Stories that persuade with data

What is inside our full-text articles, and how do we improve access to it?Or: Stories, that persuade with data.

Biocreative III Publishers PanelSeptember 13, 2010

Anita de Waard, a.dewaard@elsevier.com Disruptive Technologies Director, Elsevier Labs

Model of a paper: “Scientific articles are stories...

2

The Story of Goldilocks and the Three Bears

Story Grammar 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 domainShe 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 cells

So, 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.  

Episode 1

Data (Figure 1F),

Model of a paper: “Scientific articles are stories...

2

The Story of Goldilocks and the Three Bears

Story Grammar 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 domainShe 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 cells

So, 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.  

Episode 1

Data (Figure 1F),

“...that persuade (editors/authors/readers!)...”

3

“...that persuade (editors/authors/readers!)...”

3

Aristotle QuintilianQuintilian Scientific Paper

prooimion Introduction/ exordium

The introduction of a speech, where one announces the subject and purpose of the discourse, and where one usually employs the persuasive appeal to ethos in order to establish credibility with the audience.

Introduction: positioning

prothesisStatement of Facts/narratio

The speaker here provides a narrative account of what has happened and generally explains the nature of the case.

Introduction: research question

  Summary/ propostitio

The propositio provides a brief summary of what one is about to speak on, or concisely puts forth the charges or accusation. Summary of contents

pistis Proof/ confirmatio

The main body of the speech where one offers logical arguments as proof. The appeal to logos is emphasized here.

Results

  Refutation/ refutatio

As the name connotes, this section of a speech was devoted to answering the counterarguments of one's opponent. Related Work

epilogos peroratio Following the refutatio and concluding the classical oration, the peroratio conventionally employed appeals through pathos, and often included a summing up.

Discussion: summary, implications.

“...that persuade (editors/authors/readers!)...”

3

Aristotle QuintilianQuintilian Scientific Paper

prooimion Introduction/ exordium

The introduction of a speech, where one announces the subject and purpose of the discourse, and where one usually employs the persuasive appeal to ethos in order to establish credibility with the audience.

Introduction: positioning

prothesisStatement of Facts/narratio

The speaker here provides a narrative account of what has happened and generally explains the nature of the case.

Introduction: research question

  Summary/ propostitio

The propositio provides a brief summary of what one is about to speak on, or concisely puts forth the charges or accusation. Summary of contents

pistis Proof/ confirmatio

The main body of the speech where one offers logical arguments as proof. The appeal to logos is emphasized here.

Results

  Refutation/ refutatio

As the name connotes, this section of a speech was devoted to answering the counterarguments of one's opponent. Related Work

epilogos peroratio Following the refutatio and concluding the classical oration, the peroratio conventionally employed appeals through pathos, and often included a summing up.

Discussion: summary, implications.

“... with data.”

4

“... with data.”

4

“... with data.”

4

So how do we improve access to these?

5

So how do we improve access to these?

5

1.1. Better access to ‘story’ elements:

So how do we improve access to these?

5

1.1. Better access to ‘story’ elements: • Learn from Fairy Tale annotation/Proppian Markup?

So how do we improve access to these?

5

1.1. Better access to ‘story’ elements: • Learn from Fairy Tale annotation/Proppian Markup?

So how do we improve access to these?

5

1.1. Better access to ‘story’ elements: • Learn from Fairy Tale annotation/Proppian Markup?

So how do we improve access to these?

5

1.1. Better access to ‘story’ elements: • Learn from Fairy Tale annotation/Proppian Markup?• W3C HCLS SiG Scientific discourse structure:

So how do we improve access to these?

5

1.1. Better access to ‘story’ elements: • Learn from Fairy Tale annotation/Proppian Markup?• W3C HCLS SiG Scientific discourse structure:

1.2. Element access through Linked Data:

1.2. Element access through Linked Data:

<ce:section id=#123>

1.2. Element access through Linked Data:

<ce:section id=#123> mice like cheesethis says

1.2. Element access through Linked Data:

<ce:section id=#123>

said @anita on September 8, 2010

mice like cheesethis says

but we all know she was wrong then

1.2. Element access through Linked Data:

<ce:section id=#123>

said @anita on September 8, 2010

mice like cheesethis says

but we all know she was wrong then

1.2. Element access through Linked Data:

<ce:section id=#123>

said @anita on September 8, 2010

the xml is fixed, but the structure is open!

mice like cheesethis says

allows for layers of annotation

but we all know she was wrong then

1.2. Element access through Linked Data:

<ce:section id=#123>

said @anita on September 8, 2010

the xml is fixed, but the structure is open!

mice like cheesethis says

2.1. Improve access to persuasive elements:Identify key rhetorical elements in scientific text:

7

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.

