NISO-NFAIS Supplemental Journal Article Materials Working Group: An Update on an Industry Initiative Alexander (‘Sasha’) Schwarzman, MLS American Geophysical Union Co-chair, NISO/NFAIS Working Group on Journal Article Supplemental Materials AN EXCHANGE OF IDEAS: MEETING OF LIBRARIANS San Antonio, TX 20 March 2012

Contents Introduction and examples Benefits and challenges Community response NISO-NFAIS working group Supplemental materials classification Project scope Recommended business practices Technical considerations  Identification  Preservation  Packaging  Metadata Practical challenges Future developments

Deluge! Chart courtesy of Ken Beauchamp, American Society for Clinical Investigation

Examples Cell, Volume 144, Issue 4, February 2011 doi: /j.cell Revisiting the Central Dogma One Molecule at a Time Supplemental Data for Bustamante et al. Document S1. Extended Discussion, Two Figures, and Supplemental References (PDF 534 kb)

Examples (cont’d)

Supplemental Material for Male-Male and Male-Female Aggression May Influence Mating Associations in Wild Octopuses (Abdopus aculeatus) Christine L. Huffard, Roy L. Caldwell, and Farnis Boneka Journal of Comparative Psychology, Vol. 124, No. 1, pp. 38–46. View article Files: Huffard_Supplementary_Table_1.doc Huffard_Abdopus_fight.mpg Huffard_Abdopus_fight.mpg This content was submitted by the author as supplemental material for an article published in APA’s PsycARTICLES. The content is presented as the author submitted it. APA assumes no liability for errors or omissions and makes no warranties of any kind. APA assumes no responsibility for any reader’s use of the materials. All questions regarding the supplemental data should be directed to the corresponding author of the published article. The reader is expected to respect the intellectual property of the author and the copyright of the American Psychological Association (APA). The content should not be reused without permission from the author and APA.

Examples (cont’d)

Supporting Info for: Yu J., et al. (2005), The Genomes of Oryza sativa: A History of Duplications, PLoS Biol. 3(2), e38. … Figure S7. Figure S7. Duplicated Segments in the Beijing indica Assembly. Plotted in the Manner of Figure 6, and with a Total of 12 PanelsFigure 6 (507 KB ZIP). Table S1. Table S1. Raw Data for Beijing indica and Syngenta japonica Assemblies Read length is the number of Q20 bases. Clone sizes are specified in terms of 10th and 90th percentiles. (16 KB XLS). …

Examples (cont’d) Cell, Volume 145, Issue 5, May 2011 doi: /j.cell Vertebrate Segmentation: From Cyclic Gene Networks to Scoliosis Supplemental Data for Pourquié et al. Movie S1. Clock and Wavefront Model for Vertebrate Segmentation, Related to Figure 1 (MP kb) This model proposes that the production of somites during embryogenesis results from a molecular oscillator. Movie S2. Imaging Clock Oscillations in the Mouse Embryo, Related to Figure 1 (MOV 8211 kb) The periodic, anterior-traveling waves of cyclic gene expression. See Aulehla et al., 2008 for additional details.

What is in the Pandora’s box? Multimedia: video, audio, virtual reality Chemical, crystallographic, and protein structures, gene sequences, 3-D images Computer programs (algorithms, code, libraries, and executables) Tables, Figures, Text (Experimental procedures, Extended methodology, Survey results, Derivations, Extended bibliographies, …) Data sets (data sets are not the focus of this group)

Supplemental materials: Good idea! Enabling technology makes it possible for: authors to present supporting evidence, e.g., multimedia, data sets, computer programs; researchers to reveal in-depth studies that would not be available in print; readers to replicate experiments and verify results.

Questions to ponder Degree of importance. Are all components of supplemental materials equally important? As a busy reviewer or reader, which ones must I focus on? Discoverability. How do I (librarian, indexer) know the article has supplemental materials? (Deadbeat parent) Identification. How do I know which article is the parent of orphaned / abandoned supplemental materials? Citing and linking. How do I provide a persistent link to the supplemental materials, and how do I cite them?

