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- 1. NISO/NFAIS Supplemental Journal Article Materials Working Group: A Progress Report Alexander (‘Sasha’) Schwarzman American Geophysical Union sschwarzman@agu.org Co-chair, NISO/NFAIS Working Group on Journal Article Supplemental Materials JATS-Con 2011: Journal Article Tag Suite Conference 2011 Bethesda, MD 27 September 2011
- 2. Deluge: sup. mat. ratio Bethesda, MD 27 September 2011 JATS-Con 2011 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 Bethesda, MD 27 September 2011 JATS-Con 2011 3 Deluge: sup. mat. size
- 4. 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.) Bethesda, MD 27 September 2011 JATS-Con 2011 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 resultsBethesda, MD 27 September 2011 JATS-Con 2011 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? … 200 years? [Viability] Bethesda, MD 27 September 2011 JATS-Con 2011 6
- 7. 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
- 8. 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 Bethesda, MD 27 September 2011 JATS-Con 2011 8
- 9. 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 Bethesda, MD 27 September 2011 JATS-Con 2011 9
- 10. NISO/NFAIS Working Group Bethesda, MD 27 September 2011 JATS-Con 2011 10
- 11. 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) Bethesda, MD 27 September 2011 JATS-Con 2011 11
- 12. Supplemental content type: Additional, Integral, Related Bethesda, MD 27 September 2011 JATS-Con 2011 12
- 13. 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. Bethesda, MD 27 September 2011 JATS-Con 2011 13
- 14. 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. Bethesda, MD 27 September 2011 JATS-Con 2011 14
- 15. 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.) Bethesda, MD 27 September 2011 JATS-Con 2011 15
- 16. 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. Bethesda, MD 27 September 2011 JATS-Con 2011 16
- 17. 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 17
- 18. 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 Bethesda, MD 27 September 2011 JATS-Con 2011: The Markup Conference 18
- 19. BWG recommendations (cont’d) • 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 Bethesda, MD 27 September 2011 JATS-Con 2011: The Markup Conference 19
- 20. BWG recommendations (cont’d) • 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 Bethesda, MD 27 September 2011 JATS-Con 2011: The Markup Conference 20
- 21. BWG recommendations (cont’d) • 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 Conference 21
- 22. BWG recommendations (cont’d) • 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 Bethesda, MD 27 September 2011 JATS-Con 2011: The Markup Conference 22
- 23. 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 Bethesda, MD 27 September 2011 JATS-Con 2011 23
- 24. 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 wrapper Bethesda, MD 27 September 2011 JATS-Con 2011 24
- 25. 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. Bethesda, MD 27 September 2011 JATS-Con 2011 25
- 26. 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 Bethesda, MD 27 September 2011 JATS-Con 2011 26
- 27. 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 Bethesda, MD 27 September 2011 JATS-Con 2011 27
- 28. 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 Bethesda, MD 27 September 2011 JATS-Con 2011 28
- 29. 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 Bethesda, MD 27 September 2011 JATS-Con 2011 29
- 30. 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) Bethesda, MD 27 September 2011 JATS-Con 2011 30
- 31. 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? Bethesda, MD 27 September 2011 JATS-Con 2011 31
- 32. 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 Bethesda, MD 27 September 2011 JATS-Con 2011 32
- 33. 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)Bethesda, MD 27 September 2011 JATS-Con 2011: The Markup Conference 33
- 34. 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 Bethesda, MD 27 September 2011 JATS-Con 2011 34
- 35. 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 Bethesda, MD 27 September 2011 JATS-Con 2011 35
- 36. Sources Beebe, L. (2010), Supplemental materials for Journal articles: NISO/NFAIS Joint Working Group, Information Standards Quarterly 22(3), p.33, doi:10.3789/isqv22n3.2010.07 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/supplemental sschwarzman@agu.org Bethesda, MD 27 September 2011 JATS-Con 2011 36
- 37. Q & A
- 38. Pseudo-supplemental (example) Bethesda, MD 27 September 2011 JATS-Con 2011 38
Editor's Notes
- And JCI is not an isolated case. The situation is typical
- Average size of a Journal of Neuroscience article and supplemental material in megabytes. Values are trimmed means (5th–95th percentile) to exclude a handful of unaccountably large articles and supplemental files. Supplemental movies are excluded to facilitate comparisons because a megabyte of a movie is arguably easier to evaluate than a megabyte of text, figures, or tables. Data include only articles published in January of each year. Error bars are standard errors of the trimmed means.
