Download - Xerox2009
Identifying Biological Knowledge: Three Possible Strategies
Anita de Waard
Disruptive Technologies Director, Elsevier Labs, Amsterdam
Casimir Researcher,
UiL-OTS, Utrecht University
XRCE, Grenoble, 24 September 2009
Overview
Overview
Problem: too much discourse, tools are not yet good enough...
Overview
Problem: too much discourse, tools are not yet good enough...
1. First attempt: allow authors to validate entities
Overview
Problem: too much discourse, tools are not yet good enough...
1. First attempt: allow authors to validate entities
2. Second attempt: discourse analysis
Overview
Problem: too much discourse, tools are not yet good enough...
1. First attempt: allow authors to validate entities
2. Second attempt: discourse analysis
3. Third attempt: collaboration to identify hypotheses
Why Study Biological Discourse?
Why Study Biological Discourse?
- There is too much of it!
Why Study Biological Discourse?
- There is too much of it!
Why Study Biological Discourse?
- There is too much of it!
- Text mining and ‘fact extraction’ techniques are gaining ground to tame thistangle
Why Study Biological Discourse?
- There is too much of it!
- Text mining and ‘fact extraction’ techniques are gaining ground to tame thistangle
- Emerging area of biologicalnatural language processing (BioNLP): subfield of computational linguistics
Why Study Biological Discourse?
- There is too much of it!
- Text mining and ‘fact extraction’ techniques are gaining ground to tame thistangle
- Emerging area of biologicalnatural language processing (BioNLP): subfield of computational linguistics
- Main focus: identifying biological entities (genes, proteins, drugs) and their relationships
Example state of the art: MEDIE
Example state of the art: MEDIE
Alteration of nm23, P53, and S100A4 expression may contribute to the development of gastric
Example state of the art: MEDIE
Previous studies have implicated miR-34a as a tumor suppressor gene whose transcription is activated by p53.
Alteration of nm23, P53, and S100A4 expression may contribute to the development of gastric
Example state of the art: MEDIE
Previous studies have implicated miR-34a as a tumor suppressor gene whose transcription is activated by p53.
Alteration of nm23, P53, and S100A4 expression may contribute to the development of gastric
Add this knowledge during authoring?
First attempt: allow authors to validate entities
Improve time + quality of knowledgebase entry
Improve time + quality of knowledgebase entry
- For database curators: save time and money
Improve time + quality of knowledgebase entry
- For database curators: save time and money
- For authors: lower the threshold to submitting papers with metadata
Improve time + quality of knowledgebase entry
- For database curators: save time and money
- For authors: lower the threshold to submitting papers with metadata
- Structured Digital Abstract: an editorial experiment to increase the reach of online published articles
Improve time + quality of knowledgebase entry
- For database curators: save time and money
- For authors: lower the threshold to submitting papers with metadata
- Structured Digital Abstract: an editorial experiment to increase the reach of online published articles
- SDA encodes in a schema information contained in the article
D-07-02772Testis-specific poly(A) polymerase (TPAP) is a cytoplasmic poly(A) polymerase that is highly expressed in round spermatids. We identified germ cell-specific gene 1 (GSG1) as a TPAP interaction partner protein using yeast two-hybrid and coimmunoprecipitation assays. Subcellular fractionation analysis showed that GSG1 is exclusively localized in the endoplasmic reticulum (ER) of mouse testis where TPAP is also present. In NIH3T3 cells cotransfected with TPAP and GSG1, both proteins colocalize in the ER. Moreover, expression of GSG1 stimulates TPAP targeting to the ER, suggesting that interactions between the two proteins lead to the redistribution of TPAP from the cytosol to the ER.
MINT-6168263:Gsg1 (uniprotkb:Q8R1W2), TPAP (uniprotkb:Q9WVP6) and Calmegin (uniprotkb:P52194) colocalize (MI:0403) by cosedimentation (MI:0027)
MINT-6168204, MINT-6168178:Gsg1 (uniprotkb:Q8R1W2) and TPAP (uniprotkb:Q9WVP6) colocalize (MI:0403) by fluorescence microscopy (MI:0416)
MINT-6167930:Gsg1 (uniprotkb:Q8R1W2) physically interacts (MI:0218) with TPAP (uniprotkb:Q9WVP6) by two-hybrid (MI:0018)
D-07-02772Testis-specific poly(A) polymerase (TPAP) is a cytoplasmic poly(A) polymerase that is highly expressed in round spermatids. We identified germ cell-specific gene 1 (GSG1) as a TPAP interaction partner protein using yeast two-hybrid and coimmunoprecipitation assays. Subcellular fractionation analysis showed that GSG1 is exclusively localized in the endoplasmic reticulum (ER) of mouse testis where TPAP is also present. In NIH3T3 cells cotransfected with TPAP and GSG1, both proteins colocalize in the ER. Moreover, expression of GSG1 stimulates TPAP targeting to the ER, suggesting that interactions between the two proteins lead to the redistribution of TPAP from the cytosol to the ER.
MINT-6168263:Gsg1 (uniprotkb:Q8R1W2), TPAP (uniprotkb:Q9WVP6) and Calmegin (uniprotkb:P52194) colocalize (MI:0403) by cosedimentation (MI:0027)
MINT-6168204, MINT-6168178:Gsg1 (uniprotkb:Q8R1W2) and TPAP (uniprotkb:Q9WVP6) colocalize (MI:0403) by fluorescence microscopy (MI:0416)
MINT-6167930:Gsg1 (uniprotkb:Q8R1W2) physically interacts (MI:0218) with TPAP (uniprotkb:Q9WVP6) by two-hybrid (MI:0018)
D-07-02772Testis-specific poly(A) polymerase (TPAP) is a cytoplasmic poly(A) polymerase that is highly expressed in round spermatids. We identified germ cell-specific gene 1 (GSG1) as a TPAP interaction partner protein using yeast two-hybrid and coimmunoprecipitation assays. Subcellular fractionation analysis showed that GSG1 is exclusively localized in the endoplasmic reticulum (ER) of mouse testis where TPAP is also present. In NIH3T3 cells cotransfected with TPAP and GSG1, both proteins colocalize in the ER. Moreover, expression of GSG1 stimulates TPAP targeting to the ER, suggesting that interactions between the two proteins lead to the redistribution of TPAP from the cytosol to the ER.