Questions to ponder (cont’d) Viability and preservation. Will it be possible to render (read, play, execute, etc.) sup. mat. in 20 years? 200 years? It is likely that sup. mat. will have to undergo periodic conversion. Then, do I look at the original or the converted object? Are they equivalent? Transmission and packaging. When fulfilling an interlibrary loan request or transmitting sup. mat. to an archive, how do I package them with the article? How do I ensure that nothing was lost or corrupted?

Questions to ponder (cont’d) Intellectual property rights. Who has rights over sup. mat., and where are they recorded? Curatorial responsibility. Who has custody over sup. mat.: author, publisher, library, data center, institutional repository, archive, any other actor? Business models. If someone is going to provide identification, description, linking, preservation, and other processing of sup. mat., what sustainable business models could support the expense?

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

Researcher community response One camp: More supplemental materials should be made available! Technology will solve most problems! The other camp: Scholarly journal is not a data dump! An article is not an FTP site!

Publisher community response 2009: Cell imposes limits on the number and kind of supplemental materials accepted 2010: The Journal of Neuroscience bans supplemental materials altogether; intends to embed dynamic content in its articles’ PDF 2011: The Journal of Experimental Medicine limits supplemental materials only to "essential supporting information"

Chronology February 2009: NFAIS Best Practices for publishing journal articlesBest Practices November 2009: Schwarzman’s White Paper on supplemental materials survey resultsWhite Paper January 2010: NISO-NFAIS supplemental materials Thought Leader RoundtableThought Leader Roundtable August 2010: NISO-NFAIS Working Group on journal article supplemental materialsWorking Group

NISO - NFAIS Working Group

Recommended Practices: scope and general principles Definitions: sup. mat., article, data, metadata, etc. Curation and life cycle: selection, peer review, editing, presentation, providing context, referencing, citing, managing/hosting, discovery, preservation Intellectual property rights management Roles and responsibilities of authors, editors, reviewers, publishers, libraries, A&I services, repositories Business Working Group – policies Co-chairs: Linda Beebe (APA), Marie McVeigh (Thomson-Reuters ISI)

Identifiers for supplemental materials Linking to and from supplemental materials Archiving, preservation, and forward migration of supplemental materials Packaging, exchange, and delivery of supplemental materials Metadata and granularity of markup Technical Working Group – “how” Co-chairs: Dave Martinsen (ACS), Sasha Schwarzman (AGU)

Supplemental materials: Pseudo vs. truly Print model: article layout implicitly reflected functional distinction between essential and nonessential elements (body vs. appendix) Mixed electronic-print model: both essential and nonessential components are often treated as “supplemental materials” Is the material essential or not? This must be stated explicitly for machine and human reader

Pseudo-supplemental (example)

Classification facet 1: Importance Integral (“pseudo-supplemental”) Essential for full understanding of work but treated as if it were supplemental. Rationale: technical, business, or logistical limitations Additional (“truly supplemental”) Not critical for understanding the work. Relevant and useful – but still optional

Classification facet 2: Custody Publisher Recommended practices offered Institutional repository or Data center The publisher has no responsibility or authority over content and does not host it. No recommended practices offered Individual Not appropriate for hosting supplemental materials

Supplemental materials classifications: Integral, Additional, Related

Recommended business practices Integral contentAdditional content Selecting / Peer reviewing At the same level as core article May not be reviewed at the same level CopyeditingAt 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: this content is part of article Provide in-text citation and link at the appropriate point in text, rather than at the end IdentifyingDOI must be assignedDOI may be assigned References within sup. mat. Integrate references into the ref. list of the core article (Biophysical Journal) Keep references separate from the core article ref. list

Recommended business practices (cont’d) Integral contentAdditional content PreservingPreserve at the same level as the core article Provide the same level of 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 Intellectual property 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

Recommended business practices (cont’d) Identifying / linking and managing sup. mat.  Sup. mats. should be linked, bi-directionally, to and from core article  Integral and Additional content should not be mixed  If journal content is hosted by a host / aggregator it should also deliver supplemental materials  An author’s website is not an appropriate place for the sole posting of supplemental materials

Recommended business practices (cont’d) Discovering supplemental materials  Consistent placement, naming, and navigation  Indicate sup. mat. presence on ToC, landing page  Link to Integral content from within the article  Link to Additional content 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 sup. mat.

