Re: [jats-list] Using JATS to cite research data.

Subject: Re: [jats-list] Using JATS to cite research data.
From: "Ian Mulvany i.mulvany@xxxxxxxxxxxxxxxxx" <jats-list-service@xxxxxxxxxxxxxxxxxxxxxx>
Date: Fri, 9 May 2014 14:35:19 -0000
Hi Kim,

Thanks for that very insightful example on why this is an important
issue. Are the general results of this study available?
- Ian

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On Thu, May 8, 2014 at 9:39 PM, Kimberly Tryka ktryka@xxxxxxxxx
<jats-list-service@xxxxxxxxxxxxxxxxxxxxxx> wrote:
> Ian -
>
> Recently, I was involved in a project that was looking at how (whether?)
> researchers with access to data from dbGaP (http://www.ncbi.nlm.nih.gov/gap)
> were citing the data that they retrieved from the database.
>
> dbGaP does have guidelines about data citation, and many of the committees
> who grant access to the data have boilerplate language they require
> researchers to put in their publications.  Yet, there were still a
> significant number of published papers (20-25%) using dbGaP data that either
> cited their data inadequately (by simply pointing to the general dbGaP site
> rather than giving a proper accession number) or simply neglected to mention
> dbGaP at all.
>
> Even with those who did cite the data properly (in that they put the
> appropriate accession number into their publication), finding that accession
> was a bit of a game.  You made the statement:
>
>> Citations to research data is currently coded almost arbitrarily
>> across different publishers, making it hard to machine read
>> data contributions in the literature.
>
>
> As I worked through the papers citing dbGaP data I found the citations in
> many different places including sections called (not a comprehensive list):
> * Abstract
> * Accession codes/numbers
> * Acknowledgments
> * Analysis
> * Applications
> * Author Information
> * Data access/accessibility/availability/accession
> * Data and Sample Sharing
> * Database content
> * Discussion
> * Footnotes
> * Funding/Grant Support
> * Genetic Influences
> * Introduction
> * Main Text
> * Materials and Methods
> * Neurological disorders
> * Online Methods
> * Process of Phenotype Harmonization
> * References
> * Results
> * Simulations and Real Data Analysis
> * Subjects
> * Supplementary Material
> * URLs
> * Web Resources
>
> Additionally, accession numbers were buried in table footnotes and figure
> captions, as well as in, for example, tables in pdf files in supplementary
> materials.
>
> I think it would be amazing if FORCE11 (or RDA or CODATA) would come up
> with, not only with a recommendation for the format of a data citation, but
> also a recommendation for where that data citation should exist in a
> published paper.  Once there was a 'where' defined, it might then be easier
> to figure out how/whether JATS needs to be altered.
>
> ---Kim
>
>
>
> On Fri, May 2, 2014 at 9:10 AM, Ian Mulvany i.mulvany@xxxxxxxxxxxxxxxxx
> <jats-list-service@xxxxxxxxxxxxxxxxxxxxxx> wrote:
>>
>> I'd like to tap into the collective wisdom of this group in
>> preparation for a workshop that I am co-organising in June on data
>> citation.
>>
>>
>> # Introduction and Question
>> How can we best use JATS to cite research data? Does this group have
>> specific examples of data citation that they could share with me,
>> and does anyone have strong opinions about the straw man options that
>> I list at the bottom of this message?
>>
>> # Need
>> Citations to research data is currently coded almost arbitrarily
>> across different publishers, making it hard to machine read
>> data contributions in the literature.
>>
>> # Background
>> We are running a workshop in June at the British Library to propose
>> some best practices for citing research data. This is being done
>> under the umbrella of the FORCE11 Data Citation Implementation group (
>> - https://www.force11.org/datacitationimplementation), and it will
>> involve a selection of invited participants, mostly
>> representing production departments of STM publishers. Ahead of that
>> meeting I'd like to start this thread as a background discussion to
>> the viability of some of the options the organisers of the meeting are
>> thinking about. Below I list three straw man options that we have been
>> discussing, along with basic pros and cons.
>>
>> # Straw man Options
>>
>> 1 get people to agree on best practice using the existing tag set
>>   pros:
>>        - nothing new needs to be introduced to JATS
>>   cons:
>>   - probably makes adoption harder, and the creation of tooling to
>> identify data citations harder, as these tools
>>   as overloading existing tags will likely not produce a tag syntax
>> unique to research data
>>
>>
>> 2 extend the JATS tag set to support specific citation of research data
>>   pros:
>>   - clean start, produces a standard that everyone can move towards,
>> good for creation of downstream tools
>>   cons:
>>   - extending JATS can take some time, owing to the standardisation
>> process
>>
>>
>> 3 produce an extension to JATS for data citation, along the same lines
>> as http://www.ncbi.nlm.nih.gov/books/NBK47081/
>>   pros:
>>      - does not need to wait for extension of JATS to be usable
>>   cons:
>>      - highly specific extension may face a difficulty in gaining
>> adoption in publishing workflows
>>
>
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