MINT-6168263:Gsg1 (uniprotkb:Q8R1W2), TPAP (uniprotkb:Q9WVP6) and Calmegin (uniprotkb:P52194) colocalize (MI:0403) by cosedimentation (MI:0027)
MINT-6168204, MINT-6168178:Gsg1 (uniprotkb:Q8R1W2) and TPAP (uniprotkb:Q9WVP6) colocalize (MI:0403) by fluorescence microscopy (MI:0416)
MINT-6167930:Gsg1 (uniprotkb:Q8R1W2) physically interacts (MI:0218) with TPAP (uniprotkb:Q9WVP6) by two-hybrid (MI:0018)
D-07-02772Testis-specific poly(A) polymerase (TPAP) is a cytoplasmic poly(A) polymerase that is highly expressed in round spermatids. We identified germ cell-specific gene 1 (GSG1) as a TPAP interaction partner protein using yeast two-hybrid and coimmunoprecipitation assays. Subcellular fractionation analysis showed that GSG1 is exclusively localized in the endoplasmic reticulum (ER) of mouse testis where TPAP is also present. In NIH3T3 cells cotransfected with TPAP and GSG1, both proteins colocalize in the ER. Moreover, expression of GSG1 stimulates TPAP targeting to the ER, suggesting that interactions between the two proteins lead to the redistribution of TPAP from the cytosol to the ER.
MINT-6168263:Gsg1 (uniprotkb:Q8R1W2), TPAP (uniprotkb:Q9WVP6) and Calmegin (uniprotkb:P52194) colocalize (MI:0403) by cosedimentation (MI:0027)
MINT-6168204, MINT-6168178:Gsg1 (uniprotkb:Q8R1W2) and TPAP (uniprotkb:Q9WVP6) colocalize (MI:0403) by fluorescence microscopy (MI:0416)
MINT-6167930:Gsg1 (uniprotkb:Q8R1W2) physically interacts (MI:0218) with TPAP (uniprotkb:Q9WVP6) by two-hybrid (MI:0018)
D-07-02772Testis-specific poly(A) polymerase (TPAP) is a cytoplasmic poly(A) polymerase that is highly expressed in round spermatids. We identified germ cell-specific gene 1 (GSG1) as a TPAP interaction partner protein using yeast two-hybrid and coimmunoprecipitation assays. Subcellular fractionation analysis showed that GSG1 is exclusively localized in the endoplasmic reticulum (ER) of mouse testis where TPAP is also present. In NIH3T3 cells cotransfected with TPAP and GSG1, both proteins colocalize in the ER. Moreover, expression of GSG1 stimulates TPAP targeting to the ER, suggesting that interactions between the two proteins lead to the redistribution of TPAP from the cytosol to the ER.
MINT-6168263:Gsg1 (uniprotkb:Q8R1W2), TPAP (uniprotkb:Q9WVP6) and Calmegin (uniprotkb:P52194) colocalize (MI:0403) by cosedimentation (MI:0027)
MINT-6168204, MINT-6168178:Gsg1 (uniprotkb:Q8R1W2) and TPAP (uniprotkb:Q9WVP6) colocalize (MI:0403) by fluorescence microscopy (MI:0416)
MINT-6167930:Gsg1 (uniprotkb:Q8R1W2) physically interacts (MI:0218) with TPAP (uniprotkb:Q9WVP6) by two-hybrid (MI:0018)
How? Word Plugin
5
How? Word Plugin
- Okkam4MsW: a Microsoft Word plugin interact with Web Services performing NLP and semantic technologies to detect entities and contextual information
- The OKKAM repository is queried to get the right OKKAM id and alternative ids (UniProt in this case)
5
How? Word Plugin
- Okkam4MsW: a Microsoft Word plugin interact with Web Services performing NLP and semantic technologies to detect entities and contextual information
- The OKKAM repository is queried to get the right OKKAM id and alternative ids (UniProt in this case)
5
OKKAM Entity Editor in MS Word
OKKAM Entity Editor in MS Word
OKKAM Entity Editor in MS Word
OKKAM Entity Editor in MS Word
Second attempt:
discourse analysis
What else is wrong with MEDIE?
What else is wrong with MEDIE?
Alteration of nm23, P53, and S100A4 expression may contribute to the development of gastric
What else is wrong with MEDIE?
Previous studies have implicated miR-34a as a tumor suppressor gene whose transcription is activated by p53.
Alteration of nm23, P53, and S100A4 expression may contribute to the development of gastric
What else is wrong with MEDIE?
Previous studies have implicated miR-34a as a tumor suppressor gene whose transcription is activated by p53.
Alteration of nm23, P53, and S100A4 expression may contribute to the development of gastric
without some idea of the status of the sentence, it cannot be interpreted!
Discourse Analysis
Discourse AnalysisUnderlying model of text mining systems:
- Scientific paper is ‘statement of pertinent facts’
- So: finding entities and relationships will give you a summary of the knowledge within the paper
- However, information extracted this way is not very useful....
Discourse AnalysisUnderlying model of text mining systems:
- Scientific paper is ‘statement of pertinent facts’
- So: finding entities and relationships will give you a summary of the knowledge within the paper
- However, information extracted this way is not very useful....
