Presentation held at second Amicus workshop, http://amicus.uvt.nl/amicus_ws2011.htm: "Storytelling in Fairytales and Science:
Narrative structure models of scientific communication and folktales"
Unpacking Value Delivery - Agile Oxford Meetup - May 2024.pptx
Overview of scientific discourse annotatoin
1. A
brief
introduc.on
to
current
efforts
in
scien.fic
discourse
annota.on
Anita
de
Waard
Disrup/ve
Technology
Director,
Elsevier
Labs
-‐
also
on
behalf
of
HCLS/UU/D2S...
hEp://elsatglabs.com/labs/anita
Thursday, October 20, 2011
2. One
way
of
subdividing
the
field
of
Scien/fic
Discourse
Annota/on:
2
Thursday, October 20, 2011
3. One
way
of
subdividing
the
field
of
Scien/fic
Discourse
Annota/on:
Five
levels
of
markup:
2
Thursday, October 20, 2011
4. One
way
of
subdividing
the
field
of
Scien/fic
Discourse
Annota/on:
Five
levels
of
markup:
1.Sec/on:
“Discussion”,
~
several
paragraphs
(+HCLS)
2
Thursday, October 20, 2011
5. One
way
of
subdividing
the
field
of
Scien/fic
Discourse
Annota/on:
Five
levels
of
markup:
1.Sec/on:
“Discussion”,
~
several
paragraphs
(+HCLS)
2.Module:
“Research
Ques/on”,
~
paragraph
2
Thursday, October 20, 2011
6. One
way
of
subdividing
the
field
of
Scien/fic
Discourse
Annota/on:
Five
levels
of
markup:
1.Sec/on:
“Discussion”,
~
several
paragraphs
(+HCLS)
2.Module:
“Research
Ques/on”,
~
paragraph
3.Statement:
“Hypothesis”,
~
sentence/clause
(+UU)
2
Thursday, October 20, 2011
7. One
way
of
subdividing
the
field
of
Scien/fic
Discourse
Annota/on:
Five
levels
of
markup:
1.Sec/on:
“Discussion”,
~
several
paragraphs
(+HCLS)
2.Module:
“Research
Ques/on”,
~
paragraph
3.Statement:
“Hypothesis”,
~
sentence/clause
(+UU)
4.Rela/on:
“Supports”,
~
hyperlink
(En/ty:
“Gene
Name”,
~
NP)
2
Thursday, October 20, 2011
8. One
way
of
subdividing
the
field
of
Scien/fic
Discourse
Annota/on:
Five
levels
of
markup:
1.Sec/on:
“Discussion”,
~
several
paragraphs
(+HCLS)
2.Module:
“Research
Ques/on”,
~
paragraph
3.Statement:
“Hypothesis”,
~
sentence/clause
(+UU)
4.Rela/on:
“Supports”,
~
hyperlink
(En/ty:
“Gene
Name”,
~
NP)
5.Special
case
of
3&4:
Claim/Evidence
network
(+D2S)
2
Thursday, October 20, 2011
9. One
way
of
subdividing
the
field
of
Scien/fic
Discourse
Annota/on:
Five
levels
of
markup:
1.Sec/on:
“Discussion”,
~
several
paragraphs
(+HCLS)
2.Module:
“Research
Ques/on”,
~
paragraph
3.Statement:
“Hypothesis”,
~
sentence/clause
(+UU)
4.Rela/on:
“Supports”,
~
hyperlink
(En/ty:
“Gene
Name”,
~
NP)
5.Special
case
of
3&4:
Claim/Evidence
network
(+D2S)
For
each
level:
2
Thursday, October 20, 2011
10. One
way
of
subdividing
the
field
of
Scien/fic
Discourse
Annota/on:
Five
levels
of
markup:
1.Sec/on:
“Discussion”,
~
several
paragraphs
(+HCLS)
2.Module:
“Research
Ques/on”,
~
paragraph
3.Statement:
“Hypothesis”,
~
sentence/clause
(+UU)
4.Rela/on:
“Supports”,
~
hyperlink
(En/ty:
“Gene
Name”,
~
NP)
5.Special
case
of
3&4:
Claim/Evidence
network
(+D2S)
For
each
level:
a) Why?
Use
cases
2
Thursday, October 20, 2011
11. One
way
of
subdividing
the
field
of
Scien/fic
Discourse
Annota/on:
Five
levels
of
markup:
1.Sec/on:
“Discussion”,
~
several
paragraphs
(+HCLS)
2.Module:
“Research
Ques/on”,
~
paragraph
3.Statement:
“Hypothesis”,
~
sentence/clause
(+UU)
4.Rela/on:
“Supports”,
~
hyperlink
(En/ty:
“Gene
Name”,
~
NP)
5.Special
case
of
3&4:
Claim/Evidence
network
(+D2S)
For
each
level:
a) Why?
Use
cases
b) What,
by
whom?
Concepts,
ontology,
authors?
2
Thursday, October 20, 2011
12. One
way
of
subdividing
the
field
of
Scien/fic
Discourse
Annota/on:
Five
levels
of
markup:
1.Sec/on:
“Discussion”,
~
several
paragraphs
(+HCLS)
2.Module:
“Research
Ques/on”,
~
paragraph
3.Statement:
“Hypothesis”,
~
sentence/clause
(+UU)
4.Rela/on:
“Supports”,
~
hyperlink
(En/ty:
“Gene
Name”,
~
NP)
5.Special
case
of
3&4:
Claim/Evidence
network
(+D2S)
For
each
level:
a) Why?
Use
cases
b) What,
by
whom?
Concepts,
ontology,
authors?
c) How?
Manual,
automated?
2
Thursday, October 20, 2011
15. 1.
Sec/on-‐level
markup
a.Why
mark
up
sec/ons?
-‐ Search:
e.g.
search
for
en//es
in
Methods
-‐ Visualisa/on:
e.g.
structured
browse
at
sec/on
level
INTRODUCTION
3
Thursday, October 20, 2011
16. 1.
Sec/on-‐level
markup
a.Why
mark
up
sec/ons?
-‐ Search:
e.g.
search
for
en//es
in
Methods
-‐ Visualisa/on:
e.g.
structured
browse
at
sec/on
level
b.What,
by
whom?
-‐ Background/Contribu/on/
Discussion
model
for
CS INTRODUCTION
-‐ HCLS:
Ontology
of
Rhetorical
Blocks
(ORB)=
IMRaD
in
OWL
3
Thursday, October 20, 2011
17. 1.
Sec/on-‐level
markup
a.Why
mark
up
sec/ons?
-‐ Search:
e.g.
search
for
en//es
Annotation
in
Methods
-‐ Visualisa/on:
e.g.
structured
browse
at
sec/on
level
b.What,
by
whom?
