niso/nfais supplemental journal article materials working group: a progress report alexander...

NISO/NFAIS Supplemental Journal Article Materials Working Group:

A Progress Report

Alexander (‘Sasha’) SchwarzmanAmerican Geophysical Union

[email protected]

Co-chair, NISO/NFAIS Working Group on Journal Article Supplemental Materials

JATS-Con 2011: Journal Article Tag Suite Conference 2011

Bethesda, MD27 September 2011

Deluge: sup. mat. ratio

Bethesda, MD 27 September 2011 JATS-Con 2011 2

Chart courtesy of Ken Beauchamp, American Society for Clinical Investigation

Average size of a Journal of Neuroscience article and supplemental material

Source: Maunsell, J. (2010), Announcement regarding supplemental material, The Journal of Neuroscience 30(32): p.10599


Deluge: sup. mat. size

What is in the Pandora’s box?

• Multimedia• Gene sequences, protein structures, chemical

compounds, crystallographic structures, 3-D images• Computer programs (algorithms, code, libraries, and

executables)• Text, Tables, Figures (Materials and methods,

Extended methodology, Survey results, Bibliographies, Derivations, …)

• Datasets (datasets are not the only type of sup. mat.)


Supplemental materials: Yes, we can!

• Enabling technology makes it possible for:

• authors to present supporting evidence, e.g. datasets multimedia

• researchers to present in-depth studies that would not be available in print

• readers to replicate experiments and verify results


Yes, we can… But should we?

• Do I (reader, reviewer) need to look at sup. mat.? [Degree of importance]

• How do I (librarian, indexer) know sup. mat. exists? How do I find it? [Discoverability]

• How do I cite / link to sup. mat.? [Identification and Linking]

• Will sup. mat. be there in 20 years? … 200 years? [Viability]


Yes, we can… But should we? (cont’d)

• Will sup. mat. be renderable/executable? [Conversion/Forward migration]

• Do I see the original? [Preservation/Longevity]

• How do I send sup. mat. out? How do I know nothing was lost in transmission? [Packaging]

• Who has custody? [Curatorial responsibility]

• Who owns it? [Intellectual property rights]

• Who pays for curating? [Business models]Bethesda, MD 27 September 2011 JATS-Con 2011 7

Who cares? You should – if you are an …• Author / Editor• Reviewer• Reader• Publisher• Hosting platform / Institutional Repository /

Data center / Individual• A&I service• Reference linking and Citation indexing service• Librarian / Archivist / Historian of scholarship


Chronology

• February 2009: NFAIS Best Practices for publishing journal articles

• November 2009: Schwarzman’s Report on supplemental materials survey results

• January 2010: NISO/NFAIS supplemental materials Thought Leader Roundtable

• August 2010: NISO/NFAIS Working Group on journal article supplemental materials


NISO/NFAIS Working Group


Business Working Group – “what”Co-chairs: Linda Beebe (APA), Marie McVeigh (Thomson-Reuters ISI)

• Scope of & general principles for Recommended Practices• Definitions: sup. mat., article, data, metadata, multimedia• Curation and life cycle: selection, peer review, editing,

production, presentation, providing context, referencing, citing, managing/hosting, discovery, preservation

• Intellectual property rights management• Roles and responsibilities of authors, editors, peer

reviewers, publishers, libraries, A&I services, repositories• Broad principles around metadata, identifiers, archiving,

linking, packaging, and accessibility (TWG charge)


Supplemental content type: Additional, Integral, Related


Classification• Supplemental materials

Additional content (“truly supplemental”) Integral content (“pseudo-supplemental”)

For technical, business, or logistical reasons, it is treated as if it were supplemental – but it is not!

• Related content Generally resides in an official data center or institutional

repository. The publisher has no responsibility or authority over it and does not host it.

No recommended practices offered.


Additional content

Provides a relevant and useful expansion of the article in the form of text, tables, figures, multimedia, or data. May aid any reader to achieve deeper understanding of the work through added detail and context.

Examples: expanded methods sections and bibliographies; additional supporting data or results; copies of instruments/surveys; and multimedia and interactive representations of additional, relevant, and useful information.

Generally, the author has created this content and the publisher hosts it or places it on the open web.