Proposed approach: treat scientific paper as a persuasive text: specific genre, with genre characteristics and allowed persuasive techniques:
- ‘these results suggest’ (depersonification)
- ‘as fig. 2a shows’ (evidence is in the data)
- ‘oncogenes produce a stress response [Serrano, 2003]’
References and data form a “folded array of successive defense lines, behind which scientists ensconce themselves” (Latour, 1986)
Overall Research Questions
Overall Research Questions
i. How can we model the discourse/suasive moves in a biological paper?
Overall Research Questions
i. How can we model the discourse/suasive moves in a biological paper?
ii. Can this model help enable automated epistemic markup?
Overall Research Questions
i. How can we model the discourse/suasive moves in a biological paper?
ii. Can this model help enable automated epistemic markup?
iii. Can it improve knowledge representations of collections of papers?
Discourse analysis
Discourse analysis
Segmentation and classification:
Discourse analysis
Segmentation and classification:
1. Parse text into discourse segments (edu’s) containing a single rhetorical move (if possible...)
Discourse analysis
Segmentation and classification:
1. Parse text into discourse segments (edu’s) containing a single rhetorical move (if possible...)
2. Determine categories or types of discourse segments that have similar semantic/pragmatic properties
Discourse analysis
Segmentation and classification:
1. Parse text into discourse segments (edu’s) containing a single rhetorical move (if possible...)
2. Determine categories or types of discourse segments that have similar semantic/pragmatic properties
3. Look at a number of linguistic characteristics and see if these segment types share those characteristics.
Segmentation
Segmentation
Goal: ‘one new thought per segment’:
Figure 4A shows that following RASV12 stimulation, p53 was stabilized and activated, and its target gene, p21cip1, was induced in all cases, indicating an intact p53 pathway in these cells.
Segmentation
Goal: ‘one new thought per segment’:
a. Figure 4a shows thatb. following RASV12 stimulationc. p53 was stabilized and activatedd. and the target gene, p21cip1, was induced in all cases,e. indicating an intact p53 pathway in these cells.
Figure 4A shows that following RASV12 stimulation, p53 was stabilized and activated, and its target gene, p21cip1, was induced in all cases, indicating an intact p53 pathway in these cells.
Segmentation
Goal: ‘one new thought per segment’:
a. Figure 4a shows thatb. following RASV12 stimulationc. p53 was stabilized and activatedd. and the target gene, p21cip1, was induced in all cases,e. indicating an intact p53 pathway in these cells.
Figure 4A shows that following RASV12 stimulation, p53 was stabilized and activated, and its target gene, p21cip1, was induced in all cases, indicating an intact p53 pathway in these cells.
IntratextualMethod
Result Result
Implication
Segmentation
Goal: ‘one new thought per segment’:
a. Figure 4a shows thatb. following RASV12 stimulationc. p53 was stabilized and activatedd. and the target gene, p21cip1, was induced in all cases,e. indicating an intact p53 pathway in these cells.
Figure 4A shows that following RASV12 stimulation, p53 was stabilized and activated, and its target gene, p21cip1, was induced in all cases, indicating an intact p53 pathway in these cells.
IntratextualMethod
Result Result
Implication
Segmentation
Goal: ‘one new thought per segment’:
Segment Types
Segment TypesSegment Description Example
Fact a known fact, generally without explicit citation
mature miR-373 is a homolog of miR-372
Hypothesis a proposed idea, not supported by evidence
This could for instance be a result of high mdm2 levels
Problem unresolved, contradictory, or unclear issue
However, further investigation is required to demonstrate the exact mechanism of LATS2 actionGoal research goal To identify novel functions of miRNAs,
Method experimental method Using fluorescence microscopy and luciferase assays,
Result a restatement of the outcome of an experiment
all constructs yielded high expression levels of mature miRNAs
Implication an interpretation of the results, in light of earlier hypotheses and facts
our procedure is sensitive enough to detect mild growth differences
Segment TypesSegment Description Example
Fact a known fact, generally without explicit citation
mature miR-373 is a homolog of miR-372
Hypothesis a proposed idea, not supported by evidence
This could for instance be a result of high mdm2 levels
Problem unresolved, contradictory, or unclear issue
However, further investigation is required to demonstrate the exact mechanism of LATS2 actionGoal research goal To identify novel functions of miRNAs,
Method experimental method Using fluorescence microscopy and luciferase assays,
Result a restatement of the outcome of an experiment
all constructs yielded high expression levels of mature miRNAs
Implication an interpretation of the results, in light of earlier hypotheses and facts
our procedure is sensitive enough to detect mild growth differences
‘Other-segments’, related to (referenced) other work:
Segment TypesSegment Description Example
Fact a known fact, generally without explicit citation
mature miR-373 is a homolog of miR-372
Hypothesis a proposed idea, not supported by evidence
This could for instance be a result of high mdm2 levels
Problem unresolved, contradictory, or unclear issue
However, further investigation is required to demonstrate the exact mechanism of LATS2 actionGoal research goal To identify novel functions of miRNAs,
Method experimental method Using fluorescence microscopy and luciferase assays,
Result a restatement of the outcome of an experiment
all constructs yielded high expression levels of mature miRNAs