-‐ Background/Contribu/on/
Discussion
model
for
CS INTRODUCTION
-‐ HCLS:
Ontology
of
Rhetorical
Blocks
(ORB)=
IMRaD
in
OWL
3
Thursday, October 20, 2011
18. 1.
Sec/on-‐level
markup
a.Why
mark
up
sec/ons?
-‐ Search:
e.g.
search
for
en//es
Annotation
in
Methods
-‐ Visualisa/on:
e.g.
structured
browse
at
sec/on
level
b.What,
by
whom?
-‐ Background/Contribu/on/
Discussion
model
for
CS INTRODUCTION
-‐ HCLS:
Ontology
of
Rhetorical
Blocks
(ORB)=
IMRaD
in
OWL
c. Automate?
-‐ Yes
-‐[Hovy/Ramakrishnan] 3
Thursday, October 20, 2011
20. 2.a.
Module-‐level
markup:
why?
-‐ BeEer
search:
e.g.
query
inside
‘Research
ques/on’
-‐ Ini/al
idea:
content
reuse,
e.g.
-‐ Write
Methods
sec/ons
once,
import/link
many
-‐ Different
way
of
crea/ng
a
collec/on
of
scholarly
content:
not
standalone
narra/ve,
but
connected
set
of
modules
5
Thursday, October 20, 2011
22. 2.b.
Module-‐level
markup:
What,
by
whom?
-‐ Kircz,
’98:
“a
much
more
radical
approach
would
be
to
[break]
apart
the
linear
text
into
independent
modules,
each
with
its
own
unique
cogni/ve
character.”
6
Thursday, October 20, 2011
23. 2.b.
Module-‐level
markup:
What,
by
whom?
-‐ Kircz,
’98:
“a
much
more
radical
approach
would
be
to
[break]
apart
the
linear
text
into
independent
modules,
each
with
its
own
unique
cogni/ve
character.”
6
Thursday, October 20, 2011
24. 2.b.
Module-‐level
markup:
What,
by
whom?
-‐ Kircz,
’98:
“a
much
more
radical
approach
would
be
to
[break]
apart
the
linear
text
into
independent
modules,
each
with
its
own
unique
cogni/ve
character.”
-‐ Harmsze,
‘00:
modular
model
for
physics
papers
6
Thursday, October 20, 2011
25. 2.b.
Module-‐level
markup:
What,
by
whom?
-‐ Kircz,
’98:
“a
much
more
radical
approach
would
be
to
[break]
apart
the
linear
text
into
independent
modules,
each
with
its
own
unique
cogni/ve
character.”
-‐ Harmsze,
‘00:
modular
model
for
physics
papers
6
Thursday, October 20, 2011
26. 2.b.
Module-‐level
markup:
What,
by
whom?
-‐ Kircz,
’98:
“a
much
more
radical
approach
would
be
to
[break]
apart
the
linear
text
into
independent
modules,
each
with
its
own
unique
cogni/ve
character.”
-‐ Harmsze,
‘00:
modular
model
for
physics
papers
-‐ LiquidPub,
2010:
Structured
Knowledge
Objects
6
Thursday, October 20, 2011
27. 2.b.
Module-‐level
markup:
What,
by
whom?
-‐ Kircz,
’98:
“a
much
more
radical
approach
would
be
to
[break]
apart
the
linear
text
into
independent
modules,
each
with
its
own
unique
cogni/ve
character.”
-‐ Harmsze,
‘00:
modular
model
for
physics
papers
-‐ LiquidPub,
2010:
Structured
Knowledge
Objects
6
Thursday, October 20, 2011
28. 2.b.
Module-‐level
markup:
What,
by
whom?
-‐ Kircz,
’98:
“a
much
more
radical
approach
would
be
to
[break]
apart
the
linear
text
into
independent
modules,
each
with
its
own
unique
cogni/ve
character.”
-‐ Harmsze,
‘00:
modular
model
for
physics
papers
-‐ LiquidPub,
2010:
Structured
Knowledge
Objects
-‐ HCLS:
Medium-‐grained
structure:
core
narra/ve
components 6
Thursday, October 20, 2011
29. 2.b.
Module-‐level
markup:
What,
by
whom?
-‐ Kircz,
’98:
“a
much
more
radical
approach
would
be
to
[break]
apart
the
linear
text
into
independent
modules,
each
with
its
own
unique
cogni/ve
character.”
-‐ Harmsze,
‘00:
modular
model
for
physics
papers
-‐ LiquidPub,
2010:
Structured
Knowledge
Objects
-‐ HCLS:
Medium-‐grained
structure:
core
narra/ve
components 6
Thursday, October 20, 2011
30. Story
grammar
model
for
science
The Story of Goldilocks and Story Grammar Paper The AXH Domain of Ataxin-1 Mediates
the Three Bears Neurodegeneration through Its Interaction with Gfi-1/
Senseless Proteins
Once upon a time Time Setting Background The mechanisms mediating SCA1 pathogenesis are still not fully
understood, but some general principles have emerged.
a little girl named Goldilocks Characters Objects of study the Drosophila Atx-1 homolog (dAtx-1) which lacks a polyQ tract,
She went for a walk in the forest. Location Experimental studied and compared in vivo effects and interactions to those of
Pretty soon, she came upon a setup the human protein
house.
She knocked and, when no one Goal Theme Research Gain insight into how Atx-1's function contributes to SCA1
answered, goal pathogenesis. How these interactions might contribute to the
disease process and how they might cause toxicity in only a
she walked right in. subset of neurons in SCA1 is not fully understood.
Atx-1 may play a role in the regulation of gene expression
Attempt Hypothesis
At the table in the kitchen, there Name Episode 1 Name dAtX-1 and hAtx-1 Induce Similar Phenotypes When
were three bowls of porridge. Overexpressed in Files
Goldilocks was hungry. Subgoal Subgoal test the function of the AXH domain
She tasted the porridge from the Attempt Method overexpressed dAtx-1 in flies using the GAL4/UAS system
first bowl. (Brand and Perrimon, 1993) and compared its effects to those of
This porridge is too hot! she Outcome Results hAtx-1.
Overexpression of dAtx-1 by Rhodopsin1(Rh1)-GAL4, which
exclaimed. drives expression in the differentiated R1-R6 photoreceptor cells
(Mollereau et al., 2000 and O'Tousa et al., 1985), results in
neurodegeneration in the eye, as does overexpression of hAtx-1
[82Q]. Although at 2 days after eclosion, overexpression of either
So, she tasted the porridge from Activity Data (data not shown),
Atx-1 does not show obvious morphological changes in the
the second bowl.
photoreceptor cells
This porridge is too cold, she said Outcome Results both genotypes show many large holes and loss of cell integrity
at 28 days
So, she tasted the last bowl of Activity Data (Figures 1B-1D).
porridge.
