reengineering the scientific research paper
DESCRIPTION
Talk for Harvard Digital Scholarship SummitTRANSCRIPT
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Stories, that persuade with data.What’s inside scientific papers, and should it be reengineered?
Anita de Waard, [email protected] Disruptive Technologies Director, Elsevier Labs
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Scientific papers are stories, that persuade with data.The Story of Goldilocks and the Three Bears
Story Part Paper The AXH Domain of Ataxin-1 Mediates 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
Setting
Objects of study the Drosophila Atx-1 homolog (dAtx-1) which lacks a polyQ tract,
She went for a walk in the forest. Pretty soon, she came upon a house.
Location
Setting
Experimental setup
studied and compared in vivo effects and interactions to those of the human protein
She knocked and, when no one answered,
Goal Theme Researchgoal
Gain insight into how Atx-1's function contributes to SCA1 pathogenesis. How these interactions might contribute to the disease process and how they might cause toxicity in only a subset of neurons in SCA1 is not fully understood.she walked right in. Attempt
Theme
Hypothesis Atx-1 may play a role in the regulation of gene expression
At the table in the kitchen, there were three bowls of porridge.
Name Episode 1 Name dAtX-1 and hAtx-1 Induce Similar Phenotypes When Overexpressed in Files
Goldilocks was hungry. Subgoal
Episode 1
Subgoal test the function of the AXH domain
She tasted the porridge from the first bowl.
Attempt
Episode 1
Method overexpressed dAtx-1 in flies using the GAL4/UAS system (Brand and Perrimon, 1993) and compared its effects to those of hAtx-1.
This porridge is too hot! she exclaimed.
Outcome
Episode 1
Results Overexpression of dAtx-1 by Rhodopsin1(Rh1)-GAL4, which 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 Atx-1 does not show obvious morphological changes in the photoreceptor cellsSo, she tasted the porridge from the
second bowl.Activity
Episode 1
Data (data not shown),
This porridge is too cold, she said Outcome
Episode 1
Results both genotypes show many large holes and loss of cell integrity at 28 days
So, she tasted the last bowl of porridge.
Activity
Episode 1
Data (Figures 1B-1D).
Ahhh, this porridge is just right, she said happily and
Outcome
Episode 1
Results Overexpression of dAtx-1 using the GMR-GAL4 driver also induces eye abnormalities. The external structures of the eyes that overexpress dAtx-1 show disorganized ommatidia and loss of interommatidial bristles she ate it all up. Outcome
Episode 1
Data (Figure 1F),
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Scientific papers are stories, that persuade with data.The Story of Goldilocks and the Three Bears
Story Part Paper The AXH Domain of Ataxin-1 Mediates 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
Setting
Objects of study the Drosophila Atx-1 homolog (dAtx-1) which lacks a polyQ tract,
She went for a walk in the forest. Pretty soon, she came upon a house.
Location
Setting
Experimental setup
studied and compared in vivo effects and interactions to those of the human protein
She knocked and, when no one answered,
Goal Theme Researchgoal
Gain insight into how Atx-1's function contributes to SCA1 pathogenesis. How these interactions might contribute to the disease process and how they might cause toxicity in only a subset of neurons in SCA1 is not fully understood.she walked right in. Attempt
Theme
Hypothesis Atx-1 may play a role in the regulation of gene expression
At the table in the kitchen, there were three bowls of porridge.
Name Episode 1 Name dAtX-1 and hAtx-1 Induce Similar Phenotypes When Overexpressed in Files
Goldilocks was hungry. Subgoal
Episode 1
Subgoal test the function of the AXH domain
She tasted the porridge from the first bowl.
Attempt
Episode 1
Method overexpressed dAtx-1 in flies using the GAL4/UAS system (Brand and Perrimon, 1993) and compared its effects to those of hAtx-1.
This porridge is too hot! she exclaimed.
Outcome
Episode 1
Results Overexpression of dAtx-1 by Rhodopsin1(Rh1)-GAL4, which 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 Atx-1 does not show obvious morphological changes in the photoreceptor cellsSo, she tasted the porridge from the
second bowl.Activity
Episode 1
Data (data not shown),
This porridge is too cold, she said Outcome
Episode 1
Results both genotypes show many large holes and loss of cell integrity at 28 days
So, she tasted the last bowl of porridge.
