice. Having discussed the 
>assignment of DOIs to tissue samples with colleagues, they have raised 
>a very valid issue in the circumstance of the results form several 
>hundred tissues samples being reported in the same article. If current 
>recommendations are followed such as those of DataCite, then the 
>citation format for datasets is very similar for that of conventional 
>written publications, in which case the reference section would extend 
>to several pages. While I am aware that DOIs can be assigned to data 
>collections and that supplements to articles are also becoming common, 
>neither of these solutions are particularly appropriate. In the first 
>case it would mean having to define a collection for every article 
>which is not practicable and in the second instance the data are 
>becoming dissociated from the written article which is basically 
>counter to the purpose of data citation. As this is surely a potential 
>issue in any discipline, if anyone is aware of an alternative solution I would be grateful for further information.
>
>Kind regards,
>Miriam Casula
>________________________________
>
>AMC Disclaimer : http://www.amc.nl/disclaimer
>
>________________________________
>
>

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