- In his article, Todd Carpenter, NISO’s managing director, referred to supplemental materials as “Pandora’s box” Supplemental materials are not just datasets.
- It seemed like such a good idea! Who could possibly quibble with it?
- So, what’s the problem? As Debbie says, “Just because we can doesn’t mean we should”
- Reference linking and Citation indexing services: CrossRef, ISI Web of Knowledge, Scopus, PubMed Central The community has responded to the challenge in various ways. Researchers appear to be split on the issue: while some argue that more supplemental materials should be made available and are optimistic about the technology’s ability to solve some of the above problems, others argue that a scholarly journal “is not a data dump” and an article “is not an FTP site.” Different publishers too responded in different ways. In 2009, Cell imposed strict limits on the number and kind of supplemental materials that could be accepted. In 2010, The Journal of Neuroscience banned supplemental materials altogether and announced that it would embed dynamic content in its articles’ PDF format. In 2011, The Journal of Experimental Medicine introduced a policy limiting supplemental materials only to “essential supporting information 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, http://www.jneurosci.org/content/30/32/10599.full
- NFAIS Best Practices for publishing journal articles: One key recommendation on supplemental materials was that the journal make a clear connection between an article and the supplemental materials that accompany it. Once published, the supplemental materials should be considered part of the journal’s archival record and should not be changed without a clear statement of correction. Publishers, the document noted, should always supply a recommended citation as well as good, descriptive metadata for those materials. A&i services covering the journal article should include the presence of supplemental data in the article record, indicating file types and DOI.
- Mixture of publishers, librarians, archivists, A&I and citation linking services, independent consultants. Governmental and non-governmental organizations, commercial and non-commercial, academic and non-academic ones.
- This represents my own view, and not that of the NISO/NFAIS Working Group Institutional repositories and official data centers: GenBank, Protein Data Bank, World Data Centers, Pangaea, etc. Images and Tables, if essential, have been integrated into the article for 300 years but what if it is multimedia or chemical structures or datasets that are essential? Let’s consider two tables, one is essential and the other is not: the former appears in the main article, whereas the latter is tucked into an Appendix or Online supplement. The essential table is marked up using a CALS or XHTML model, the non-essential is not tagged. Now let’s consider a video: one is essential, the other is supplemental: while the non-essential one can still be dumped in an online supplement, the essential video may or may not be integrated into the main article. And it may or may not have metadata attached to it. The distinction is not just “what cannot be printed” vs. what can. A non-essential table can be printed but is still “truly supplemental.” An essential video cannot be printed but is not supplemental at all. The distinction is conceptual, based on the degree of importance of a particular object to the scholarly discourse. The fact that a particular object is not integrated into the article because of technical or business reasons should not obscure the fact that there is nothing supplemental about such content. I refer to such content as “pseudo-supplemental – it *pretends* to be supplemental while it is not. The adjective “supplemental” is a homonym: the content critical/essential for understanding the article’s conclusions isn’t supplemental at all but, confusingly, the same term is being used to refer to both types of content.