Ahhh, this porridge is just right, Outcome Results Overexpression of dAtx-1 using the GMR-GAL4 driver also
she said happily and induces eye abnormalities. The external structures of the eyes
7 that overexpress dAtx-1 show disorganized ommatidia and loss
she ate it all up. Data (Figure 1F),
of interommatidial bristles
Thursday, October 20, 2011
33. 2.c.
Module-‐level
markup:
how?
-‐ Automated
recogni/on:
very
difficult:
-‐ How
do
you
know
where
the
boundaries
are?
8
Thursday, October 20, 2011
34. 2.c.
Module-‐level
markup:
how?
-‐ Automated
recogni/on:
very
difficult:
-‐ How
do
you
know
where
the
boundaries
are?
-‐ Even
difficult
for
author
to
iden/fy!
8
Thursday, October 20, 2011
35. 2.c.
Module-‐level
markup:
how?
-‐ Automated
recogni/on:
very
difficult:
-‐ How
do
you
know
where
the
boundaries
are?
-‐ Even
difficult
for
author
to
iden/fy!
-‐ Author
creates:
templates.
8
Thursday, October 20, 2011
36. 2.c.
Module-‐level
markup:
how?
-‐ Automated
recogni/on:
very
difficult:
-‐ How
do
you
know
where
the
boundaries
are?
-‐ Even
difficult
for
author
to
iden/fy!
-‐ Author
creates:
templates.
-‐ XPharm,
2001:
modular
text
book
in
pharmacology:
8
Thursday, October 20, 2011
37. 2.c.
Module-‐level
markup:
how?
-‐ Automated
recogni/on:
very
difficult:
-‐ How
do
you
know
where
the
boundaries
are?
-‐ Even
difficult
for
author
to
iden/fy!
-‐ Author
creates:
templates.
-‐ XPharm,
2001:
modular
text
book
in
pharmacology:
8
Thursday, October 20, 2011
38. 2.c.
Module-‐level
markup:
how?
-‐ Automated
recogni/on:
very
difficult:
-‐ How
do
you
know
where
the
boundaries
are?
-‐ Even
difficult
for
author
to
iden/fy!
-‐ Author
creates:
templates.
-‐ XPharm,
2001:
modular
text
book
in
pharmacology:
-‐ Only
works
if
you
pay
authors!
8
Thursday, October 20, 2011
39. 2.c.
Module-‐level
markup:
how?
-‐ Automated
recogni/on:
very
difficult:
-‐ How
do
you
know
where
the
boundaries
are?
-‐ Even
difficult
for
author
to
iden/fy!
-‐ Author
creates:
templates.
-‐ XPharm,
2001:
modular
text
book
in
pharmacology:
-‐ Only
works
if
you
pay
authors!
-‐ Mo/f
detec/on
work
might
offer
help?
8
Thursday, October 20, 2011
41. 3.
Statement-‐level
markup
a.Why?
-‐ Automated
summarisa/on?
-‐ Towards
claim-‐evidence
networks
9
Thursday, October 20, 2011
42. 3.
Statement-‐level
markup
a.Why?
-‐ Automated
summarisa/on?
-‐ Towards
claim-‐evidence
networks
b.How,
by
whom?
-‐ Comparison
of
three
groups:
1.Liakata
et
al.:
CoreSC
2.Ananiadou
et
al.:
Metaknowledge
annota/on
3.De
Waard/Pander
Maat:
Discourse
Segment
Types
-‐ Annotated
three
texts:
compare
schemes,
levels,
annota/on
overlap
9
Thursday, October 20, 2011
43. 3.1
Liakata
et
al.:
Core-‐Scien/fic
Concepts
(CoreSC)
Annota/on
Scheme
s
Thursday, October 20, 2011
44. 3.1
Liakata
et
al.:
Core-‐Scien/fic
Concepts
(CoreSC)
Annota/on
Scheme
Three-‐layer,
ontology-‐mo/vated
annota/on
scheme
for
sentence
annota/on,
which
views
a
paper
as
the
humanly
readable
representa0on
of
a
scien0fic
inves0ga0on:
[45-‐page
guideline:
Liakata
&
Soldatova
2008]
-‐ 1st
layer:
Core
Scien4fic
Concepts
(CoreSCs):
Hypothesis,
Mo/va/on,
Goal,
Object,
Background,
Method,
Experiment,
Model,
Observa/on,
Result,
Conclusion
-‐ 2nd
layer:
Proper4es
of
CoreSCs.
s
Novelty
(New/Old)
and
Advantage
(advantage/disadvantage)
-‐ 3rd
layer:
Concept
Iden4fiers:
linking
sentences
together
which
refer
to
the
same
instance
of
a
CoreSC
Thursday, October 20, 2011
46. 3.1
CoreSC
Annota/on
tool:
• Automated
annota/on
with
CoreSC
system
well
underway!
Thursday, October 20, 2011
47. 3.2.
Ananiadou
et
al:
Metaknowledge
annota/on:
Knowledge
Type Certainty
Level
•
Inves4ga4on
•L3
•
Observa4on
•L2
•
Analysis
•L1
•
General
Par4cipants Bio-‐Event Class
/
Type
•
Theme(s) (Centred
on
an
Event
(Grounded
to
an
event
•
Actor(s) Trigger) ontology)
Source Manner Polarity
•
High
•
Other •
Nega4ve
•
Low
•
Current •
Posi4ve
•
Neutral
Thursday, October 20, 2011
48. 3.2
Example
of
Metaknowledge
annota/on:
S3 = These results suggest that Y has no effect on
expression of X
Knowledge Certainty Lexical
Event Manner Source
Type Level Polarity
E1 General L3 Posi4ve Neutral Current
E2 Analysis L2 Nega4ve Neutral Current
Thursday, October 20, 2011
49. 3.2
Example
of
Metaknowledge
annota/on:
S3 = These results suggest that Y has no effect on
expression of X
Knowledge Certainty Lexical
Event Manner Source
Type Level Polarity
E1 General L3 Posi4ve Neutral Current
E2 Analysis L2 Nega4ve Neutral Current
Thursday, October 20, 2011
50. 3.2
Example
of
Metaknowledge
annota/on:
S3 = These results suggest that Y has no effect on
expression of X
Knowledge Certainty Lexical
Event Manner Source
Type Level Polarity
E1 General L3 Posi4ve Neutral Current
E2 Analysis L2 Nega4ve Neutral Current
Thursday, October 20, 2011
51. 3.2
Example
of
Metaknowledge
annota/on:
S3 = These results suggest that Y has no effect on
expression of X
Knowledge Certainty Lexical
Event Manner Source
Type Level Polarity
E1 General L3 Posi4ve Neutral Current
E2 Analysis L2 Nega4ve Neutral Current
• Manual
annota/on
underway
of
the
GENIA
event
corpus
(1000
MEDLINE
abstracts)
Thursday, October 20, 2011
52. 3.3
de
Waard/Pander
Maat:
Discourse
Segment
Types
Both seminomas and the EC component of
nonseminomas share features with ES cells. To
exclude that the detection of miR-371-3 merely
reflects its expression pattern in ES cells, we tested
by RPA miR-302a-d, another ES cells-specific
miRNA cluster (Suh et al, 2004). In many of the
miR-371-3 expressing seminomas and
nonseminomas, miR-302a-d was undetectable (Figs
S7 and S8), suggesting that miR-371-3 expression
is a selective event during tumorigenesis.