Activity
Episode 1
Data (Figures 1B-1D).
Ahhh, this porridge is just right, she said happily and
Outcome
Episode 1
Results Overexpression of dAtx-1 using the GMR-GAL4 driver also induces eye abnormalities. The external structures of the eyes that overexpress dAtx-1 show disorganized ommatidia and loss of interommatidial bristles she ate it all up. Outcome
Episode 1
Data (Figure 1F),
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Story analysis of scientific text: ORB vs. Medium-grained structure
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See work at http://www.w3.org/wiki/HCLSIG/SWANSIOC
Story analysis of scientific text: ORB vs. Medium-grained structure
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Episode-level access through Linked Data standards:
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Episode-level access through Linked Data standards:
<ce:section id=#123>
said @anita on April 5, 2011
mice like cheesethis says
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but we all know she was deluded then
Episode-level access through Linked Data standards:
<ce:section id=#123>
said @anita on April 5, 2011
mice like cheesethis says
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allows for layers of annotation
but we all know she was deluded then
Episode-level access through Linked Data standards:
<ce:section id=#123>
said @anita on April 5, 2011
the xml is fixed, but the structure is open!
mice like cheesethis says
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Satellite Format: Linked Data repository for all Elsevier content
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Satellite Format: Linked Data repository for all Elsevier content
Dublin Core and SKOS
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Satellite Format: Linked Data repository for all Elsevier content
SWAN’s PAV (Provenance, Authoring and Versioning) ontology
Dublin Core and SKOS
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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 m i R - 3 7 1 - 3 e x p r e s s i n g s e m i n o m a s a n d nonseminomas, miR-302a-d was undetectable (Figs S7 and S8), suggesting that miR-371-3 expression is a selective event during tumorigenesis.
Scientific papers are stories, that persuade with data.
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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 m i R - 3 7 1 - 3 e x p r e s s i n g s e m i n o m a s a n d nonseminomas, miR-302a-d was undetectable (Figs S7 and S8), suggesting that miR-371-3 expression is a selective event during tumorigenesis.
Both seminomas and the EC component of nonseminomas share features with ES cells.To exclude thatthe 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 thatmiR-371-3 expression is a selective event during tumorigenesis.
Scientific papers are stories, that persuade with data.
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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 m i R - 3 7 1 - 3 e x p r e s s i n g s e m i n o m a s a n d nonseminomas, miR-302a-d was undetectable (Figs S7 and S8), suggesting that miR-371-3 expression is a selective event during tumorigenesis.
Both seminomas and the EC component of nonseminomas share features with ES cells.To exclude thatthe 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 thatmiR-371-3 expression is a selective event during tumorigenesis.
Fact
Hypothesis
Method
Result
Implication
Goal
Reg-Implication
Scientific papers are stories, that persuade with data.
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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 m i R - 3 7 1 - 3 e x p r e s s i n g s e m i n o m a s a n d nonseminomas, miR-302a-d was undetectable (Figs S7 and S8), suggesting that miR-371-3 expression is a selective event during tumorigenesis.
Both seminomas and the EC component of nonseminomas share features with ES cells.To exclude thatthe 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 thatmiR-371-3 expression is a selective event during tumorigenesis.
Fact
Hypothesis
Method
Result
Implication
Goal
Reg-Implication
Conceptual knowledge
Scientific papers are stories, that persuade with data.
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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 m i R - 3 7 1 - 3 e x p r e s s i n g s e m i n o m a s a n d nonseminomas, miR-302a-d was undetectable (Figs S7 and S8), suggesting that miR-371-3 expression is a selective event during tumorigenesis.
Both seminomas and the EC component of nonseminomas share features with ES cells.To exclude thatthe 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 thatmiR-371-3 expression is a selective event during tumorigenesis.
Fact
Hypothesis
Method
Result
Implication
Goal
Reg-Implication
Conceptual knowledge
ExperimentalEvidence
Scientific papers are stories, that persuade with data.