Integral content

Essential for the full understanding of the work by the general scientist or reader in the journal’s discipline, but placed outside the article for technical, business, or logistical reasons.

Examples: descriptions of methods needed to evaluate a study, review, or technical report; detailed results required to comprehend outcomes; tables, figures, or multimedia with primary data required to verify/fully understand the work.

In general, the publisher maintains responsibility for hosting and curating this content in the same way the article itself is treated. (For some specialized journals, content held in an external repository may be considered integral.)


Related contentOther content the author wishes to make the reader aware

of because it may add to the understanding of the work or to the replication or verification of the results.

Examples: data used, created, or deposited by authors and held in external repositories, gene sequences, protein structures, crystallographic structures, digital recordings, 3-D images, and chemical compounds.

Generally resides in an official data center or institutional repository. Because the publisher lacks any authority over this type of content, no recommended practices are offered. However, some recommendations on preservation plans and repositories are included.


BWG recommendations

Integral content Additional content

Selecting / Peer reviewing

At the same level as core article

May not be reviewed at the same level

Copyediting At the same level as core article. Should be noted if not

May not be edited at the same level. If so, should be noted

Referencing within article

Cite/link at the same level as table or fig. No ref. list entry, for this content is part of article

Provide in-text citation and link at the appropriate point in text, rather than at the end

Citing from other pub’s

Not to be cited separately. Cite article as a whole

Can be cited separately

References within sup. mat.

Integrate references into the ref. list of the core article

Keep references separate from the core article ref. list

Bethesda, MD 27 September 2011 JATS-Con 2011: The Markup Conference

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BWG recommendations (cont’d)

Integral content Additional content

Preserving Preserve at the same level as the core article

Provide the same metadata markup

Include in migration plans

Take preservation into consideration when accepting

If uncertain about preservation, have author submit to a trusted repository and link to it

Managing rights

Treat rights in the same manner as the rights for the core article

Anyone who has access to online article should also have access to Integral content

Determination of rights for Additional content may differ and should be transparent to users


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• Managing and hosting sup. materials If journal content is hosted by an aggregator

or other host, that host should also deliver supplemental materials

Use persistent identifiers to ensure links to and from core article

An author’s website is not an appropriate place for the sole posting of supplemental materials


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• Discovering supplemental materials Consistent placement, naming, and navigation Indicate presence in the table of contents Link to the Integral content from within the article Link to the Additional content “above the fold” on

the first PDF or HTML page of the article Aid A&I services by including metadata that

indicate the purpose and format of the supplemental materials


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• Linking to and from supplemental materials Provide bidirectional linking to and from both

Additional and Integral content Assign separate DOIs for Additional and Integral

content

• Providing context for supplemental materials Do not supply README files. Include the following elements either on a

landing page or within the content itself:Bethesda, MD 27 September 2011 JATS-Con 2011: The Markup

Conference21


• Providing context for sup. materials (cont’d) Article citation and DOI Title and/or succinct statement about the content For multimedia: player, file extension, and size List multiple files Browser information, if supplemental content

rendition is browser-dependent A separate DOI or other unique identifier


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Technical Working Group – “how”Co-chairs: Dave Martinsen (ACS), Sasha Schwarzman (AGU)

• Metadata, persistent identifiers, and granularity of markup needed to support practices recommended by the BWG

• Referencing and linking to and from supplemental materials, handling cited references within

• Archiving, preservation, and forward migration of supplemental materials

• Packaging, exchange, and delivery of supplemental materials

• Technical support for accessibility practices recommended by the BWG


Metadata schema

• Supplemental material

• Core (parent) article metadata

• Type: (Additional | Integral | Related)

• Core article item being supplemented (figure, table, etc.)

• Descriptive metadata

• Physical metadata

• Object or Object group or Object wrapperBethesda, MD 27 September 2011 JATS-Con 2011 24

Object group vs. Object wrapper

• Object group contains logically different objects that share some common metadata, e.g., a series of graphs or images

• Object wrapper contains objects that are associated with or represent various aspects of the same logical object, e.g.,A chemical structure represented by: a connection table, an image of a molecule in a static orientation, and an interactive application allowing manipulation by the viewer.

Protein-related information represented by: analytical measurements, chemical structure, and derived structures.


