The role of annotations in scholarly communications Dan Whaley, Founder, hypothes.is

2. To enable
an open
conversation
over all
knowledge

3. “Wholly new forms of encyclopedias will
appear, ready made with a mesh of
associative trails running through them,
ready to be dropped into the memex and
there amplified.”
– Vannevar Bush,
“As We May Think” (1945)

4. Tim Berners-Lee http://www.w3.org/History/1989/proposal.html
One must
also be able
to annotate
links, as well
as nodes, ...
”
“

7. the web
w/ comments

8. the web

9. the web
D.I.Y.

10. w3.org/annotation
(Est. August 19, 2014)

11. Web Annotations are ...
like the Web.
• Interoperable
• Federated
• Support mixed formats
• Characterized by open source
implementations

13. Relating documents
URL
doi
ISBN
PDF ID

14. Four modes
address body
target
/ URI selection
Annotation
Comment
Highlight
Bookmark

15. discussiontaggingbookmarking note taking

16. discussiontaggingbookmarking note taking
• Not standards based
• Not interoperable
• Not open source
• Separate from the
target
• Not federated

17. Use cases:
• Public debate and discussion
• Post-pub commentary
• Pre-pub annotated reviews
• Personal research
• Leveraging semantic relationships from
community data sets
• Tagging with vocabularies
• Copy-editing
• Critical review of images and data

18. Organizations building standards-compliant
applications

19. Bring annotation to
biosciences.
Research objects
and data sets
Identifiers

20. Provides a communication channel for information about research resources
NIFbot
1
2
3
1. Research resource identifier:
unique identifier for software
2. Annotation with information
supplied via the
Neuroscience Information
Framework
3. Links to validation
information in the literature

21. 1
2
3
4
1. Text mining used to
assign RRID
2. Automated population
of RRID information
3. Link to RRID resolving
service
4. Link to validation
report from F1000
Research
NIFbot
NIFbot

22. Shortly, as a layer over any article:
• Are there any additional notes by the authors?
• Has the paper been retracted?
• What do my peers think of it?
• Exactly which antibodies and reagents does it
use?
• Have any issues been reported with them?
• Who else has tried to reproduce this protocol?
• What are helpful suggestions others have for
doing so?

23. “Continuous Ambient Search”

24. Bring annotation to
scholarly peer-review.
Pre-publication Post-publication

30. Benefits of an annotated review
• In context, while reading
• Precise
• Copy-edits are more natural
• Threaded discussion between authors and
reviewers
• Selected discussions can persist post-
publication
• Via ORCID iDs annotation can become part of
a reviewer’s CV.

31. AnnotatorJS
Annotator Store
github/openannotation
github/openannotation
github/hypothesis
Software.

32. Different ways that it be implemented
Browser plug-in
Embedding
Link
<script>
Long term? Shipped natively
in browsers
Now?

33. What’s coming?
• Groups & social features
• Image & video annotation
• Moderation, voting, flexible peer-
review models
• Copy-editing features
• Semantic tagging & controlled
vocabularies
• Offline functionality

34. Try it yourself!