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Realms of persuasive experimental discourse:
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(3) c. miR-371-3 expression is a selective event during tumorigenesis.
(1) Both seminomas and the EC component of nonseminomas share features with ES cells.
(2) b. the detection of miR-371-3 merely reflects its expression pattern in ES cells,
(2) c. we tested by RPA miR-302a-d, another ES cells-specific miRNA cluster (Suh et al, 2004).
(3) a. In many of the miR-371-3 expressing seminomas and nonseminomas, miR-302a-d was undetectable (Figs S7 and S8),
(2) a. To exclude that (3) b. suggesting that
Realms of persuasive experimental discourse:
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(3) c. miR-371-3 expression is a selective event during tumorigenesis.
(1) Both seminomas and the EC component of nonseminomas share features with ES cells.
(2) b. the detection of miR-371-3 merely reflects its expression pattern in ES cells,
(2) c. we tested by RPA miR-302a-d, another ES cells-specific miRNA cluster (Suh et al, 2004).
(3) a. In many of the miR-371-3 expressing seminomas and nonseminomas, miR-302a-d was undetectable (Figs S7 and S8),
Concepts, models, ‘facts’
Experiment
Transitions(2) a. To exclude that (3) b. suggesting that
Realms of persuasive experimental discourse:
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(3) c. miR-371-3 expression is a selective event during tumorigenesis.
(1) Both seminomas and the EC component of nonseminomas share features with ES cells.
(2) b. the detection of miR-371-3 merely reflects its expression pattern in ES cells,
(2) c. we tested by RPA miR-302a-d, another ES cells-specific miRNA cluster (Suh et al, 2004).
(3) a. In many of the miR-371-3 expressing seminomas and nonseminomas, miR-302a-d was undetectable (Figs S7 and S8),
Concepts, models, ‘facts’
Experiment
Transitions(2) a. To exclude that (3) b. suggesting that
Realms of persuasive experimental discourse:
‘State’ present tense
‘Narrative’ past tense
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Fact creation through citations:
To investigate the possibility that miR-372 and miR-373 suppress the expression of LATS2, we...
Therefore, these results point to LATS2 as a mediator of the miR-372 and miR-373 effects on cell proliferation and tumorigenicity,
Voorhoeve et al, Cell, 2006:
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Fact creation through citations:
To investigate the possibility that miR-372 and miR-373 suppress the expression of LATS2, we...
Therefore, these results point to LATS2 as a mediator of the miR-372 and miR-373 effects on cell proliferation and tumorigenicity,
Voorhoeve et al, Cell, 2006:
Hypothesis
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Fact creation through citations:
To investigate the possibility that miR-372 and miR-373 suppress the expression of LATS2, we...
Therefore, these results point to LATS2 as a mediator of the miR-372 and miR-373 effects on cell proliferation and tumorigenicity,
Voorhoeve et al, Cell, 2006:
Hypothesis
Implication
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... two miRNAs, miRNA-372 and-373, function as potential novel oncogenes in testicular germ cell tumors by inhibition of LATS2 expression, which suggests that Lats2 is an important tumor suppressor (Voorhoeve et al., 2006).
Raver-Shapira et.al, JMolCell 2007
Fact creation through citations:
To investigate the possibility that miR-372 and miR-373 suppress the expression of LATS2, we...
Therefore, these results point to LATS2 as a mediator of the miR-372 and miR-373 effects on cell proliferation and tumorigenicity,
Voorhoeve et al, Cell, 2006:
Hypothesis
Implication
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... two miRNAs, miRNA-372 and-373, function as potential novel oncogenes in testicular germ cell tumors by inhibition of LATS2 expression, which suggests that Lats2 is an important tumor suppressor (Voorhoeve et al., 2006).
Raver-Shapira et.al, JMolCell 2007
Fact creation through citations:
To investigate the possibility that miR-372 and miR-373 suppress the expression of LATS2, we...