Metadata schema (cont’d)

• Object or Object group or Object wrapper Core article item being supplemented Descriptive metadata Physical metadata Object or Object group or Object wrapper


Descriptive metadata

• ID• version• label• contrib_group• content_descriptor• title• language • alt_title• accessibility_long_desc• summary

• subject_descriptor• physical_form_descriptor• ref_count• publication_info• creation_date• preservation_level• copyright• license• open_access


Physical metadata

• creation_application platform software (name, version) application_information

• ext_link• filename• fixity

fixity_method fixity_value

• format• format_registry

• mime_subtype• mime_type• primary_representation?• relationship• rendering-application

platform software (name, version) application_information

• size• validity


TWG: Conceptual challenges:• Heterogeneity: an archive or a document may

contain both Additional and Integral content

• Relationships: related but different objects; alternate representations of the same object

• Recurrence: an archive (ZIP, TAR, RAR) or a document (PDF, MS Word) may contain nested objects and groups

• Hierarchical structure: an archive may contain a tree with many branches and sub-branches


Challenges: conceptual (cont’d)

• Granularity down: what level to choose —entire sup. mat., groups, objects, …?

• Granularity up: link to a specific item within the article or to the article as a whole?

• Should Related content be marked up?

• What is the extent of differences in marking up Integral and Additional content? (Think about tables; now think about videos)


Challenges (practical)

• Is sup. mat. importance “in the eye of the beholder?” (what’s Additional to you is Integral to me) — some beholders are more equal than others: a decision made upfront determines downstream processing

• Real costs, hypothetical benefits

• Business models: is sup. mat. a money maker or a money waster?


Integration with JATS• supplementary-material wrapper already

contains such typically supplemental objects as figure, media, table – but not a structural section!

• Parameterized list of supplementary-material attributes can be extended to include metadata developed by the NISO Working Group

• Attribute lists of elements that could be supplemental, e.g., table, figure, media, section, etc., can be extended as well

• alternatives can hold Object wrappers/groups


Integration with JATS (cont’d)

• What is currently missing is mechanism for indicating whether sup. mat. is Additional, Integral, or Related. A dedicated attribute could be introduced for that purpose, e.g., @importance (Additional | Integral | Related)

(Note: Elsevier 5.1 has the @role attribute that could be used to categorize sections, figures, and e-components)

• Or the @specific-use attribute could be used for that purpose (expedient – but overload danger)


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What does the future hold?

“… over time the concept of supplemental material will gradually give way to a more modern concept of a hierarchical or layered presentation in which a reader can define which level of detail best fits their interests and needs.”

Marcus, E. (2009), Taming supplemental material, Cell 139(1), p.11, doi:10.1016/j.cell.2009.09.021


Stakeholders group

A larger group to be kept apprised of development, to serve as a source of feedback on drafts, and to provide community vetting of a final document. The group list is open; anyone who would like to track the progress of this project and would like to potentially provide feedback on draft work can sign up by visiting: www.niso.org/lists/suppinfo


SourcesBeebe, L. (2010), Supplemental materials for Journal articles: NISO/NFAIS Joint Working

Group, Information Standards Quarterly 22(3), p.33, doi:10.3789/isqv22n3.2010.07

Carpenter, T. (2009), Journal article supplementary materials: A Pandora’s box of issues needing best practices, Against the Grain 21(6), p.84

Marcus, E. (2009), Taming supplemental material, Cell 139(1), p.11, doi:10.1016/j.cell.2009.09.021

Maunsell, J. (2010), Announcement regarding supplemental material, The Journal of Neuroscience 30(32): p.10599

NFAIS (2009), Best practices for publishing journal articles, 30 pp., http://www.nfais.org/files/file/Best_Practices_Final_Public.pdf

Schwarzman, S. (2010), Supplemental materials survey, Information Standards Quarterly 22(3), p.23, doi:10.3789/isqv22n3.2010.05

http://www.agu.org/dtd/Presentations/sup-mat/10.3789_isqv22n3.2010.05.pdf

NISO/NFAIS Supplemental journal article materials project

http://www.niso.org/workrooms/[email protected]


niso/nfais supplemental journal article materials working group: a progress report alexander...

Documents

type of sup

linkingwill sup

contdwill sup

figures materials

group whatcochairs

datasets datasets

protein structures

crystallographic structures