2.1. Improve access to persuasive elements:Identify key rhetorical elements in scientific text:

7

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.

2.1. Improve access to persuasive elements:Identify key rhetorical elements in scientific text:

7

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

2.1. Improve access to persuasive elements:Identify key rhetorical elements in scientific text:

7

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

2.1. Improve access to persuasive elements:Identify key rhetorical elements in scientific text:

7

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

2.1. Improve access to persuasive elements:Identify key rhetorical elements in scientific text:

7

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

2.1. Improve access to persuasive elements:Identify key rhetorical elements in scientific text:

7

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

2.1. Improve access to persuasive elements:Identify key rhetorical elements in scientific text:

7

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

2.1. Improve access to persuasive elements:Identify key rhetorical elements in scientific text:

7

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

2.1. Improve access to persuasive elements:Identify key rhetorical elements in scientific text:

7

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

2.1. Improve access to persuasive elements:Identify key rhetorical elements in scientific text:

7

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

2.2. Realms in experimental discourse

(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,

2.2. Realms in experimental discourse

(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) a. To exclude that

2.2. Realms in experimental discourse

(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

2.2. Realms in experimental discourse

(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

2.2. Realms in experimental discourse

(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

2.2. Realms in experimental discourse

(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’

(2) a. To exclude that (3) b. suggesting that

2.2. Realms in experimental discourse

(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

(2) a. To exclude that (3) b. suggesting that

2.2. Realms in experimental discourse

(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

2.2. Realms in experimental discourse

2.3. Hypotheses, Evidence and Relationships:

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2.3. Hypotheses, Evidence and Relationships:

9

2.3. Hypotheses, Evidence and Relationships:

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2.3. Hypotheses, Evidence and Relationships:

9

2.3. Hypotheses, Evidence and Relationships:

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2.3. Hypotheses, Evidence and Relationships:

Hypothesis 22: Intramembrenous Aβ dimer may be toxic.

Derived from: POSTAT_CONTRIBUTION(This essay explores the possibility that a fraction of these Abeta peptides never leave the membrane lipid bilayer after they are generated, but instead exert their toxic effects by competing with and compromising the functions of intramembranous segments of membrane-bound proteins that serve many critical functions.

9

2.3. Hypotheses, Evidence and Relationships:

9

2.3. Hypotheses, Evidence and Relationships:

9

• Collective of groups working on representing scientific text as – discourse elements– linked by rhetorical relationships– connected to data

2.3. Hypotheses, Evidence and Relationships:

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• Collective of groups working on representing scientific text as – discourse elements– linked by rhetorical relationships– connected to data

• Current efforts: – W3C HCLS SiG: development of a Rhetorical Document Structure– Unification of ScholOnto, CiTO, SWAN, SALT relations

2.3. Hypotheses, Evidence and Relationships:

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• Collective of groups working on representing scientific text as – discourse elements– linked by rhetorical relationships– connected to data

• Current efforts: – W3C HCLS SiG: development of a Rhetorical Document Structure– Unification of ScholOnto, CiTO, SWAN, SALT relations

• Developing an Annotation Framework with Harvard/MGH:– Access to collection of full-text content on Alzheimer’s– Allow standoff annotation through Harvard’s Annotation Ontology– Run several hypothesis/event identification tools - access through

U-Compare, UMIA, SciKnowMine– Allow layering of annotations– Test with users in Alzheimer community!