Therefore, these results point to LATS2 as a mediator of the miR-372 and miR-373 effects on cell proliferation and tumorigenicity,
Voorhoeve et al, Cell, 2006:
Hypothesis
Implication
Cited Implication
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... two miRNAs, miRNA-372 and-373, function as potential novel oncogenes in testicular germ cell tumors by inhibition of LATS2 expression, which suggests that Lats2 is an important tumor suppressor (Voorhoeve et al., 2006).
Raver-Shapira et.al, JMolCell 2007
miR-372 and miR-373 target the Lats2 tumor suppressor (Voorhoeve et al., 2006)
Yabuta, JBioChem 2007:
Fact creation through citations:
To investigate the possibility that miR-372 and miR-373 suppress the expression of LATS2, we...
Therefore, these results point to LATS2 as a mediator of the miR-372 and miR-373 effects on cell proliferation and tumorigenicity,
Voorhoeve et al, Cell, 2006:
Hypothesis
Implication
Cited Implication
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... two miRNAs, miRNA-372 and-373, function as potential novel oncogenes in testicular germ cell tumors by inhibition of LATS2 expression, which suggests that Lats2 is an important tumor suppressor (Voorhoeve et al., 2006).
Raver-Shapira et.al, JMolCell 2007
miR-372 and miR-373 target the Lats2 tumor suppressor (Voorhoeve et al., 2006)
Yabuta, JBioChem 2007:
Fact creation through citations:
To investigate the possibility that miR-372 and miR-373 suppress the expression of LATS2, we...
Therefore, these results point to LATS2 as a mediator of the miR-372 and miR-373 effects on cell proliferation and tumorigenicity,
Voorhoeve et al, Cell, 2006:
Hypothesis
Implication
Cited Implication
Fact
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“[Y]ou can transform a fact into fiction or a fiction into fact just by adding or subtracting references [and data]”
– Bruno Latour, ‘Science in Action’,1987
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“[Y]ou can transform a fact into fiction or a fiction into fact just by adding or subtracting references [and data]”
– Bruno Latour, ‘Science in Action’,1987
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How is this rhetoric instantiated?Rhetorical goal
Utterance {Proposition} S = H, B
V = C, E
Indicate lack of knowledge
{The role of untranslated exons in the CCR3 gene} has not been studied.
NN 0
Evaluate other work
Recently, CCR3 has been shown to {be upregulated on neutrophils by interferons in vitro [..]}
N, D 3
Offer hypotheses
it is thought that {these transcription factors affect transcription of the gene through interactions with the RNA transcription complex.}
NN, R 2
Interpret results these data suggested that {5' untranslated exon 1 may have a regulatory function.}
A, D 2
Assess validity of interpretations
Since {this was not the case with other lines,} {we suspect {it is integration-site specific}}
A, D 1
State correspondence to expectations
While we expected {the transcript to be about 1 kb in size (Figure 4A),} {two bands ~4 and 5 kb were apparent.}
A, D 2, S+
Comparison to other work
It is important that {this data be viewed with {what is known about other myeloid-specific promoters,}}
A,R/NN/D
2, F+
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11
Eventually: trace roots of a claim: how many independent data points is it based on?
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11
PHC Growth arrestundergo
Eventually: trace roots of a claim: how many independent data points is it based on?
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11
PHC Growth arrestundergo
Eventually: trace roots of a claim: how many independent data points is it based on?
Paper A:implication
results
method
goal
fact
fact
data 1
data 2 data 3
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11
PHC Growth arrestundergo
Eventually: trace roots of a claim: how many independent data points is it based on?
Paper A:implication
results
method
goal
fact
fact
Paper B:
data 4
data 5 data 6
implication
results
method
goal
fact
fact
data 1
data 2 data 3
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11
PHC Growth arrestundergo
Eventually: trace roots of a claim: how many independent data points is it based on?
Paper A:implication
results
method
goal
fact
fact
Paper B:
data 4
data 5 data 6
implication
results
method
goal
fact
fact
data 1
data 2 data 3
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11
PHC Growth arrestundergo
Eventually: trace roots of a claim: how many independent data points is it based on?
Paper A:implication
results
method
goal
fact
fact
Paper B:
data 4
data 5 data 6
implication
results
method
goal
fact
fact
data 1
data 2 data 3
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11
PHC Growth arrestundergo
Eventually: trace roots of a claim: how many independent data points is it based on?
