2012-08-14-OSA-Pubs-IT_Presentation

Online Supplemental
Journal Article Materials:
A Recommended Practice
Alexander (‘Sasha’) Schwarzman
Content Technology Architect
OSA – The Optical Society
Co-chair, NISO/NFAIS Working Group on
Supplemental Journal Article Materials
OSA PUBS-IT MEETING
Washington, DC
14 August 2012

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
14 August 2012 OSA Pubs-IT meeting 2

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

Examples
Supplemental 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]

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
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)

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
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)
Cell, Volume 145, Issue 5, 650-663 27 May 2011
doi:10.1016/j.cell.2011.05.011
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 (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.

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 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

NISO/NFAIS Working Group

Business Working Group – policies
Co-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

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

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 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

Recommended business practices
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
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

Recommended business practices
(cont’d)
Integral content Additional content
Preserving 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

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

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.

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

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

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

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

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

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

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

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.

Manifest
• Journal title or identifier
• Article DOI
• DOIs for article components
• DOIs for the supplemental materials
• Supplemental material types:
Integral, Additional, both

Manifest (cont’d)
• File names
• File sizes
• Description of each file
• Copyright information

Supporting Documentation
• Non-normative sup. mat. DTD
• Tag Library
• Tagged samples
http://supplemental.niso.org/

Sources
Beebe, 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/isqv22n3.2010.07
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,
http://dx.doi.org/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,
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 Project
Part B: Technical Recommendations – Draft available for Public Comment at
http://www.niso.org/workrooms/supplemental
until 15 September 2012
aschwarzman@osa.org

2012-08-14-OSA-Pubs-IT_Presentation

Recommended

Recommended

More Related Content

Similar to 2012-08-14-OSA-Pubs-IT_Presentation

Similar to 2012-08-14-OSA-Pubs-IT_Presentation (20)

More from aschwarzman

More from aschwarzman (11)

2012-08-14-OSA-Pubs-IT_Presentation