Thursday, October 20, 2011
53. 3.3
de
Waard/Pander
Maat:
Discourse
Segment
Types
Both seminomas and the EC component of
Both seminomas and the EC component of
nonseminomas share features with ES cells.
nonseminomas share features with ES cells. To
exclude thatthat detection of miR-371-3 merely
To exclude the
reflects its expression pattern in ES cells,reflects its
the detection of miR-371-3 merely we tested
by RPA miR-302a-d, another ES cells-specific
expression pattern in ES cells,
miRNA cluster RPA miR-302a-d, another ES cells-
we tested by (Suh et al, 2004). In many of the
m i R - 3 7 miRNAx p r e s s(Suh et e m2004). a s a n d
specific 1 - 3 e cluster i n g s al, i n o m
nonseminomas, miR-302a-d was undetectable (Figs
In many of the miR-371-3 expressing seminomas
S7 and S8), suggesting that miR-371-3undetectable
and nonseminomas, miR-302a-d was expression
is a selective event during tumorigenesis.
(Figs S7 and S8),
suggesting that
miR-371-3 expression is a selective event during
tumorigenesis.
Thursday, October 20, 2011
54. 3.3
de
Waard/Pander
Maat:
Discourse
Segment
Types
Both seminomas and the EC component of
Both seminomas and the EC component of Fact
nonseminomas share features with ES cells.
nonseminomas share features with ES cells. To
exclude thatthat detection of miR-371-3 merely
To exclude the
reflects its expression pattern in ES cells,reflects its
the detection of miR-371-3 merely we tested
by RPA miR-302a-d, another ES cells-specific
expression pattern in ES cells,
miRNA cluster RPA miR-302a-d, another ES cells-
we tested by (Suh et al, 2004). In many of the
m i R - 3 7 miRNAx p r e s s(Suh et e m2004). a s a n d
specific 1 - 3 e cluster i n g s al, i n o m
nonseminomas, miR-302a-d was undetectable (Figs
In many of the miR-371-3 expressing seminomas
S7 and S8), suggesting that miR-371-3undetectable
and nonseminomas, miR-302a-d was expression
is a selective event during tumorigenesis.
(Figs S7 and S8),
suggesting that
miR-371-3 expression is a selective event during
tumorigenesis.
Thursday, October 20, 2011
55. 3.3
de
Waard/Pander
Maat:
Discourse
Segment
Types
Both seminomas and the EC component of
Both seminomas and the EC component of Fact
nonseminomas share features with ES cells.
nonseminomas share features with ES cells. To
exclude thatthat detection of miR-371-3 merely
To exclude the
reflects its expression pattern in ES cells,reflects its
the detection of miR-371-3 merely we tested Hypothesis
by RPA miR-302a-d, another ES cells-specific
expression pattern in ES cells,
miRNA cluster RPA miR-302a-d, another ES cells-
we tested by (Suh et al, 2004). In many of the
m i R - 3 7 miRNAx p r e s s(Suh et e m2004). a s a n d
specific 1 - 3 e cluster i n g s al, i n o m
nonseminomas, miR-302a-d was undetectable (Figs
In many of the miR-371-3 expressing seminomas
S7 and S8), suggesting that miR-371-3undetectable
and nonseminomas, miR-302a-d was expression
is a selective event during tumorigenesis.
(Figs S7 and S8),
suggesting that
miR-371-3 expression is a selective event during
tumorigenesis.
Thursday, October 20, 2011
56. 3.3
de
Waard/Pander
Maat:
Discourse
Segment
Types
Both seminomas and the EC component of
Both seminomas and the EC component of Fact
nonseminomas share features with ES cells.
nonseminomas share features with ES cells. To
exclude thatthat detection of miR-371-3 merely
To exclude the
reflects its expression pattern in ES cells,reflects its
the detection of miR-371-3 merely we tested Hypothesis
by RPA miR-302a-d, another ES cells-specific
expression pattern in ES cells,
miRNA cluster RPA miR-302a-d, another ES cells-
we tested by (Suh et al, 2004). In many of the
m i R - 3 7 miRNAx p r e s s(Suh et e m2004). a s a n d
specific 1 - 3 e cluster i n g s al, i n o m Method
nonseminomas, miR-302a-d was undetectable (Figs
In many of the miR-371-3 expressing seminomas
S7 and S8), suggesting that miR-371-3undetectable
and nonseminomas, miR-302a-d was expression
is a selective event during tumorigenesis.
(Figs S7 and S8),
suggesting that
miR-371-3 expression is a selective event during
tumorigenesis.
Thursday, October 20, 2011
57. 3.3
de
Waard/Pander
Maat:
Discourse
Segment
Types
Both seminomas and the EC component of
Both seminomas and the EC component of Fact
nonseminomas share features with ES cells.
nonseminomas share features with ES cells. To
exclude thatthat detection of miR-371-3 merely
To exclude the
reflects its expression pattern in ES cells,reflects its
the detection of miR-371-3 merely we tested Hypothesis
by RPA miR-302a-d, another ES cells-specific
expression pattern in ES cells,
miRNA cluster RPA miR-302a-d, another ES cells-
we tested by (Suh et al, 2004). In many of the
m i R - 3 7 miRNAx p r e s s(Suh et e m2004). a s a n d
specific 1 - 3 e cluster i n g s al, i n o m Method
nonseminomas, miR-302a-d was undetectable (Figs
In many of the miR-371-3 expressing seminomas
S7 and S8), suggesting that miR-371-3undetectable
and nonseminomas, miR-302a-d was expression Result
is a selective event during tumorigenesis.
(Figs S7 and S8),
suggesting that
miR-371-3 expression is a selective event during
tumorigenesis.
