1. Supplemental Materials to a Journal Article Alexander (Sasha) Schwarzman American Geophysical Union sschwarzman@agu.org Co-chair, NISO/NFAIS Working Group on Journal Article Supplemental Materials Balisage 2011: The Markup Conference Montréal, 3 August 2011

2. Deluge: sup. mat. ratio Montréal, 3 August 2011Balisage 2011: The Markup Conference 2 Chart courtesy of Ken Beauchamp, American Society for Clinical Investigation

3. 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 Montréal, 3 August 2011Balisage 2011: The Markup Conference 3 Deluge: sup. mat. size

4. What is in the Pandoras 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.) Montréal, 3 August 2011Balisage 2011: The Markup Conference 4

5. 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 Montréal, 3 August 2011Balisage 2011: The Markup Conference 5

6. 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] Montréal, 3 August 2011Balisage 2011: The Markup Conference 6

7. Yes, we can. But should we? (contd) 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] Montréal, 3 August 2011Balisage 2011: The Markup Conference 7

8. 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 Montréal, 3 August 2011Balisage 2011: The Markup Conference 8

9. Classification attempt Montréal, 3 August 2011Balisage 2011: The Markup Conference 9

10. Pseudo-supplemental (example) Montréal, 3 August 2011Balisage 2011: The Markup Conference 10

11. Chronology February 2009: NFAIS Best Practices for publishing journal articlesBest Practices November 2009: Schwarzmans Report on supplemental materials survey resultsReport January 2010: NISO/NFAIS supplemental materials Thought Leader RoundtableThought Leader Roundtable August 2010: NISO/NFAIS Working Group on journal article supplemental materialsWorking Group Montréal, 3 August 2011Balisage 2011: The Markup Conference 11

12. NISO/NFAIS Working Group Montréal, 3 August 2011Balisage 2011: The Markup Conference 12

13. 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) Montréal, 3 August 2011Balisage 2011: The Markup Conference 13

14. 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 Montréal, 3 August 2011Balisage 2011: The Markup Conference 14

15. 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/suppinfowww.niso.org/lists/suppinfo Montréal, 3 August 2011Balisage 2011: The Markup Conference 15

16. 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. Montréal, 3 August 2011Balisage 2011: The Markup Conference 16

17. 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. Montréal, 3 August 2011Balisage 2011: The Markup Conference 17

18. Integral content Essential for the full understanding of the work by the general scientist or reader in the journals 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.) Montréal, 3 August 2011Balisage 2011: The Markup Conference 18

19. Related content Other 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. Montréal, 3 August 2011Balisage 2011: The Markup Conference 19

20. 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) Montréal, 3 August 2011Balisage 2011: The Markup Conference 20

21. 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 wrapper Montréal, 3 August 2011Balisage 2011: The Markup Conference 21

22. 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. Montréal, 3 August 2011Balisage 2011: The Markup Conference 22

23. Metadata schema (contd) Object or Object group or Object wrapper Parent article item being supplemented Descriptive metadata Physical metadata Object or Object group or Object wrapper Montréal, 3 August 2011Balisage 2011: The Markup Conference 23

24. 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 Montréal, 3 August 2011Balisage 2011: The Markup Conference 24

25. 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 Montréal, 3 August 2011Balisage 2011: The Markup Conference 25

26. 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 Montréal, 3 August 2011Balisage 2011: The Markup Conference 26

27. Challenges: conceptual (contd) 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) Montréal, 3 August 2011Balisage 2011: The Markup Conference 27

28. Challenges (practical) Is sup. mat. importance in the eye of the beholder? (whats 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? Montréal, 3 August 2011Balisage 2011: The Markup Conference 28

29. 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 elements or/and groups @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) Montréal, 3 August 2011Balisage 2011: The Markup Conference 29

30. 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 Montréal, 3 August 2011Balisage 2011: The Markup Conference 30

31. Sources Beebe, L. (2010), Supplemental materials for Journal articles: NISO/NFAIS Joint Working Group, Information Standards Quarterly 22(3), p.33, doi:10.3789/isqv22n3.2010.0710.3789/isqv22n3.2010.07 Carpenter, T. (2009), Journal article supplementary materials: A Pandoras 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.2009.09.02110.1016/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 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/isqv22n3.2010.0510.3789/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/supplemental sschwarzman@agu.org Montréal, 3 August 2011Balisage 2011: The Markup Conference 31