Paper A:implication
results
method
goal
fact
fact
Paper B:
data 4
data 5 data 6
implication
results
method
goal
fact
fact
underpinning
data 1
data 2 data 3
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11
PHC Growth arrestundergo
Eventually: trace roots of a claim: how many independent data points is it based on?
Paper A:implication
results
method
goal
fact
fact
Paper B:
data 4
data 5 data 6
implication
results
method
goal
fact
fact
data 1
data 2 data 3
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11
PHC Growth arrestundergo
Eventually: trace roots of a claim: how many independent data points is it based on?
Paper A:implication
results
method
goal
fact
fact
Paper B:
data 4
data 5 data 6
implication
results
method
goal
fact
fact
data 1
data 2 data 3
method link
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Scientific papers are stories, that persuade with data.
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Scientific papers are stories, that persuade with data.
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Scientific papers are stories, that persuade with data.
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Sometimes the link to data is good:
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And sometimes it’s not so good:
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And sometimes it’s not so good:
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And sometimes it’s not so good:
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And sometimes it’s not so good:
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Data-driven papers? Work done with Ed Hovy, Phil Bourne, Gully Burns and Cartic Ramakrishnan
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Data-driven papers? Work done with Ed Hovy, Phil Bourne, Gully Burns and Cartic Ramakrishnan
1. Research: Each item in the system has metadata (including provenance) and relations to other data items added to it.
metadata
metadata
metadata
metadata
metadata
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Data-driven papers? Work done with Ed Hovy, Phil Bourne, Gully Burns and Cartic Ramakrishnan
1. Research: Each item in the system has metadata (including provenance) and relations to other data items added to it.
metadata
metadata
metadata
metadata
metadata
2. Workflow: All data items created in the lab are added to a (lab-owned) workflow system.
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Data-driven papers? Work done with Ed Hovy, Phil Bourne, Gully Burns and Cartic Ramakrishnan
1. Research: Each item in the system has metadata (including provenance) and relations to other data items added to it.
metadata
metadata
metadata
metadata
metadata
2. Workflow: All data items created in the lab are added to a (lab-owned) workflow system.
Rats were subjected to two grueling tests(click on fig 2 to see underlying data). These results suggest that the neurological pain pro-
3. Authoring: A paper is written in an authoring tool which can pull data with provenance from the workflow tool in the appropriate representation into the document.
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Data-driven papers? Work done with Ed Hovy, Phil Bourne, Gully Burns and Cartic Ramakrishnan
1. Research: Each item in the system has metadata (including provenance) and relations to other data items added to it.
metadata
metadata
metadata
metadata
metadata
2. Workflow: All data items created in the lab are added to a (lab-owned) workflow system.
4. Editing and review: Once the co-authors agree, the paper is ‘exposed’ to the editors, who in turn expose it to reviewers. Reports are stored in the authoring/editing system, the paper gets updated, until it is validated.
Review
Edit
Revise
Rats were subjected to two grueling tests(click on fig 2 to see underlying data). These results suggest that the neurological pain pro-
3. Authoring: A paper is written in an authoring tool which can pull data with provenance from the workflow tool in the appropriate representation into the document.
![Page 54: Reengineering the scientific research paper](https://reader033.vdocuments.net/reader033/viewer/2022052618/554ea5a7b4c905977e8b48db/html5/thumbnails/54.jpg)
5. Publishing and distribution: When a paper is published, a collection of validated information is exposed to the world. It remains connected to its related data item, and its heritage can be traced.
Data-driven papers? Work done with Ed Hovy, Phil Bourne, Gully Burns and Cartic Ramakrishnan
1. Research: Each item in the system has metadata (including provenance) and relations to other data items added to it.
metadata
metadata
metadata
metadata
metadata
2. Workflow: All data items created in the lab are added to a (lab-owned) workflow system.
4. Editing and review: Once the co-authors agree, the paper is ‘exposed’ to the editors, who in turn expose it to reviewers. Reports are stored in the authoring/editing system, the paper gets updated, until it is validated.