Recommended business practices (cont’d) Providing context for sup. materials Include on a landing page or within the content:  Core 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  Sup. mat. DOI or another identifier, if assigned

Technical considerations Heterogeneity: an archive (ZIP, TAR, RAR), a document (PDF, MS Word), or a virtual collection (web page) may contain both Integral and Additional content. The two may need to be treated differently in terms of identification, linking, preservation, and metadata assignment

Technical considerations (cont’d)

Supplemental Material for Male-Male and Male-Female Aggression May Influence Mating Associations in Wild Octopuses (Abdopus aculeatus) Christine L. Huffard, Roy L. Caldwell, and Farnis Boneka Journal of Comparative Psychology, Vol. 124, No. 1, pp. 38–46. View article Files: Huffard_Supplementary_Table_1.doc Huffard_Abdopus_fight.mpg Huffard_Abdopus_fight.mpg This content was submitted by the author as supplemental material for an article published in APA’s PsycARTICLES. The content is presented as the author submitted it. APA assumes no liability for errors or omissions and makes no warranties of any kind. APA assumes no responsibility for any reader’s use of the materials. All questions regarding the supplemental data should be directed to the corresponding author of the published article. The reader is expected to respect the intellectual property of the author and the copyright of the American Psychological Association (APA). The content should not be reused without permission from the author and APA.

Technical considerations (cont’d) Hierarchy and Recurrence: an archive may contain a tree with many branches and sub- branches with nested objects and groups Granularity down: what to identify — entire sup. mat., groups, objects, …? At what level do you stop? Granularity up: link to a specific item within the core article or to the core article as a whole?

Technical considerations (cont’d) Supporting Info for: Yu J., et al. (2005), The Genomes of Oryza sativa: A History of Duplications, PLoS Biol. 3(2), e38. Figure S6. Figure S6. Coordinated Annotation of the Individual Chromosomes for Beijing indica and Syngenta japonica We depict all the genetic markers, nr-KOME cDNAs, FGENESH gene predictions, and transposable elements identified by RepeatMasker. Genes are depicted as WH (colored blue) or NH (colored red) based on their similarity to Arabidopsis. TEs are decomposed into classes I, II, and III. Correspondence between indica and japonica is indicated by drawing a connecting line between the 5′ ends of the nr-KOME cDNAs that clearly align to both assemblies. (9.6 MB ZIP).

Examples (cont’d) Cell, Volume 145, Issue 5, May 2011 doi: /j.cell Vertebrate Segmentation: From Cyclic Gene Networks to Scoliosis Supplemental Data for Pourquié et al. Movie S1. Clock and Wavefront Model for Vertebrate Segmentation, Related to Figure 1 (MP kb) This model proposes that the production of somites during embryogenesis results from a molecular oscillator. Movie S2. Imaging Clock Oscillations in the Mouse Embryo, Related to Figure 1 (MOV 8211 kb) The periodic, anterior-traveling waves of cyclic gene expression. See Aulehla et al., 2008 for additional details.

Technical considerations (cont’d) Supplemental objects types: Individual (atomic) items Physical containers (e.g., ZIP, PDF) with:  unrelated objects  logically different objects that share some common metadata, e.g., a series of graphs or images Logical wrappers

Technical considerations (cont’d) Logical wrapper: a shell around multiple physical representations 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.

Identification 1. All Integral Supplemental content MUST be assigned its own identifier Rationale: Any content item that is critical to the understanding of the article but which is located and maintained separately from the article body should be uniquely identified to enhance linking reliability (e.g., hosting of the content item may diverge from that of the article body).