Implication an interpretation of the results, in light of earlier hypotheses and facts
our procedure is sensitive enough to detect mild growth differences
‘Other-segments’, related to (referenced) other work:
Regulatory segments, acting as matrix sentences framing other segments:
Linguistic and structural properties
Linguistic and structural properties
Linguistic and structural properties1. Position in text
- Section of the paper (Introduction, Results, Discussion)
- Beginning/middle/end of section
- First/second/third part of sentence
Linguistic and structural properties1. Position in text
- Section of the paper (Introduction, Results, Discussion)
- Beginning/middle/end of section
- First/second/third part of sentence
2. Verb:
- Tense, aspect, voice
- Verb class: Thing (increase), Thing-Thing (inhibit), Person-Thing (examine, observe, operate, implicate), Person: Report
- Lexicon
Linguistic and structural properties1. Position in text
- Section of the paper (Introduction, Results, Discussion)
- Beginning/middle/end of section
- First/second/third part of sentence
2. Verb:
- Tense, aspect, voice
- Verb class: Thing (increase), Thing-Thing (inhibit), Person-Thing (examine, observe, operate, implicate), Person: Report
- Lexicon
3. Metadiscourse markers [Hyland, 2003]:
- Connectives
- Endophorics, Evidentials
- Hedges, Boosters
- Person markers
Results: Section and Sequence
Results: Section and Sequence
1. Voorhoeve, 2006: Cell - 427 segments
Results: Section and Sequence
1. Voorhoeve, 2006: Cell - 427 segments
2. Louiseau, 2008: European Neuropsychopharmacology - 281 segments
Results: Section and Sequence
1. Voorhoeve, 2006: Cell - 427 segments
2. Louiseau, 2008: European Neuropsychopharmacology - 281 segments
- Introduction (90): Other-Result (24), Other-Implication (11), Problem (9), Fact (8)
Results: Section and Sequence
1. Voorhoeve, 2006: Cell - 427 segments
2. Louiseau, 2008: European Neuropsychopharmacology - 281 segments
- Introduction (90): Other-Result (24), Other-Implication (11), Problem (9), Fact (8)
- Result (334): Goal (26) -> Method (68) -> Result (105) -> Reg-Implication (23) ->Implication (50)
Results: Section and Sequence
1. Voorhoeve, 2006: Cell - 427 segments
2. Louiseau, 2008: European Neuropsychopharmacology - 281 segments
- Introduction (90): Other-Result (24), Other-Implication (11), Problem (9), Fact (8)
- Result (334): Goal (26) -> Method (68) -> Result (105) -> Reg-Implication (23) ->Implication (50)
- Discussion (187):Implication (27), Result (21), Other-Result (24), Hypothesis (19), Problem (17)
Results: Verb Tense
Results: Verb Tense
- Realm of the Present: Fact (82%), Hypothesis (71%), Implication (62%)
Results: Verb Tense
- Realm of the Present: Fact (82%), Hypothesis (71%), Implication (62%)
- Realm of the Past: Result (82%), Method (76%) - 50% Passive, of Method 50% Past Perfect
Results: Verb Tense
- Realm of the Present: Fact (82%), Hypothesis (71%), Implication (62%)
- Realm of the Past: Result (82%), Method (76%) - 50% Passive, of Method 50% Past Perfect
- Realm of the Modal: 44% in Hypothesis
Results: Verb Tense
- Realm of the Present: Fact (82%), Hypothesis (71%), Implication (62%)
- Realm of the Past: Result (82%), Method (76%) - 50% Passive, of Method 50% Past Perfect
- Realm of the Modal: 44% in Hypothesis
- Realm of the To-Infinitive: 50% is Goal, 75% of Goal is to-infinitive (Purpose Clause)
Results: Verb Type
Results: Verb Type
- Thing - Thing: high in experimental (Method, Result) and conceptual (Problem, Hypothesis, Fact, Implication) segments:
‣ Need to differentiate between ‘concept’ things and ‘experimental’ things!
Results: Verb Type
- Thing - Thing: high in experimental (Method, Result) and conceptual (Problem, Hypothesis, Fact, Implication) segments:
‣ Need to differentiate between ‘concept’ things and ‘experimental’ things!
- Person - Implicate: high in Hypothesis, Implication, Problem
Results: Verb Type
- Thing - Thing: high in experimental (Method, Result) and conceptual (Problem, Hypothesis, Fact, Implication) segments:
‣ Need to differentiate between ‘concept’ things and ‘experimental’ things!
- Person - Implicate: high in Hypothesis, Implication, Problem
- Person - Operate: high in Methods (90%)
Results: Verb Type
- Thing - Thing: high in experimental (Method, Result) and conceptual (Problem, Hypothesis, Fact, Implication) segments:
‣ Need to differentiate between ‘concept’ things and ‘experimental’ things!
- Person - Implicate: high in Hypothesis, Implication, Problem
- Person - Operate: high in Methods (90%)
- Person - Examine: high in Goal (87%)
Results: Metadiscourse Markers
Results: Metadiscourse Markers
- Causitive: high in Implications (therefore, thus),
- Comparison: high in Results (whereas, in contrast),
- Temporality: high in Methods (next, subsequently)
- Person markers: high in Methods (50%) and Results
- Boosters: high in Results (indeed, surprisingly, interestingly)
- Hedges: high in Implication, Reg-Implication (raises the possibility that, explains at least in part)
- but modals and ‘suggest’ verbs are left out
Discourse as a Fact-oryhypothesis
fact fact fact
problem
i. How can we model the discourse moves in a biological paper?
goalto
Discourse as a Fact-oryhypothesis
fact fact fact
problem
i. How can we model the discourse moves in a biological paper?
goalto
Discourse as a Fact-oryhypothesis
fact fact fact
problem
i. How can we model the discourse moves in a biological paper?
goalto
wemethod
resultresulting in
Discourse as a Fact-oryhypothesis
fact fact fact
problem
i. How can we model the discourse moves in a biological paper?
goalto
wemethod
resultresulting in
Discourse as a Fact-oryhypothesis
fact fact fact
problem
i. How can we model the discourse moves in a biological paper?