Thursday, October 20, 2011
58. 3.3
de
Waard/Pander
Maat:
Discourse
Segment
Types
Both seminomas and the EC component of
Both seminomas and the EC component of Fact
nonseminomas share features with ES cells.
nonseminomas share features with ES cells. To
exclude thatthat detection of miR-371-3 merely
To exclude the
reflects its expression pattern in ES cells,reflects its
the detection of miR-371-3 merely we tested Hypothesis
by RPA miR-302a-d, another ES cells-specific
expression pattern in ES cells,
miRNA cluster RPA miR-302a-d, another ES cells-
we tested by (Suh et al, 2004). In many of the
m i R - 3 7 miRNAx p r e s s(Suh et e m2004). a s a n d
specific 1 - 3 e cluster i n g s al, i n o m Method
nonseminomas, miR-302a-d was undetectable (Figs
In many of the miR-371-3 expressing seminomas
S7 and S8), suggesting that miR-371-3undetectable
and nonseminomas, miR-302a-d was expression Result
is a selective event during tumorigenesis.
(Figs S7 and S8),
suggesting that
miR-371-3 expression is a selective event during
Implication
tumorigenesis.
Thursday, October 20, 2011
59. 3.3
de
Waard/Pander
Maat:
Discourse
Segment
Types
Both seminomas and the EC component of
Both seminomas and the EC component of Fact
nonseminomas share features with ES cells.
nonseminomas share features with ES cells. To
exclude thatthat detection of miR-371-3 merely
To exclude the Goal
reflects its expression pattern in ES cells,reflects its
the detection of miR-371-3 merely we tested Hypothesis
by RPA miR-302a-d, another ES cells-specific
expression pattern in ES cells,
miRNA cluster RPA miR-302a-d, another ES cells-
we tested by (Suh et al, 2004). In many of the
m i R - 3 7 miRNAx p r e s s(Suh et e m2004). a s a n d
specific 1 - 3 e cluster i n g s al, i n o m Method
nonseminomas, miR-302a-d was undetectable (Figs
In many of the miR-371-3 expressing seminomas
S7 and S8), suggesting that miR-371-3undetectable
and nonseminomas, miR-302a-d was expression Result
is a selective event during tumorigenesis.
(Figs S7 and S8),
suggesting that
miR-371-3 expression is a selective event during
Implication
tumorigenesis.
Thursday, October 20, 2011
60. 3.3
de
Waard/Pander
Maat:
Discourse
Segment
Types
Both seminomas and the EC component of
Both seminomas and the EC component of Fact
nonseminomas share features with ES cells.
nonseminomas share features with ES cells. To
exclude thatthat detection of miR-371-3 merely
To exclude the Goal
reflects its expression pattern in ES cells,reflects its
the detection of miR-371-3 merely we tested Hypothesis
by RPA miR-302a-d, another ES cells-specific
expression pattern in ES cells,
miRNA cluster RPA miR-302a-d, another ES cells-
we tested by (Suh et al, 2004). In many of the
m i R - 3 7 miRNAx p r e s s(Suh et e m2004). a s a n d
specific 1 - 3 e cluster i n g s al, i n o m Method
nonseminomas, miR-302a-d was undetectable (Figs
In many of the miR-371-3 expressing seminomas
S7 and S8), suggesting that miR-371-3undetectable
and nonseminomas, miR-302a-d was expression Result
is a selective event during tumorigenesis.
(Figs S7 and S8),
suggesting that Reg-Implication
miR-371-3 expression is a selective event during
Implication
tumorigenesis.
Thursday, October 20, 2011
61. 3.3
de
Waard/Pander
Maat:
Discourse
Segment
Types
Conceptual
Both seminomas and the EC component of
Both seminomas and the EC component of knowledge
Fact
nonseminomas share features with ES cells.
nonseminomas share features with ES cells. To
exclude thatthat detection of miR-371-3 merely
To exclude the Goal
reflects its expression pattern in ES cells,reflects its
the detection of miR-371-3 merely we tested Hypothesis
by RPA miR-302a-d, another ES cells-specific
expression pattern in ES cells,
miRNA cluster RPA miR-302a-d, another ES cells-
we tested by (Suh et al, 2004). In many of the
m i R - 3 7 miRNAx p r e s s(Suh et e m2004). a s a n d
specific 1 - 3 e cluster i n g s al, i n o m Method
nonseminomas, miR-302a-d was undetectable (Figs
In many of the miR-371-3 expressing seminomas
S7 and S8), suggesting that miR-371-3undetectable
and nonseminomas, miR-302a-d was expression Result
is a selective event during tumorigenesis.
(Figs S7 and S8),
suggesting that Reg-Implication
miR-371-3 expression is a selective event during
Implication
tumorigenesis.
Thursday, October 20, 2011
62. 3.3
de
Waard/Pander
Maat:
Discourse
Segment
Types
Conceptual
Both seminomas and the EC component of
Both seminomas and the EC component of knowledge
Fact
nonseminomas share features with ES cells.
nonseminomas share features with ES cells. To
exclude thatthat detection of miR-371-3 merely
To exclude the Goal
reflects its expression pattern in ES cells,reflects its
the detection of miR-371-3 merely we tested Hypothesis
by RPA miR-302a-d, another ES cells-specific
expression pattern in ES cells,
miRNA cluster RPA miR-302a-d, another ES cells-
we tested by (Suh et al, 2004). In many of the
m i R - 3 7 miRNAx p r e s s(Suh et e m2004). a s a n d
specific 1 - 3 e cluster i n g s al, i n o m Method
Experimental
nonseminomas, miR-302a-d was undetectable (Figs
In many of the miR-371-3 expressing seminomas
Evidence
S7 and S8), suggesting that miR-371-3undetectable
and nonseminomas, miR-302a-d was expression Result
is a selective event during tumorigenesis.
(Figs S7 and S8),
suggesting that Reg-Implication
miR-371-3 expression is a selective event during
Implication
tumorigenesis.
Thursday, October 20, 2011
64. 3.3
Iden/fica/on
of
DSTs:
-‐ Verb
form:
tense,
e.g.
-‐ Concepts
in
‘state’
(gnomic)
present:
‘Dopaminergic
innerva/on
plays
a
major
role
in
the
control
of
mood
and
its
perturba/on’
-‐ Experiments
in
‘event’
past:
‘Four
out
of
seven
cell
lines
expressed
this
cluster’
15
Thursday, October 20, 2011
65. 3.3
Iden/fica/on
of
DSTs:
-‐ Verb
form:
tense,
e.g.