2.4. Three dimensions of annotation:

measure

2.4. Three dimensions of annotation:

measure

document

claim

triple

entity

collection

Granularity2.4. Three dimensions of annotation:

measure

document

claim

triple

entity

collection

Granularity2.4. Three dimensions of annotation:

automated

manual

semi-automated

Meansmeasure

document

claim

triple

entity

collection

Granularity2.4. Three dimensions of annotation:

reader/curator/data miningtypesetter/productionauthor/editor

Moment

automated

manual

semi-automated

Meansmeasure

document

claim

triple

entity

collection

Granularity2.4. Three dimensions of annotation:

Entity Markupreader/curator/data miningtypesetter/productionauthor/editor

Moment

automated

manual

semi-automated

Meansmeasure

document

claim

triple

entity

collection

Granularity2.4. Three dimensions of annotation:

Hypothesis markup

Entity Markupreader/curator/data miningtypesetter/productionauthor/editor

Moment

automated

manual

semi-automated

Meansmeasure

document

claim

triple

entity

collection

Granularity2.4. Three dimensions of annotation:

Hypothesis markup

Entity Markupreader/curator/data miningtypesetter/productionauthor/editor

Moment

automated

manual

semi-automated

Meansmeasure

3.1. Research data

... gets created...

3.1. Research data

... gets created... ... and destroyed!

3.1. Research data

3.2. Data-driven papers? Work done with Ed Hovy, Phil Bourne, Gully Burns and Cartic Ramakrishnan

3.2. 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

3.2. 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.

3.2. 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.

3.2. 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

EditRevise

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.

3.2. 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

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.

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

EditRevise

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.

Some other publisher

6. User applications: distributed applications run on this ‘exposed data’ universe.

3.2. 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

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.

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

EditRevise

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.

3.3. Small step: ScienceDirect app store

3.4. Social Change! Some next steps:

3.4. Social Change! Some next steps:

• January 2011: ‘Beyond the PDF’ workshop, Phil Bourne: linking data to papers; develop virtual community around that

3.4. Social Change! Some next steps:

• January 2011: ‘Beyond the PDF’ workshop, Phil Bourne: linking data to papers; develop virtual community around that

• June 2011: ‘Executable Paper Challenge’ @ ICCS: ask computer scientists to submit ideas for ‘executable papers’ - embedded code or data

3.4. Social Change! Some next steps:

• January 2011: ‘Beyond the PDF’ workshop, Phil Bourne: linking data to papers; develop virtual community around that

• June 2011: ‘Executable Paper Challenge’ @ ICCS: ask computer scientists to submit ideas for ‘executable papers’ - embedded code or data

• August 2011: Dagstuhl Workshop ‘Future of Research Communications’ (Ed Hovy, Ivan Herman, Tim Clark, Anita de Waard):

3.4. Social Change! Some next steps:

• January 2011: ‘Beyond the PDF’ workshop, Phil Bourne: linking data to papers; develop virtual community around that

• June 2011: ‘Executable Paper Challenge’ @ ICCS: ask computer scientists to submit ideas for ‘executable papers’ - embedded code or data

• August 2011: Dagstuhl Workshop ‘Future of Research Communications’ (Ed Hovy, Ivan Herman, Tim Clark, Anita de Waard):

–Involve key parties (scientists, publishers, funding bodies, libraries) to map out main bottlenecks

3.4. Social Change! Some next steps:

• January 2011: ‘Beyond the PDF’ workshop, Phil Bourne: linking data to papers; develop virtual community around that

• June 2011: ‘Executable Paper Challenge’ @ ICCS: ask computer scientists to submit ideas for ‘executable papers’ - embedded code or data

• August 2011: Dagstuhl Workshop ‘Future of Research Communications’ (Ed Hovy, Ivan Herman, Tim Clark, Anita de Waard):

–Involve key parties (scientists, publishers, funding bodies, libraries) to map out main bottlenecks

–Write white paper

3.4. Social Change! Some next steps:

• January 2011: ‘Beyond the PDF’ workshop, Phil Bourne: linking data to papers; develop virtual community around that

• June 2011: ‘Executable Paper Challenge’ @ ICCS: ask computer scientists to submit ideas for ‘executable papers’ - embedded code or data

• August 2011: Dagstuhl Workshop ‘Future of Research Communications’ (Ed Hovy, Ivan Herman, Tim Clark, Anita de Waard):

–Involve key parties (scientists, publishers, funding bodies, libraries) to map out main bottlenecks

–Write white paper–Implement?!

3.4. Social Change! Some next steps:

Questions? Interested in collaboration?

a.dewaard@elsevier.com

http://elsatglabs.com/labs/anita

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