goalto
wemethod
resultresulting in
Discourse as a Fact-ory
suggests that
implication
discussion
hypothesis
fact fact fact
problem
i. How can we model the discourse moves in a biological paper?
goalto
wemethod
resultresulting in
Discourse as a Fact-ory
suggests that
implication
discussion
hypothesis
fact fact fact
problem
i. How can we model the discourse moves in a biological paper?
goalto
wemethod
resultresulting in
Discourse as a Fact-ory
suggests that
implication
discussion
hypothesis
fact fact fact
problem
introduction
i. How can we model the discourse moves in a biological paper?
goalto
wemethod
resultresulting in
Discourse as a Fact-ory
suggests that
implication
discussion
hypothesis
fact fact fact
problem
introduction
results
i. How can we model the discourse moves in a biological paper?
goalto
wemethod
resultresulting in
Discourse as a Fact-ory
suggests that
implication
discussion
hypothesis
fact fact fact
problem
introduction
results
discussion
i. How can we model the discourse moves in a biological paper?
goalto
wemethod
resultresulting in
Discourse as a Fact-ory
suggests that
implication
discussion
Own viewShared view
hypothesis
fact fact fact
problem
introduction
results
discussion
i. How can we model the discourse moves in a biological paper?
goalto
hypothetical realm: (might, would)
realm of activity: (to test, to see)
realm of models: present
realm of experience:
past
wemethod
resultresulting in
Discourse as a Fact-ory
suggests that
implication
discussion
Own viewShared view
hypothesis
fact fact fact
problem
introduction
results
discussion
i. How can we model the discourse moves in a biological paper?
ii. Is this useful for enabling automated epistemic markup?
ii. Is this useful for enabling automated epistemic markup?
✓ first efforts seem promising: simple markers (‘suggest’ verbs, connectives, etc.) already help:
ii. Is this useful for enabling automated epistemic markup?
✓ first efforts seem promising: simple markers (‘suggest’ verbs, connectives, etc.) already help:
6> It is thus emerging that A_1-42-induced memory deficits may involve subtler neuronal alternations leading to synaptic deficits, prior to frank neurodegeneration in AD brains.
ii. Is this useful for enabling automated epistemic markup?
✓ first efforts seem promising: simple markers (‘suggest’ verbs, connectives, etc.) already help:
6> It is thus emerging that A_1-42-induced memory deficits may involve subtler neuronal alternations leading to synaptic deficits, prior to frank neurodegeneration in AD brains.TRIPLET(that A_1_GENE:+ - 42 - induced memory deficits,involve,subtler neuronal alternations)
ii. Is this useful for enabling automated epistemic markup?
✓ first efforts seem promising: simple markers (‘suggest’ verbs, connectives, etc.) already help:
6> It is thus emerging that A_1-42-induced memory deficits may involve subtler neuronal alternations leading to synaptic deficits, prior to frank neurodegeneration in AD brains.TRIPLET(that A_1_GENE:+ - 42 - induced memory deficits,involve,subtler neuronal alternations)
ii. Is this useful for enabling automated epistemic markup?
✓ first efforts seem promising: simple markers (‘suggest’ verbs, connectives, etc.) already help:
6> It is thus emerging that A_1-42-induced memory deficits may involve subtler neuronal alternations leading to synaptic deficits, prior to frank neurodegeneration in AD brains.TRIPLET(that A_1_GENE:+ - 42 - induced memory deficits,involve,subtler neuronal alternations)
‣ issue: segment parsing is difficult!
ii. Is this useful for enabling automated epistemic markup?
✓ first efforts seem promising: simple markers (‘suggest’ verbs, connectives, etc.) already help:
6> It is thus emerging that A_1-42-induced memory deficits may involve subtler neuronal alternations leading to synaptic deficits, prior to frank neurodegeneration in AD brains.TRIPLET(that A_1_GENE:+ - 42 - induced memory deficits,involve,subtler neuronal alternations)
‣ issue: segment parsing is difficult!
‣ issue: verb tense is not always accessible
ii. Is this useful for enabling automated epistemic markup?
✓ first efforts seem promising: simple markers (‘suggest’ verbs, connectives, etc.) already help:
6> It is thus emerging that A_1-42-induced memory deficits may involve subtler neuronal alternations leading to synaptic deficits, prior to frank neurodegeneration in AD brains.TRIPLET(that A_1_GENE:+ - 42 - induced memory deficits,involve,subtler neuronal alternations)
‣ issue: segment parsing is difficult!
‣ issue: verb tense is not always accessible
‣ bionlp: not that much work on full text, since commercial publishers are difficult :-)!
ii. Is this useful for enabling automated epistemic markup?
✓ first efforts seem promising: simple markers (‘suggest’ verbs, connectives, etc.) already help:
6> It is thus emerging that A_1-42-induced memory deficits may involve subtler neuronal alternations leading to synaptic deficits, prior to frank neurodegeneration in AD brains.TRIPLET(that A_1_GENE:+ - 42 - induced memory deficits,involve,subtler neuronal alternations)
‣ issue: segment parsing is difficult!
‣ issue: verb tense is not always accessible
‣ bionlp: not that much work on full text, since commercial publishers are difficult :-)!
‣ possible challenge at biolink 2011: watch this space...
Concepts
KnownFact KnownFact
Concepts
KnownFact KnownFact
Hypothesis
To investigate the possibility that miR-372 and miR-373 suppress the
expression of LATS2, we...
Concepts
KnownFact KnownFact
Experiment 1
Goal
Result
Data
Method
Hypothesis
To investigate the possibility that miR-372 and miR-373 suppress the
expression of LATS2, we...
Concepts
KnownFact KnownFact
Experiment 1
Goal
Result
Data
Method
Hypothesis
To investigate the possibility that miR-372 and miR-373 suppress the
expression of LATS2, we...
