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About
This page belongs to a [http://www.ncbi.nlm.nih.gov/books/NBK280240/ paper] [http://jats.nlm.nih.gov/jats-con/2015/schedule2015a.html#2-900 presented] on April 22, 2015 (from 9.00 to 9.45am EDT) as part of [http://jats.nlm.nih.gov/jats-con/2015/schedule2015.html JATS-Con 2015] in the [http://www.nlm.nih.gov/about/lhcaud_gen.html Lister Hill Auditorium] at the National Library of Medicine in Bethesda, Maryland.
Daniel Mietchen, Johanna McEntyre, Jeff Beck, Chris Maloney; Force11 Data Citation Implementation Group
Abstract
Data referred to in articles is usually not cited in a consistent or structured fashion. To address this, Force 11 have developed the [https://www.force11.org/datacitation Joint Declaration of Data Citation Principles]. [http://jats.nlm.nih.gov/publishing/tag-library/1.1d1/index.html JATS 1.1d1] has provisions for citing articles and other sources, but does not offer straightforward ways of expressing some of the concepts needed for data citation. In order to facilitate the citation of data in JATS-tagged documents in a way that is compliant with the Joint Declaration of Data Citation Principles, the [https://www.force11.org/datacitationimplementation Force11 Data Citation Implementation Group] held a meeting in June of last year, at which several new elements, attributes and values for attributes were suggested to be added to JATS. These have since been submitted to the [http://www.niso.org/apps/group_public/workgroup.php?wg_abbrev=jats-sc JATS Standing Committee], which largely accepted them, so they are now included in the draft standard [http://jats.nlm.nih.gov/publishing/tag-library/1.1d2/index.html JATS 1.1d2]. This talk will provide background on the decision criteria behind the elements that were proposed, and how they were selected for JATS 1.1d2. It will in addition provide suggested examples for use of the new tags.
The full paper is available via [http://www.ncbi.nlm.nih.gov/books/NBK280240/ http://www.ncbi.nlm.nih.gov/books/NBK280240/].
In scholarly literature, whenever and wherever a claim relies upon data, the corresponding data should be cited.
;Unique Identification
A data citation should include a persistent method for identification that is machine actionable, globally unique, and widely used by a community.
;Access
Data citations should facilitate access to the data themselves and to such associated metadata, documentation, code, and other materials, as are necessary for both humans and machines to make informed use of the referenced data.
;Interoperability and Flexibility
Data citation methods should be sufficiently flexible to accommodate the variant practices among communities, but should not differ so much that they compromise interoperability of data citation practices across communities.
= NIH Public Access Policy =
{{cquote|[http://grants.nih.gov/grants/NIH-Public-Access-Plan.pdf NIH will explore ways to advance data as a legitimate form of scholarship through data citation and other means.]}}
Options to extend JATS functionality
= Getting new elements added to JATS itself =
NISO [http://www.niso.org/workrooms/ali/ Access and License Indicators (ALI)], available in [http://jatspan.org/niso/publishing-1.1d3/ JATS 1.1d3]
= A superset extension of JATS =
[http://taxpub.sourceforge.net/ TaxPub]
Catapano T. TaxPub: An Extension of the NLM/NCBI Journal Publishing DTD for Taxonomic Descriptions. In: Journal Article Tag Suite Conference (JATS-Con) Proceedings 2010 [Internet]. Bethesda (MD): National Center for Biotechnology Information (US); 2010. Available from: http://www.ncbi.nlm.nih.gov/books/NBK47081/
Penev L, Catapano T, Agosti D, et al. Implementation of TaxPub, an NLM DTD extension for domain-specific markup in taxonomy, from the experience of a biodiversity publisher. In: Journal Article Tag Suite Conference (JATS-Con) Proceedings 2012 [Internet]. Bethesda (MD): National Center for Biotechnology Information (US); 2012. Available from: http://www.ncbi.nlm.nih.gov/books/NBK100351/
Process
Survey of
existing citation infrastructure in JATS 1.0
data citation practices
Remote discussions via the Force11 Data Citation Implementation Working Group
One-day workshop in London in June 2014
Decision to go for extending JATS rather than a superset extension
Agreement reached on set of suggestions for new elements, attributes and attribute values
Submission of suggestions to JATS Standing Committee
Response from JATS Standing Committee
Incorporation into JATS 1.1d2
Recommendation by JATS Standing Committee to NISO: adopt JATS 1.1d3 as JATS 1.1
For elements [http://jatspan.org/niso/publishing-1.1d3/#p=elem-ext-link <ext-link>] and [http://jatspan.org/niso/publishing-1.1d3/#p=elem-pub-id <pub-id>]
[http://jatspan.org/niso/publishing-1.1d3/#p=attr-pub-id-type @pub-id-type] used to be used to specify the authority; now it should only be used to specify the type of identifier
For example, a DOI might be described with assigning-authority="crossref"
=Linking attributes for [http://jatspan.org/niso/publishing-1.1d3/#p=elem-pub-id <nowiki><</nowiki>pub-id<nowiki>></nowiki>]=
Many identifiers are associated with URLs, so can be rendered as hyperlinks
Indeed, in the linked data world, many identifiers are HTTP URIs.
Therefore, the "[http://jatspan.org/niso/publishing-1.1d1/#p=pe-might-link-atts might-link attributes]" were added.
Standing Committee has indicated that they will revisit this issue in light of the [http://projectcredit.net/ CRediT] - Contributor Role Taxonomy, which has just been published
The following example shows how the "accession" value might be used. Note that it is accompanied by an @assigning-authority, to make clear the provenance of the identifier.
HeinzD.W.,
BaaseW.A.,
et. al.
How amino-acid insertions are allowed in an alpha-helix of T4
Müller, C et al. (2005): Audio record of a 'singing iceberg' from the Weddell Sea, Antarctica. doi:10.1594/PANGAEA.339110, Supplement to: Müller, Christian; Schlindwein, Vera; Eckstaller, Alfons; Miller, Heinz (2005): Singing Icebergs. Science, 310, 12, doi:10.1126/science.1117145
Possible tagging solution:
MüllerC,
et al.
(2005):
Audio record of a 'singing iceberg' from the Weddell Sea,