-‐ Concepts
in
‘state’
(gnomic)
present:
‘Dopaminergic
innerva/on
plays
a
major
role
in
the
control
of
mood
and
its
perturba/on’
-‐ Experiments
in
‘event’
past:
‘Four
out
of
seven
cell
lines
expressed
this
cluster’
-‐ Seman4c
verb
class:
-‐ Research
verbs
(Inves/ga/on,
Predic/on,
Procedure,
Observa/on,
Interpreta/on)
-‐ Discourse
verbs
-‐ Proper/es
and
rela/onships
-‐
between
things
and
concepts
15
Thursday, October 20, 2011
66. 3.3
Iden/fica/on
of
DSTs:
-‐ Verb
form:
tense,
e.g.
-‐ Concepts
in
‘state’
(gnomic)
present:
‘Dopaminergic
innerva/on
plays
a
major
role
in
the
control
of
mood
and
its
perturba/on’
-‐ Experiments
in
‘event’
past:
‘Four
out
of
seven
cell
lines
expressed
this
cluster’
-‐ Seman4c
verb
class:
-‐ Research
verbs
(Inves/ga/on,
Predic/on,
Procedure,
Observa/on,
Interpreta/on)
-‐ Discourse
verbs
-‐ Proper/es
and
rela/onships
-‐
between
things
and
concepts
-‐ Modality
-‐ Types:
Source
{Author,
others,
unknown},
Basis
{Data,
Reasoning,
0},
Value
{Certain,
probable,
possible,
unknown}
-‐ Markers:
Modal
aux,
verb
class
Interpreta/on,
epistemic
adverbs
15
Thursday, October 20, 2011
68. 3.
Same
Statement
annotated
three
ways:
CoreSC:
<annotationART atype="GSC" type="Res" conceptID="Res24" novelty="None" advantage="None">
Here we show that BOB.1/OBF.1 regulates Btk gene expression.
</annotationART>
BioEvent/MetaKnowledge:
<sentence id="S6">Here we show that
<term id="T13" sem="Protein_family_or_group">
<gene-or-gene-product id="G9">BOB.1</gene-or-gene-product>/
<gene-or-gene-product id="G10">OBF.1</gene-or-gene-product>
</term> regulates
<term id="T14" sem="Biological_process">
<term id="T15" sem="DNA_domain_or_region">
<gene-or-gene-product id="G11">Btk
</gene-or-gene-product> gene
</term> expression
</term>.
</sentence>
Discourse Segments:
<segment segID ="286" section = "D" segtype = "RegImplication">
Here we show that
</segment>
<segment segID ="287" section = "D" segtype = "Implication">
Thursday, October 20, 2011
69. 3.
Same
Statement
annotated
three
ways:
CoreSC:
<annotationART atype="GSC" type="Res" conceptID="Res24" novelty="None" advantage="None">
Here we show that BOB.1/OBF.1 regulates Btk gene expression.
</annotationART>
BioEvent/MetaKnowledge:
<sentence id="S6">Here we show that
<term id="T13" sem="Protein_family_or_group">
<gene-or-gene-product id="G9">BOB.1</gene-or-gene-product>/
<gene-or-gene-product id="G10">OBF.1</gene-or-gene-product>
</term> regulates
<term id="T14" sem="Biological_process">
<term id="T15" sem="DNA_domain_or_region">
<gene-or-gene-product id="G11">Btk
</gene-or-gene-product> gene
</term> expression
</term>.
</sentence>
Discourse Segments:
<segment segID ="286" section = "D" segtype = "RegImplication">
Here we show that
</segment>
<segment segID ="287" section = "D" segtype = "Implication">
BOB.1/OBF.1 regulates Btk gene expression.
</segment>
Thursday, October 20, 2011
70. 3.
Same
Statement
annotated
three
ways:
CoreSC:
<annotationART atype="GSC" type="Res" conceptID="Res24" novelty="None" advantage="None">
Here we show that BOB.1/OBF.1 regulates Btk gene expression.
</annotationART>
BioEvent/MetaKnowledge:
<sentence id="S6">Here we show that
<term id="T13" sem="Protein_family_or_group">
<gene-or-gene-product id="G9">BOB.1</gene-or-gene-product>/
<gene-or-gene-product id="G10">OBF.1</gene-or-gene-product>
</term> regulates
<term id="T14" sem="Biological_process">
<term id="T15" sem="DNA_domain_or_region">
<gene-or-gene-product id="G11">Btk
</gene-or-gene-product> gene
</term> expression
</term>.
</sentence>
Discourse Segments:
<segment segID ="286" section = "D" segtype = "RegImplication">
Here we show that
</segment>
<segment segID ="287" section = "D" segtype = "Implication">
BOB.1/OBF.1 regulates Btk gene expression.
</segment>
Thursday, October 20, 2011
71. 3.
Comparing
statement-‐level
annota/on
models
Who Why What How
Liakata:
CoreSC Iden/fy
main
Sentence Manual
corpus,
components
of
automated
scien/fic
inves/ga/on
annota/on
tools
-‐
for
machine
learning working
on
automated
detec/on
Ananiadou:
Enhance
informa/on
Events
(intra-‐ Manual
corpus,
MetaKnowledge/ extrac/on
for
senten/al):
can
be
working
on
BioEvents biomedical
texts
to
several
per
automated
detec/on
enable
metadiscourse
sentence,
or
one
in
annota/on more
sentences
de
Waard: Iden/fy
mechanisms
Clause Manual,
ideas
(but
no
Discourse
Segment
of
conveying
real
plans!)
for
Types (epistemic)
knowledge
automated
in
scien/fic
discourse iden/fica/on
Thursday, October 20, 2011
72. 4.
Rela.ons
a.Why?
-‐ Argumenta/on
visualisa/on
b.What,
by
whom?
-‐ Harmsze
(1999):
Ontology
of
content
rela/onships
-‐ IBIS,
ClaiMaker
(2001)
-‐ Diligent
argumenta/on
ontology
(2005)
-‐ SALT:
RST
(2007)
-‐ SWAN
(2010)
c. How?
-‐ So
far:
Manually 18
Thursday, October 20, 2011
73. 4.
Rela.ons
a.Why?
-‐ Argumenta/on
visualisa/on
b.What,
by
whom?
-‐ Harmsze
(1999):
Ontology
of
content
rela/onships
-‐ IBIS,
ClaiMaker
(2001)
-‐ Diligent
argumenta/on
ontology
(2005)
-‐ SALT:
RST
(2007)
-‐ SWAN
(2010)
c. How?
-‐ So
far:
Manually 18
Thursday, October 20, 2011
74. 4.
Rela.ons
a.Why?
-‐ Argumenta/on
visualisa/on
b.What,
by
whom?
-‐ Harmsze
(1999):
Ontology
of
content
rela/onships
-‐ IBIS,
ClaiMaker
(2001)
-‐ Diligent
argumenta/on
ontology
(2005)
-‐ SALT:
RST
(2007)
-‐ SWAN
(2010)
c. How?