Implication
Therefore, these results point toLATS2 as a mediator of the miR-372 and miR-373 effects on cell proliferation and tumorigenicity,
Concepts
KnownFact KnownFact
Experiment 1
Goal
Result
Data
Method
Hypothesis
To investigate the possibility that miR-372 and miR-373 suppress the
expression of LATS2, we...
Implication
Therefore, these results point toLATS2 as a mediator of the miR-372 and miR-373 effects on cell proliferation and tumorigenicity,
Voorhoeve, 2006
Concepts
KnownFact KnownFact
Experiment 1
Goal
Result
Data
Method
Goal
Experiment 2
Data
Method Result
Hypothesis
To investigate the possibility that miR-372 and miR-373 suppress the
expression of LATS2, we...
Implication
Therefore, these results point toLATS2 as a mediator of the miR-372 and miR-373 effects on cell proliferation and tumorigenicity,
Voorhoeve, 2006
Concepts
KnownFact KnownFact
Experiment 1
Goal
Result
Data
Method
Goal
Experiment 2
Data
Method Result
Hypothesis
To investigate the possibility that miR-372 and miR-373 suppress the
expression of LATS2, we...
Implication
Therefore, these results point toLATS2 as a mediator of the miR-372 and miR-373 effects on cell proliferation and tumorigenicity,
Fact
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
Voorhoeve, 2006
Concepts
KnownFact KnownFact
Experiment 1
Goal
Result
Data
Method
Goal
Experiment 2
Data
Method Result
Hypothesis
To investigate the possibility that miR-372 and miR-373 suppress the
expression of LATS2, we...
Implication
Therefore, these results point toLATS2 as a mediator of the miR-372 and miR-373 effects on cell proliferation and tumorigenicity,
Fact
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
Voorhoeve, 2006
Fact creation vs. Latour (1986)
Fact creation vs. Latour (1986)
Future research:
Future research:
‣ Need co-annotators to verify semantic types
Future research:
‣ Need co-annotators to verify semantic types
‣ Need to scale up with more (types of) texts!
Future research:
‣ Need co-annotators to verify semantic types
‣ Need to scale up with more (types of) texts!
I. How is a scientific fact created, as it moves from a hedged claim to a throughout successive citations?
Future research:
‣ Need co-annotators to verify semantic types
‣ Need to scale up with more (types of) texts!
I. How is a scientific fact created, as it moves from a hedged claim to a throughout successive citations?
II. Can we identify a rhetorically successful text, using these segments and characteristics?
Future research:
‣ Need co-annotators to verify semantic types
‣ Need to scale up with more (types of) texts!
I. How is a scientific fact created, as it moves from a hedged claim to a throughout successive citations?
II. Can we identify a rhetorically successful text, using these segments and characteristics?
III. Can we help authors create such texts (guidelines, tools?
Third attempt:
collaboration!
Improve ‘what is claimed about an entity’
insulin ::: GB000841
maintaining glucose homeostasis
... diabetes defect) to overcome insulin resistance in maintaining glucose homeostasis, hyperglycemia and glucose intolerance ...improve glucose
homeostasis... in T2D is able to increase insulin secretion and improve glucose homeostasis.
improves glucose homeostasis
... SIRT1, whose administration to insulin-resistant animals improves glucose homeostasis.
is capable glucose homeostasis
S15511 is a novel insulin sensitizer that is capable of improving glucose homeostasis in nondiabetic rats.
maintains glucose homeostasis
Pancreatic beta-cells possess a well-regulated insulin secretory property that maintains systemic glucose homeostasis.
may be involved
glucose homeostasis
... similar way to those of insulin, PANDER may be involved in glucose homeostasis.
participates glucose homeostasis
Fine-tuning of insulin secretion from pancreatic beta-cells participates in blood glucose homeostasis.
Improve ‘what is claimed about an entity’
insulin ::: GB000841
maintaining glucose homeostasis
... diabetes defect) to overcome insulin resistance in maintaining glucose homeostasis, hyperglycemia and glucose intolerance ...improve glucose
homeostasis... in T2D is able to increase insulin secretion and improve glucose homeostasis.
improves glucose homeostasis
... SIRT1, whose administration to insulin-resistant animals improves glucose homeostasis.
is capable glucose homeostasis
S15511 is a novel insulin sensitizer that is capable of improving glucose homeostasis in nondiabetic rats.
maintains glucose homeostasis
Pancreatic beta-cells possess a well-regulated insulin secretory property that maintains systemic glucose homeostasis.
may be involved
glucose homeostasis
... similar way to those of insulin, PANDER may be involved in glucose homeostasis.
participates glucose homeostasis
Fine-tuning of insulin secretion from pancreatic beta-cells participates in blood glucose homeostasis.
When insulin secretion cannot be increased adequately (type I diabetes defect) to overcome insulin resistance in maintaining glucose homeostasis, hyperglycemia and glucose intolerance ensues. Insulin resistance and glucose intolerance has been well recognized in patients with advanced chronic kidney diseases (CKD).
.. Incretin metabolism is abnormal in T2D, evidenced by a decreased incretin effect, reduction in nutrient-mediated secretion of GIP and GLP-1 in T2D, and resistance to GIP. GLP-1, on the other hand, when administered intravenously in T2D is able to increase insulin secretion and improve glucose homeostasis.
SIRT1, a NAD(+)-dependent protein deacetylase that regulates transcription factors involved in key cellular processes, has been implicated as a mediator of the beneficial effects of calorie restriction. In a recent issue of Nature, Milne et al. (2007) describe novel potent activators of SIRT1, whose administration to insulin-resistant animals improves glucose homeostasis.
