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 --- Head of Technology - eLife Submit now - http://submit.elifesciences.org/ twitter: @IanMulvany 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 >> > > JATS-List info and archive > EasyUnsubscribe (by email)
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