-‐ So
far:
Manually 18
Thursday, October 20, 2011
75. 4.
Rela.ons
a.Why?
-‐ Argumenta/on
visualisa/on
b.What,
by
whom?
-‐ Harmsze
(1999):
Ontology
of
content
rela/onships
-‐ IBIS,
ClaiMaker
(2001)
-‐ Diligent
argumenta/on
ontology
(2005)
-‐ SALT:
RST
(2007)
-‐ SWAN
(2010)
c. How?
-‐ So
far:
Manually 18
Thursday, October 20, 2011
76. 4.
Rela.ons
a.Why?
-‐ Argumenta/on
visualisa/on
b.What,
by
whom?
-‐ Harmsze
(1999):
Ontology
of
content
rela/onships
-‐ IBIS,
ClaiMaker
(2001)
-‐ Diligent
argumenta/on
ontology
(2005)
-‐ SALT:
RST
(2007)
-‐ SWAN
(2010)
c. How?
-‐ So
far:
Manually 18
Thursday, October 20, 2011
81. 5.Claim-‐Evidence
Networks
(statement
+
rela/ons)
a.Why?
Show
argumenta/on
across
body
of
work
b.What,
by
whom?
-‐ Buckingham
Shum,
1999
19
Thursday, October 20, 2011
82. 5.Claim-‐Evidence
Networks
(statement
+
rela/ons)
a.Why?
Show
argumenta/on
across
body
of
work
b.What,
by
whom?
-‐ Buckingham
Shum,
1999
19
Thursday, October 20, 2011
83. 5.Claim-‐Evidence
Networks
(statement
+
rela/ons)
a.Why?
Show
argumenta/on
across
body
of
work
b.What,
by
whom?
-‐ Buckingham
Shum,
1999
-‐ SWAN:
Clark,
Ciccarese
et
al.,
2005
19
Thursday, October 20, 2011
84. 5.Claim-‐Evidence
Networks
(statement
+
rela/ons)
a.Why?
Show
argumenta/on
across
body
of
work
b.What,
by
whom?
-‐ Buckingham
Shum,
1999
-‐ SWAN:
Clark,
Ciccarese
et
al.,
2005
19
Thursday, October 20, 2011
85. 5.Claim-‐Evidence
Networks
(statement
+
rela/ons)
a.Why?
Show
argumenta/on
across
body
of
work
b.What,
by
whom?
-‐ Buckingham
Shum,
1999
-‐ SWAN:
Clark,
Ciccarese
et
al.,
2005
-‐ Nanopublica/ons:
Mons,
2010
19
Thursday, October 20, 2011
86. 5.Claim-‐Evidence
Networks
(statement
+
rela/ons)
a.Why?
Show
argumenta/on
across
body
of
work
b.What,
by
whom?
-‐ Buckingham
Shum,
1999
-‐ SWAN:
Clark,
Ciccarese
et
al.,
2005
-‐ Nanopublica/ons:
Mons,
2010
19
Thursday, October 20, 2011
87. 5.Claim-‐Evidence
Networks
(statement
+
rela/ons)
a.Why?
Show
argumenta/on
across
body
of
work
b.What,
by
whom?
-‐ Buckingham
Shum,
1999
-‐ SWAN:
Clark,
Ciccarese
et
al.,
2005
-‐ Nanopublica/ons:
Mons,
2010
-‐ Nanopublica/ons
+
SWAN,
2011
19
Thursday, October 20, 2011
88. 5.Claim-‐Evidence
Networks
(statement
+
rela/ons)
a.Why?
Show
argumenta/on
across
body
of
work
b.What,
by
whom?
-‐ Buckingham
Shum,
1999
-‐ SWAN:
Clark,
Ciccarese
et
al.,
2005
-‐ Nanopublica/ons:
Mons,
2010
-‐ Nanopublica/ons
+
SWAN,
2011
c.How?
19
Thursday, October 20, 2011
89. 5.Claim-‐Evidence
Networks
(statement
+
rela/ons)
a.Why?
Show
argumenta/on
across
body
of
work
b.What,
by
whom?
-‐ Buckingham
Shum,
1999
-‐ SWAN:
Clark,
Ciccarese
et
al.,
2005
-‐ Nanopublica/ons:
Mons,
2010
-‐ Nanopublica/ons
+
SWAN,
2011
c.How?
-‐ So
far:
manually 19
Thursday, October 20, 2011
90. 5.Claim-‐Evidence
Networks
(statement
+
rela/ons)
a.Why?
Show
argumenta/on
across
body
of
work
b.What,
by
whom?
-‐ Buckingham
Shum,
1999
-‐ SWAN:
Clark,
Ciccarese
et
al.,
2005
-‐ Nanopublica/ons:
Mons,
2010
-‐ Nanopublica/ons
+
SWAN,
2011
c.How?
-‐ So
far:
manually 19
Thursday, October 20, 2011
91. D2S
Use
case:
Claim-‐Evidence
Network
in
Medicine
B. Elsevier-published
A. Philips’ Electronic Patient Records Clinical Guideline
C. Elsevier (or other publisher’s)
Research Report or Data
20
Thursday, October 20, 2011
92. D2S
Use
case:
Claim-‐Evidence
Network
in
Medicine
Step 1: Patient data +
diagnosis link to Guideline
recommendation
B. Elsevier-published
A. Philips’ Electronic Patient Records Clinical Guideline
C. Elsevier (or other publisher’s)
Research Report or Data
20
Thursday, October 20, 2011
93. D2S
Use
case:
Claim-‐Evidence
Network
in
Medicine
Step 1: Patient data +
diagnosis link to Guideline
recommendation
B. Elsevier-published
A. Philips’ Electronic Patient Records Clinical Guideline
Step 2: Guideline recommendation
links to evidence in report or data
C. Elsevier (or other publisher’s)
Research Report or Data
20
Thursday, October 20, 2011
94. D2S
Use
case:
Claim-‐Evidence
Network
in
Medicine
Step 1: Patient data +
diagnosis link to Guideline
recommendation
B. Elsevier-published
A. Philips’ Electronic Patient Records Clinical Guideline
Step 2: Guideline recommendation
links to evidence in report or data
C. Elsevier (or other publisher’s)
Research Report or Data
Related
HCLS
Use
Case:
Accelerate
uptake
of
medical
research
on
drug-‐drug
interac/on
in
product
inserts 20
Thursday, October 20, 2011
95. Five
levels
of
scien/fic
discourse
annota/on
21
Thursday, October 20, 2011
96. Five
levels
of
scien/fic
discourse
annota/on
Why What/Who How
Automated!
Sec/on Search,
UI ABCDE,
ORB/HCLS
Publisher
helps?