S15511 is a novel insulin sensitizer that is capable of improving glucose homeostasis in nondiabetic rats.... However, the mechanisms behind the insulin-sensitizing effect of S15511 are unknown. The aim of our study was to explore whether S15511 improves insulin sensitivity in skeletal muscles. S15511 treatment was associated with an increase in insulin-stimulated glucose transport in type IIb fibers, while type I fibers were unaffected. Pancreatic beta-cells possess a well-regulated insulin secretory property that maintains systemic glucose homeostasis. Although it has long been thought that differentiated beta-cells are nearly static, recent studies have shown that beta-cell mass dynamically changes throughout the lifetime. In this article, recent progress of regenerative medicine of the pancreas is reviewed.... Our results showed that glucose up-regulated PANDER mRNA and protein levels in a time- and dose-dependent manner in MIN6 cells and pancreatic islets. ...Because PANDER is expressed by pancreatic beta-cells and in response to glucose in a similar way to those of insulin, PANDER may be involved in glucose homeostasis.
Fine-tuning of insulin secretion from pancreatic beta-cells participates in blood glucose homeostasis. ... Our data identify miR124a and miR96 as novel regulators of the expression of proteins playing a critical role in insulin exocytosis and in the release of other hormones and neurotransmitters.
Improve ‘what is claimed about an entity’
insulin ::: GB000841
maintaining glucose homeostasis
... diabetes defect) to overcome insulin resistance in maintaining glucose homeostasis, hyperglycemia and glucose intolerance ...improve glucose
homeostasis... in T2D is able to increase insulin secretion and improve glucose homeostasis.
improves glucose homeostasis
... SIRT1, whose administration to insulin-resistant animals improves glucose homeostasis.
is capable glucose homeostasis
S15511 is a novel insulin sensitizer that is capable of improving glucose homeostasis in nondiabetic rats.
maintains glucose homeostasis
Pancreatic beta-cells possess a well-regulated insulin secretory property that maintains systemic glucose homeostasis.
may be involved
glucose homeostasis
... similar way to those of insulin, PANDER may be involved in glucose homeostasis.
participates glucose homeostasis
Fine-tuning of insulin secretion from pancreatic beta-cells participates in blood glucose homeostasis.
When insulin secretion cannot be increased adequately (type I diabetes defect) to overcome insulin resistance in maintaining glucose homeostasis, hyperglycemia and glucose intolerance ensues. Insulin resistance and glucose intolerance has been well recognized in patients with advanced chronic kidney diseases (CKD).
.. Incretin metabolism is abnormal in T2D, evidenced by a decreased incretin effect, reduction in nutrient-mediated secretion of GIP and GLP-1 in T2D, and resistance to GIP. GLP-1, on the other hand, when administered intravenously in T2D is able to increase insulin secretion and improve glucose homeostasis.
SIRT1, a NAD(+)-dependent protein deacetylase that regulates transcription factors involved in key cellular processes, has been implicated as a mediator of the beneficial effects of calorie restriction. In a recent issue of Nature, Milne et al. (2007) describe novel potent activators of SIRT1, whose administration to insulin-resistant animals improves glucose homeostasis.
S15511 is a novel insulin sensitizer that is capable of improving glucose homeostasis in nondiabetic rats.... However, the mechanisms behind the insulin-sensitizing effect of S15511 are unknown. The aim of our study was to explore whether S15511 improves insulin sensitivity in skeletal muscles. S15511 treatment was associated with an increase in insulin-stimulated glucose transport in type IIb fibers, while type I fibers were unaffected. Pancreatic beta-cells possess a well-regulated insulin secretory property that maintains systemic glucose homeostasis. Although it has long been thought that differentiated beta-cells are nearly static, recent studies have shown that beta-cell mass dynamically changes throughout the lifetime. In this article, recent progress of regenerative medicine of the pancreas is reviewed.... Our results showed that glucose up-regulated PANDER mRNA and protein levels in a time- and dose-dependent manner in MIN6 cells and pancreatic islets. ...Because PANDER is expressed by pancreatic beta-cells and in response to glucose in a similar way to those of insulin, PANDER may be involved in glucose homeostasis.
Fine-tuning of insulin secretion from pancreatic beta-cells participates in blood glucose homeostasis. ... Our data identify miR124a and miR96 as novel regulators of the expression of proteins playing a critical role in insulin exocytosis and in the release of other hormones and neurotransmitters.
