Supplemental Materials to a Journal Article Alexander (Sasha) Schwarzman American Geophysical Union [email protected] Co-chair, NISO/NFAIS Working Group

Supplemental Materials to a Journal Article

Alexander (‘Sasha’) SchwarzmanAmerican Geophysical Union

[email protected]

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

Balisage 2011: The Markup Conference Montréal, 3 August 2011

Deluge: sup. mat. ratio

Montréal, 3 August 2011 Balisage 2011: The Markup Conference 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? [Hosting]


Yes, we can. But should we? (cont’d)

• Will sup. mat. be readable/playable/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]


Whose problem?• Author / Editor• Reviewer• Reader• Publisher• Hosting platform / Repository / Data center /

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


Classification attempt


Pseudo-supplemental (example)


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, citation, data, multimedia• Curation and life cycle: selection, peer review, editing,

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

• 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)


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


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


BWG definitions

• Supplemental materials Additional content (“truly supplemental”) Integral content (“pseudo-supplemental”)

• Related content Generally resides in an official data center or

institutional repository. The author may not have been the creator, and the publisher has no responsibility or authority over this content 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.


What to mark up?

• Additional content Metadata (at least)

• Integral content Metadata (necessary) Full text, if text/tables (possibly)

• Related content Minimal, if any, markup (e.g., ext. link)


Metadata schema

• Supplemental material

• Parent article metadata (ID, verification code)

• Type: (Additional | Integral | Related)

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

• Descriptive metadata

• Physical metadata

• Object or Object group or Object wrapperMontréal, 3 August 2011 Balisage 2011: The Markup Conference 21

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 Parent 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


Challenges: conceptual• 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 existing Tag Sets• Incorporating sup. mat. metadata schema into

content models of elements & groups that could be Integral or Additional: table, figure, media, alternatives, fig-group, section, etc.

• Indicating element’s or/and group’s @importance, i.e., additional, integral

• Providing version-specific appearance instructions, e.g., @specific-use="HTML-only"

• Can be done: supplementary-material (JATS), @role (Elsevier 5.1)


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


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]


Documents

Supplemental Materials to a Journal Article Alexander (Sasha) Schwarzman American Geophysical Union [email protected] Co-chair, NISO/NFAIS Working Group