2012-03-20-AGU-Librarians_Presentation

NISO-NFAIS Supplemental Journal
Article Materials Working Group:
An Update on an Industry Initiative
Alexander (‘Sasha’) Schwarzman, MLS
American Geophysical Union
sschwarzman@agu.org
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, 480-497 18 February 2011
doi:10.1016/j.cell.2011.01.033
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
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. 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)
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

• 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

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 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:
this content is part of article
Provide in-text citation and
link at the appropriate point in
text, rather than at the end
Identifying DOI must be assigned DOI 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

(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

(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

(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.

(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
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.

• 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?

Supporting Info for: Yu J., et al. (2005), The Genomes of
Oryza sativa: A History of Duplications, PLoS Biol. 3(2), e38.
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).

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

• 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:
http://dx.doi.org/10.1109/TUFFC.2009.1248/mm9
http://dx.doi.org/10.1787/oif-2008-table2-en

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:
http://dx.doi.org/10.5061/dryad.125
http://dx.doi.org/10.1371/journal.pbio.0030038.st004

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:
http://dx.doi.org/10.1371/journal.pbio.0030038.g002
http://dx.doi.org/10.1371/journal.pbio.0030038.t003

5. Supplemental content packages (e.g., a container
holding several supplemental items) MAY be
assigned external identifiers.
Rationale: Enhance linking reliability.
Examples:
http://dx.doi.org/10.1037/0097-7403.32.3.322.supp
http://dx.doi.org/10.1037/0735-7044.122.4.777.supp
http://dx.doi.org/10.1371/journal.pbio.0030038.sg008
http://dx.doi.org/10.1172/JCI200521773DS4
http://dx.doi.org/10.2210/pdb2fpe/pdb
http://dx.doi.org/10.1787/548525556001

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.

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 http://www.udfr.org or
PRONOM
http://www.nationalarchives.gov.uk/PRONOM/

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?

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
<!ELEMENT supp_mat_metadata
(core_article_metadata,
supp_mat_descriptive,
supp_mat_object_metadata+ ) >
<!ATTLIST supp_mat_metadata
supp-mat-type
(integral | additional |
integral-and-additional)
#REQUIRED >

Metadata schema (cont’d)
<!ELEMENT core_article_metadata
(core_article_identifier+,
core_article_verification*) >
<!ELEMENT supp_mat_descriptive
(supp_mat_identifier*, version?,
label?, titles?, caption?,
contrib_group*, summary*,
history?, language*,
content_descriptor?,
subject_descriptor_group*,
accessibility_long_desc*,
publisher?, copyright*, license*,
open_access*, provenance?,
preservation*) >

<!ELEMENT supp_mat_object_metadata
(core_element_metadata*,
supp_mat_descriptive?,
supp_mat_physical?,
supp_mat_object_metadata*) >
<!ATTLIST supp_mat_object_metadata
supp-mat-type
(integral | additional |
integral-and-additional)
#IMPLIED
relationship-of-objects
(unrelated | single |
logical-set | alternatives)
#IMPLIED >

<!ELEMENT supp_mat_physical
(ext_link | file_metadata)+ >
<!ELEMENT file_metadata
(filename,
((mime_type, mime_subtype?) |
((format, format_registry?,
validity?),
(mime_type, mime_subtype?)?)),
size?, fixity?,
creating_application?,
rendering_application*) >

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?

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:10.1016/j.cell.2009.09.021

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

2012-03-20-AGU-Librarians_Presentation

More Related Content

What's hot

Similar to 2012-03-20-AGU-Librarians_Presentation

More from aschwarzman

2012-03-20-AGU-Librarians_Presentation