Review
Edit
Revise
Rats were subjected to two grueling tests(click on fig 2 to see underlying data). These results suggest that the neurological pain pro-
3. Authoring: A paper is written in an authoring tool which can pull data with provenance from the workflow tool in the appropriate representation into the document.
![Page 55: Reengineering the scientific research paper](https://reader033.vdocuments.net/reader033/viewer/2022052618/554ea5a7b4c905977e8b48db/html5/thumbnails/55.jpg)
5. Publishing and distribution: When a paper is published, a collection of validated information is exposed to the world. It remains connected to its related data item, and its heritage can be traced.
Some other publisher
6. User applications: distributed applications run on this ‘exposed data’ universe.
Data-driven papers? Work done with Ed Hovy, Phil Bourne, Gully Burns and Cartic Ramakrishnan
1. Research: Each item in the system has metadata (including provenance) and relations to other data items added to it.
metadata
metadata
metadata
metadata
metadata
2. Workflow: All data items created in the lab are added to a (lab-owned) workflow system.
4. Editing and review: Once the co-authors agree, the paper is ‘exposed’ to the editors, who in turn expose it to reviewers. Reports are stored in the authoring/editing system, the paper gets updated, until it is validated.
Review
Edit
Revise
Rats were subjected to two grueling tests(click on fig 2 to see underlying data). These results suggest that the neurological pain pro-
3. Authoring: A paper is written in an authoring tool which can pull data with provenance from the workflow tool in the appropriate representation into the document.
![Page 56: Reengineering the scientific research paper](https://reader033.vdocuments.net/reader033/viewer/2022052618/554ea5a7b4c905977e8b48db/html5/thumbnails/56.jpg)
One step: encouraging submission of structured workflows
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Another step: ScienceDirect app store
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Another step: ScienceDirect app store
- Eclipse SDK platform accessing all ScienceDirect/Scopus content-Build applications on top of content-Offer to users in marketplace
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A third step: Executable Paper ChallengeGoal: invite computer science community to help develop formats that:
- add executable files and reproducible data to computer science papers;
- handle storage and validation of very large files
- help validation of data and code, and decrease the reviewer’s workload
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A third step: Executable Paper ChallengeGoal: invite computer science community to help develop formats that:
- add executable files and reproducible data to computer science papers;
- handle storage and validation of very large files
- help validation of data and code, and decrease the reviewer’s workload
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In Summary:
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In Summary:1. Stories:
- ORB, Satellite: link to any part of content - bring it on!
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In Summary:1. Stories:
- ORB, Satellite: link to any part of content - bring it on!
2. Persuasion:
- Logical structure for biological propositions; trace a claim through successive citations
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In Summary:1. Stories:
- ORB, Satellite: link to any part of content - bring it on!
2. Persuasion:
- Logical structure for biological propositions; trace a claim through successive citations
3. Data:
- Better data linking, better structuring of methods.
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In Summary:1. Stories:
- ORB, Satellite: link to any part of content - bring it on!
2. Persuasion:
- Logical structure for biological propositions; trace a claim through successive citations
3. Data:
- Better data linking, better structuring of methods.
In conclusion: is the research paper going away?
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In Summary:1. Stories:
- ORB, Satellite: link to any part of content - bring it on!
2. Persuasion:
- Logical structure for biological propositions; trace a claim through successive citations
3. Data:
- Better data linking, better structuring of methods.
In conclusion: is the research paper going away?
I don’t think so! But it will be:
- Structured better: authors will need to justify claims directly
- Connected better: more traceable, better links to data and workflow components, and to other work
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Thank you!
W3C group on Discourse Structure: http://www.w3.org/wiki/HCLSIG/SWANSIOC SciVerse: http://developer.sciverse.comPangea project: http://bit.ly/98haOw Parsing rhetoric: http://elsatglabs.com/labs/anita/Fact creation demo: http://elsatglabs.com/labs/anita/demos/LATSDemo102007/Methods Navigator: http://www.methodsnavigator.comSciVerse APIs: http://developer.sciverse.comExecutable Paper Challenge: http://www.executablepapers.com
Or mail me at: Anita de Waard, [email protected]