Online Supplemental Journal Article Materials: A Recommended Practice

Alexander (‘Sasha’) SchwarzmanContent Technology Architect

OSA – The Optical Society

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

OSA PUBS-IT MEETING

Washington, DC14 August 2012

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Contents• Introduction and

examples• Benefits and challenges• Community response• NISO/NFAIS working

group• Supplemental materials

classification

• Recommendation scope• Recommended business

practices• Recommended

technical practices• Draft for Public

Comment

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Deluge!

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Chart courtesy of Ken Beauchamp, American Society for Clinical Investigation

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ExamplesSupplemental Information for Garland, E. C., et al. (2011),

Dynamic horizontal cultural transmission of humpback whale song at the ocean basin scale, Current Biology 21(8), 687–691, http://dx.doi.org/10.1016/j.cub.2011.03.019

• Document S1. Two Figures, Table S2, Supplemental Experimental Procedures, and Acknowledgments. [PDF, 209K]

• Document S2. Table S1. [XLS, 37K]• Audio S1. Audio of the Blue Song Type Presented in Figure 2.

[MP3, 4788K]• Audio S2. Audio of the Dark Red Song Type Presented in

Figure 3. [MP3, 1922K]

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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. Duplicated Segments in the Beijing indica Assembly. Plotted

in the Manner of Figure 6, and with a Total of 12 Panels(507 KB ZIP).Table S1. Raw Data for Beijing indica and Syngenta japonica AssembliesRead length is the number of Q20 bases. Clone sizes are specified in

terms of 10th and 90th percentiles.(16 KB XLS).…

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Examples (cont’d)

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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 BonekaJournal of Comparative Psychology, Vol. 124, No. 1, pp. 38–46. View articleFiles: Huffard_Supplementary_Table_1.docHuffard_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.

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Examples (cont’d)Cell, Volume 145, Issue 5, 650-663 27 May 2011doi:10.1016/j.cell.2011.05.011Vertebrate 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 (MP4 2539 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.

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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)

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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.

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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?

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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?

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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?

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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

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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!

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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"

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Chronology• February 2009: NFAIS Best Practices for

publishing journal articles• November 2009: Schwarzman’s White Paper

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

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NISO/NFAIS Working Group

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Business Working Group – policiesCo-chairs: Linda Beebe (APA), Marie McVeigh (Thomson-Reuters ISI)

• Recommended Practices: scope and general principles• Definitions: sup. mat., article, data, metadata, etc.• Roles and responsibilities of publishers, editors, peer

reviewers, libraries, A&I services, repositories• Curation and life cycle: selection, peer review, editing,

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

• Intellectual property rights management

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

• Metadata• Persistent identifiers • Preservation• Packaging and exchange• Supporting documentation

non-normative DTD Tag Library tagged samples

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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

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Pseudo-supplemental (example)

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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

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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

• IndividualNot appropriate for hosting supplemental materials

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Supplemental materials classification

Importance

Curated by

Integral Additional

Publisher Recommended practices offered

Institutional repository or Data center No recommended practices offered

[large data sets]

Individual Not appropriate

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Recommended business practicesIntegral 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

Identifying DOI must be assigned DOI may be assigned

Cross-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

Reference in other pub’s

Cite article as a whole. Do not cite Integral Content separately

There has to be enough metadata if cited separately

Reference citations within sup. mat.

Integrate references into the ref. list of the core article(Biophysical Journal)

Keep references separate from the core article ref. list

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Recommended business practices (cont’d)

Integral content Additional contentPreserving Preserve 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

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Managing and hosting

• Do not mix Integral and Additional content• 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

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Discoverability and findability

• Consistent placement, naming, and navigation: Across all articles in a journal On ToC – indicate presence of sup. mat. In the article – locate links near the top of screen view In the sup. mat. – navigation should match article’s

• Aid A&I services by including metadata that indicate the purpose and format of the sup. mat.

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Maintaning links

• Supplemental materials should be linked, bi-directionally, to and from core article

• Assign and register DOIs to minimize the broken links problem Assign separate DOIs for Integral and Additional

content When sup. mat. is hosted by an external repository,

sup. mat. must be assigned a DOI; publisher is responsible for ensuring that the link works when its target moves

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Providing context

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 used

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Minimal sup. mat. metadata

• Sup. mat. DOI(s), for each individual sup. mat. object or for their set(s)

• Article DOI• Relationship type of sup. mat. to the article:

Integral, Additional, or both• Descriptive metadata for sup. mat., e.g., title

or summary• File formats of sup. mat. files

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Extended sup. mat. metadata Physical metadata Formats Label Caption Contributors Dates (history) Keywords Publisher Copyright and licensing Source (provenance) Preservation level Versions

Relationship among sup. mat. objects:- single- unrelated- alternatives- logical set

Reference to an article object Validity Fixity Application and platform

• created with• to be used for rendering

Article metadata, e.g., citation

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Metadata location

• Text or XML file, part of article package• Another supplemental material file• Integrating into the article DTD• HTML <meta> tags• Embedding in sup. mat. file, e.g., ‘properties’

of MS Office documents, PDF’s XMP limited use fixity and file size should not be embedded

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Persistent identifiers

• All Integral sup. mat’s should be assigned a DOI• All sup. mat’s associated with more than one

article should be assigned a DOI• Aggregate sup. mat’s should be assigned a DOI• Sup. mat’s uniquely identified by sufficient

metadata may be assigned a DOI• Logical wrappers around or physical containers

with sup. mat’s may be assigned a DOI

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Preservation

• Publisher should state publicly its preservation strategy• WG recommends migration over emulation• Retention

Integral objects: original + two latest converted Additional objects: original + the latest converted

• File formats Publisher uses formal registries, e.g., PRONOM, UDFR Publisher defines formats it will support, and either

converts non-conformant objects or doesn’t guarantee their availability in the future

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Packaging and exchange

• Article and all its components should be transferable in a single package, e.g., to fulfill interlibrary loan request, or to perform a deposit to an archive or a repository.

• 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.

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Manifest

• Journal title or identifier• Article DOI• DOIs for article components• DOIs for the supplemental materials• Supplemental material types:

Integral, Additional, both

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Manifest (cont’d)

• File names• File sizes• Description of each file• Copyright information

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Supporting Documentation

• Non-normative sup. mat. DTD• Tag Library• Tagged samples

http://supplemental.niso.org/

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

Standards Quarterly 22(3), p.33, http://dx.doi.org/10.3789/isqv22n3.2010.07Carpenter, T. (2009), Journal article supplementary materials: A Pandora’s box of issues needing best

practices, Against the Grain 21(6), p.84Marcus, E. (2009), Taming supplemental material, Cell 139(1), p.11,

http://dx.doi.org/10.1016/j.cell.2009.09.021Maunsell, J. (2010), Announcement regarding supplemental material, The Journal of Neuroscience 30(32):

p.10599NFAIS (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,

http://dx.doi.org/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 ProjectPart B: Technical Recommendations – Draft available for Public Comment at

http://www.niso.org/workrooms/supplementaluntil 15 September 2012

aschwarzman@osa.org

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Q & A