Harmsze/Kircz,
LiquidPub,
Module Content
reuse
HCLS
Manual:
templates
Teufel,
Ananiadou,
Summaries;
Working
towards
Statement towards
networks
Liakata,
automated
detec/on
UU
SALT,
ScholOnto,
Diligent,
Manual:
some
tools,
Rela/ons Networks
SWAN never
took
off...
Claim/ Argumenta/on
ScholOnto,
SWAN,
Manual-‐
towards
Evidence networks Nanopublica/ons,
D2S automa/on?
21
Thursday, October 20, 2011
97. Five
levels
of
scien/fic
discourse
annota/on
Why What/Who How
Automated!
Sec/on Search,
UI ABCDE,
ORB/HCLS
Publisher
helps?
Harmsze/Kircz,
LiquidPub,
Module Content
reuse
HCLS
Manual:
templates
Teufel,
Ananiadou,
Summaries;
Working
towards
Statement towards
networks
Liakata,
automated
detec/on
UU
SALT,
ScholOnto,
Diligent,
Manual:
some
tools,
Rela/ons Networks
SWAN never
took
off...
Claim/ Argumenta/on
ScholOnto,
SWAN,
Manual-‐
towards
Evidence networks Nanopublica/ons,
D2S automa/on?
21
Thursday, October 20, 2011
98. Five
levels
of
scien/fic
discourse
annota/on
Why What/Who How
Automated!
Sec/on Search,
UI ABCDE,
ORB/HCLS
Publisher
helps?
Harmsze/Kircz,
LiquidPub,
Module Content
reuse
HCLS
Manual:
templates
Teufel,
Ananiadou,
Summaries;
Working
towards
Statement towards
networks
Liakata,
automated
detec/on
UU
SALT,
ScholOnto,
Diligent,
Manual:
some
tools,
Rela/ons Networks
SWAN never
took
off...
Claim/ Argumenta/on
ScholOnto,
SWAN,
Manual-‐
towards
Evidence networks Nanopublica/ons,
D2S automa/on?
21
Thursday, October 20, 2011
99. Five
levels
of
scien/fic
discourse
annota/on
Why What/Who How
Automated!
Sec/on Search,
UI ABCDE,
ORB/HCLS
Publisher
helps?
Harmsze/Kircz,
LiquidPub,
Module Content
reuse
HCLS
Manual:
templates
Teufel,
Ananiadou,
Summaries;
Working
towards
Statement towards
networks
Liakata,
automated
detec/on
UU
SALT,
ScholOnto,
Diligent,
Manual:
some
tools,
Rela/ons Networks
SWAN never
took
off...
Claim/ Argumenta/on
ScholOnto,
SWAN,
Manual-‐
towards
Evidence networks Nanopublica/ons,
D2S automa/on?
21
Thursday, October 20, 2011
100. Five
levels
of
scien/fic
discourse
annota/on
Why What/Who How
Automated!
Sec/on Search,
UI ABCDE,
ORB/HCLS
Publisher
helps?
Harmsze/Kircz,
LiquidPub,
Module Content
reuse
HCLS
Manual:
templates
Teufel,
Ananiadou,
Summaries;
Working
towards
Statement towards
networks
Liakata,
automated
detec/on
UU
SALT,
ScholOnto,
Diligent,
Manual:
some
tools,
Rela/ons Networks
SWAN never
took
off...
Claim/ Argumenta/on
ScholOnto,
SWAN,
Manual-‐
towards
Evidence networks Nanopublica/ons,
D2S automa/on?
21
Thursday, October 20, 2011
101. Five
levels
of
scien/fic
discourse
annota/on
Why What/Who How
Automated!
Sec/on Search,
UI ABCDE,
ORB/HCLS
Publisher
helps?
Harmsze/Kircz,
LiquidPub,
Module Content
reuse
HCLS
Manual:
templates
Teufel,
Ananiadou,
Summaries;
Working
towards
Statement towards
networks
Liakata,
automated
detec/on
UU
SALT,
ScholOnto,
Diligent,
Manual:
some
tools,
Rela/ons Networks
SWAN never
took
off...
Claim/ Argumenta/on
ScholOnto,
SWAN,
Manual-‐
towards
Evidence networks Nanopublica/ons,
D2S automa/on?
21
Thursday, October 20, 2011
102. Five
levels
of
scien/fic
discourse
annota/on
Why What/Who How
Automated!
Sec/on Search,
UI ABCDE,
ORB/HCLS
Publisher
helps?
Harmsze/Kircz,
LiquidPub,
Module Content
reuse
HCLS
Manual:
templates
MoFfs?
Teufel,
Ananiadou,
Summaries;
Working
towards
Statement towards
networks
Liakata,
automated
detec/on
UU
SALT,
ScholOnto,
Diligent,
Manual:
some
tools,
Rela/ons Networks
SWAN never
took
off...
Claim/ Argumenta/on
ScholOnto,
SWAN,
Manual-‐
towards
Evidence networks Nanopublica/ons,
D2S automa/on?
21
Thursday, October 20, 2011
104. Ques.ons:
Scien/fic
discourse
-‐>
fairy
tales:
how
can
we
transfer
knowledge
here
to
scien/fic
discourse
community?
22
Thursday, October 20, 2011
105. Ques.ons:
Scien/fic
discourse
-‐>
fairy
tales:
how
can
we
transfer
knowledge
here
to
scien/fic
discourse
community?
Issue:
Scien/sts
do
not
like
being
told
that
they
write
fairy
tales!
22
Thursday, October 20, 2011
106. Ques.ons:
Scien/fic
discourse
-‐>
fairy
tales:
how
can
we
transfer
knowledge
here
to
scien/fic
discourse
community?
Issue:
Scien/sts
do
not
like
being
told
that
they
write
fairy
tales!
Fairy
tales
-‐>
scien/fic
discourse:
is
anyone
here/in
this
community
interested
in
working
on
inter-‐domain
transfer
of
tools,
technologies
and
theories?
22
Thursday, October 20, 2011
107. Ques.ons:
Scien/fic
discourse
-‐>
fairy
tales:
how
can
we
transfer
knowledge
here
to
scien/fic
discourse
community?
Issue:
Scien/sts
do
not
like
being
told
that
they
write
fairy
tales!
Fairy
tales
-‐>
scien/fic
discourse:
is
anyone
here/in
this
community
interested
in
working
on
inter-‐domain
transfer
of
tools,
technologies
and
theories?
Anita
de
Waard,
a.dewaard@elsevier.com
-‐HCLS:
hEp://www.w3.org/wiki/HCLSIG/SWANSIOC
-‐UU:
hEp://elsatglabs.com/labs/anita
-‐D2S:
hEp://www.data2seman/cs.org
22
Thursday, October 20, 2011