Identification (cont’d) 2. All supplemental content items that are applicable to more than one article SHOULD be assigned an external identifier Rationale: Linking to the content item may need to occur from various publisher platforms. Examples:

Identification (cont’d) 3. Supplemental content items that are an aggregate of (potentially many) individual elements or records SHOULD be assigned an external identifier. Rationale: The content has its own intrinsic value outside the context of the article and should be discoverable on its own. Examples:

Identification (cont’d) 4. Supplemental content items that are uniquely described by sufficient metadata MAY be assigned an external identifier. Rationale: The content has its own intrinsic value outside the context of the article and may be discoverable on its own. Any effort expended in assigning descriptive metadata can best be exploited via an external identifier. Examples:

Identification (cont’d) 5. Supplemental content packages (e.g., a container holding several supplemental items) MAY be assigned external identifiers. Rationale: Enhance linking reliability. Examples:

Preservation 1. Publishers should state publicly their preservation strategy/approaches. Out of the two main approaches (migration vs. emulation) migration is recommended as the preservation strategy. Migration involves converting objects, over the long-term, from one form to another which is usable under prevalent technology at the time.

Preservation (cont’d) 2. Retention of files – Ideally, all objects throughout the migration chain should be saved.  For the Integral Content, at least the original object plus the last two iterations of the converted objects, i.e., latest and latest-1 versions, must be saved.  For Additional Content, publishers should strive to save the original object plus the converted objects.

Preservation (cont’d) 3. Format is important – preservation techniques depend on object format. Format is not equal to mime-types, which may not carry enough information for converting and management of objects. If possible, publishers should use formats defined in formal format registries like UDFR orhttp:// PRONOM

Preservation (cont’d) Alternatively, publishers may define and publish list of file formats they support. Criteria:  Is the format open or proprietary?  Is the format widely used?  Is there already a standard format for this type of content?  Does this format have advantages over existing formats for this type of content?  Are there free/ubiquitous viewers?  Are there viewers for multiple operating systems?  Are there any concerns about long term viability?  Is there open source software related to the format?  Is the format defined/reviewed by an international standard (both formal or de facto) or a widely recognized body?

Preservation (cont’d) Limitation of formats accepted by publishers – While it is an acceptable practice to limit the formats of objects to be supported, authors should be able to deposit objects in formats outside of the acceptable list.  Conversion to archival format - publisher lists required/preferred formats for preservation/carried forward. Objects outside of the list should be converted to a supported format. Both the original and converted objects will be kept.  Two-tier service - publisher lists formats to support. Other formats will still be accepted but not guaranteed to be carried forward. Each object should have basic descriptive metadata, like label and caption, to inform users what the object is about, in case the format becomes obsolete.

Packaging Article and all its components should be transferable in a single package, e.g., to fulfill interlibrary loan request, to perform a deposit to an archive or a repository, etc. There are a number of different packaging specifications available, and this Working Group does not intend to design a new one nor require the use of any particular specifications or tools.

Packaging (cont’d) The package contains all files comprising the article and the manifest describing the contents Manifest – article-level metadata: 1.Journal ID (ISSN) 2.Core article ID (citation) 3.Core article DOI 4.Persistent links to the supplemental materials 5.List of all files contained in the package

Packaging (cont’d) Manifest – component-level metadata: 1.Type: Integral, Additional, or both 2.Component DOI 3.File name 4.File size 5.File description 6.Rendering application information 7.Detailed copyright information 8.Instructions

Metadata schema

Metadata schema (cont’d)

Metadata schema (cont’d)

Metadata schema (cont’d)

Version of record If the version of record incorporates linked or embedded essential objects then the notion of Integral Supplemental material is not applicable Additional content still has to be indicated as such, e.g., AGU’s “Auxiliary material” Is version of record the same for various actors?

Version of record (cont’d)

Practical challenges 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?

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: /j.cell

Sources Beebe, L. (2010), Supplemental materials for Journal articles: NISO/NFAIS Joint Working Group, Information Standards Quarterly 22(3), p.33, doi: /isqv22n /isqv22n 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: /j.cell /j.cell Maunsell, J. (2010), Announcement regarding supplemental material, The Journal of Neuroscience 30(32): p NFAIS (2009), Best practices for publishing journal articles, 30 pp., Schwarzman, S. (2010), Supplemental materials survey, Information Standards Quarterly 22(3), p.23, doi: /isqv22n /isqv22n NISO/NFAIS Supplemental journal article materials project

Q & A