- This is a work in progress
- Obviously, object groups contain objects but why would objects contain object groups? Because a single archive (ZIP, TAR) or a document (PDF, MS Word) may contain multiple objects and groups of objects
- label: Figure S1 content_descriptor: General type of content for the material, for example, survey, extended methodology (semi-controlled vocabulary) summary: A brief summary of the supplemental material. Typically used to describe the contents prior to downloading or for assistive devices. subject_descriptor: Subject keyword describing the supplemental material (controlled on non-controlled vocabulary) physical_form_descriptor: Table, dataset publication_info: Who published the material an author, publisher, organization, maybe different than the copyright holder preservation_level: A commitment from a publisher or archive to carry the supplemental material forward. Used to help determine the likelihood that the material will be accessible in the future. Different for Additional and Integral. Could be implicit
- fixity: checksum, etc. relationship: Relation between objects, binds objects together. RDF-like "is-a" "is-a-child", etc. The intellectual unit can be preserved as a group and tell which object is primary (or preferred). Validity – whether a file is valid in relationship to the format it claims to be; goes with format. We suggest publishers use JHOVE terminology: “well-formed”, “well-formed and valid”, “not valid”, “not well-formed”. See http://hul.harvard.edu/jhove/index.html or http://www.jhove2.org
- Then the only difference in how an integral supplemental object and a fully integrated one are marked up may be the @specific-use value
- Moving beyond the binary “Integral/Additional” divide to a “tree-ring” (concentric circles) model: assigning weights, like in relevance ranking?
- False pretenses: Pseudo-supplemental (treated as if it were supplemental but it is not) This is a screenshot of Cell article (doi:10.1016/j.cell.2011.04.005). Movie S1 (highlighted in yellow) is mentioned in the first (!) section of the article. The movie is perfectly integrated in the HTML, it can be played in context, on the right. Clearly, Movie S1 is essential to the article's science; there is nothing supplemental about it. And yet, that very movie, Movie S1, shows up when one clicks on the "Supplemental Information" tab. Why?! After all, this is not your grandfather's print-only journal that has no option but to treat non-printable content as if it were supplemental -- this is the Article of the Future (actually, of the Present now) itself! it's not as if Cell were not capable of integrating the movie; indeed, it did incorporate it into the narrative very nicely, as the screenshot demonstrates. But if you look at the PDF version, the movie is not embedded in it. They could for sure, but they chose not to. Why, furthermore, despite the successful integration of essential movie into the HTML narrative, they still placed that movie on the Supplemental Information tab?Puzzled, I contacted Keith Wollman, Cell's VP for Content and Operations. He wrote, "we don't currently embed movies in the article PDF because we are conservative about the archival nature of that PDF in response to concerns from librarians."And then it dawned on me: it is not simply paper vs. electronic divide that brings into being the concept of "pseudo-supplemental” materials: rather, it is the VoR! Whether we have an old-fashioned print-only journal or a cutting-edge one, like Cell, they make the same decision: treat essential content as if it were supplemental. Why? Whether the VoR is print or a static PDF (or maybe PDF/A), the publisher is unable or unwilling to embed dynamic objects into the VoR. On the other side of the fence are, for example, the Journal of Neuroscience, which says that they will embed the dynamic content into its PDF, or AGU journals. For the former, the VoR is dynamic PDF; for the latter, XML.There are some interesting MARKUP implications.Suppose that the Cell article contained two movies: one essential and one truly supplemental. Outside the article's context it would have been impossible to ascertain which movie bore which functional relationship to the article. A visible manifestation of that would be the fact that both movies would appear on the same Supplemental Information tab. Which means that the implicit degree of importance (normally inferred by the reader from the context) must be made explicit: this one is essential -- you must watch it; that one is supplemental -- you may skip it.Interestingly enough, J. of Neuroscience may face the same problem: they say, there is no need for supplemental materials, we'll embed them into the PDF, and that's it. Now, suppose the submission, again, contains two movies: one essential and one supplemental. Are they going to reject the supplemental movie and embed only the essential one? Or are they going to embed both? If the latter then again, the reader will not be able to differentiate which is which.