30
A network of hypotheses and evidence
30
PHC Growth arrestundergo
A network of hypotheses and evidence
30
PHC Growth arrestundergo
A network of hypotheses and evidence
Paper A:implication
results
method
goal
fact
fact
30
PHC Growth arrestundergo
A network of hypotheses and evidence
Paper A:implication
results
method
goal
fact
fact
data 1
data 2 data 3
30
PHC Growth arrestundergo
A network of hypotheses and evidence
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
30
PHC Growth arrestundergo
A network of hypotheses and evidence
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
30
PHC Growth arrestundergo
A network of hypotheses and evidence
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
30
PHC Growth arrestundergo
A network of hypotheses and evidence
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
30
PHC Growth arrestundergo
A network of hypotheses and evidence
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
30
PHC Growth arrestundergo
A network of hypotheses and evidence
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
For Example: SWAN
For Example: SWAN
For Example: SWAN
For Example: SWAN
HypER Working Group:
- Goal: Align and expand existing efforts on detection and analysis of Hypotheses, Evidence & Relationships
- Partners:
- Harvard/MGH: SWAN, ARF
- Open University: Cohere
- Oxford University: CiTO, eLearning/Rhetoric
- DERI: SALT, aTags
- University of Trento: LiquidPub
- Xerox Research: XIP hypothesis identifier
- U Tilburg: ML for Science
- Elsevier, UUtrecht: Discourse analysis of biology
HypER Working Group:
- Goal: Align and expand existing efforts on detection and analysis of Hypotheses, Evidence & Relationships
- Partners:
- Harvard/MGH: SWAN, ARF
- Open University: Cohere
- Oxford University: CiTO, eLearning/Rhetoric
- DERI: SALT, aTags
- University of Trento: LiquidPub
- Xerox Research: XIP hypothesis identifier
- U Tilburg: ML for Science
- Elsevier, UUtrecht: Discourse analysis of biology
HypER Working Group:
- Goal: Align and expand existing efforts on detection and analysis of Hypotheses, Evidence & Relationships
- Partners:
- Harvard/MGH: SWAN, ARF
- Open University: Cohere
- Oxford University: CiTO, eLearning/Rhetoric
- DERI: SALT, aTags
- University of Trento: LiquidPub
- Xerox Research: XIP hypothesis identifier
- U Tilburg: ML for Science
- Elsevier, UUtrecht: Discourse analysis of biology
HypER Working Group:
- Goal: Align and expand existing efforts on detection and analysis of Hypotheses, Evidence & Relationships
- Partners:
- Harvard/MGH: SWAN, ARF
- Open University: Cohere
- Oxford University: CiTO, eLearning/Rhetoric
- DERI: SALT, aTags
- University of Trento: LiquidPub
- Xerox Research: XIP hypothesis identifier
- U Tilburg: ML for Science
- Elsevier, UUtrecht: Discourse analysis of biology
HypER Working Group:
- Goal: Align and expand existing efforts on detection and analysis of Hypotheses, Evidence & Relationships
- Partners:
- Harvard/MGH: SWAN, ARF
- Open University: Cohere
- Oxford University: CiTO, eLearning/Rhetoric
- DERI: SALT, aTags
- University of Trento: LiquidPub
- Xerox Research: XIP hypothesis identifier
- U Tilburg: ML for Science
- Elsevier, UUtrecht: Discourse analysis of biology
HypER Working Group:
- Goal: Align and expand existing efforts on detection and analysis of Hypotheses, Evidence & Relationships
- Partners:
- Harvard/MGH: SWAN, ARF
- Open University: Cohere
- Oxford University: CiTO, eLearning/Rhetoric
- DERI: SALT, aTags
- University of Trento: LiquidPub
- Xerox Research: XIP hypothesis identifier
- U Tilburg: ML for Science
- Elsevier, UUtrecht: Discourse analysis of biology
HypER Working Group:
- Goal: Align and expand existing efforts on detection and analysis of Hypotheses, Evidence & Relationships
- Partners:
- Harvard/MGH: SWAN, ARF
- Open University: Cohere
- Oxford University: CiTO, eLearning/Rhetoric
- DERI: SALT, aTags
- University of Trento: LiquidPub
- Xerox Research: XIP hypothesis identifier
- U Tilburg: ML for Science
- Elsevier, UUtrecht: Discourse analysis of biology
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.
HypER Activities: http://hyper.wik.is
Current activities:
- Aligning discourse ontologies: joint task with W3C HCLSSig
- Aligning architectures to exchange hypotheses + evidence
- Format for a rhetorical conference paper (SALT + abcde)
- Parser test of hypothesis identification tools on pharmacology corpus
HypER Activities: http://hyper.wik.is
Current activities:
- Aligning discourse ontologies: joint task with W3C HCLSSig
- Aligning architectures to exchange hypotheses + evidence
- Format for a rhetorical conference paper (SALT + abcde)
- Parser test of hypothesis identification tools on pharmacology corpus
Further interests:
- Better structure of evidence: MyExperiment, KeFeD, ...
- Granularity of annotation/access: entity, hypothesis, discussion?
Conclusion
Conclusion
Problem: too much discourse, tools are not yet good enough...
Conclusion
Problem: too much discourse, tools are not yet good enough...
1. First attempt: allow authors to validate entities - pursue
Conclusion
Problem: too much discourse, tools are not yet good enough...
1. First attempt: allow authors to validate entities - pursue
2. Second attempt: discourse analysis - any help is great!
Conclusion
Problem: too much discourse, tools are not yet good enough...
1. First attempt: allow authors to validate entities - pursue
2. Second attempt: discourse analysis - any help is great!
3. Third attempt: collaboration to identify hypotheses: do join!
Questions?
[email protected]://elsatglabs.elsevier.com/labs/anita
References
Hyland, K. (2004). Disciplinary Discourses: Social Interactions in Academic Writing, Addison Wesley Publishing Company, 2004.
Latour, B., and Woolgar, S. (1986). Laboratory Life: The Construction of Scientific Facts. 2nd ed. Princeton, NJ: Princeton University Press, 1986. ISBN: 9780691028323.
Latour, B. (1987). Science in Action, How to Follow Scientists and Engineers through Society, (Cambridge, Ma.: Harvard University Press, 1987)
Segmentation Criteria (summary)
Finite/Non-finite
Grammatical role Segment? Example
Finite/Non-finite Subject N The extent to which miRNAs specifically affect metastasis
Finite/Non-finite Direct Object Y these miRNAs are potential novel oncogenes
Nonfinite Phrase-level adjunct (restrictive and non-restrictive)
N spanning a given miRNA genomic region
Nonfinite Clause-level adjunct Y by cloning eight miR-Vec plasmids
Finite Non-restrictive Phrase-level adjunct Y which is only active when tamoxifen is added (De Vita et al, 2005) […]
Finite Restrictive Phrase-level adjunct N that we examined
Finite Clause-level adjunct Ywhich correlates with the reported ES-cell expression pattern of the miR-371-3 cluster (Suh et al, 2004)
Basic Segment TypesSegment Description Example
Fact a known fact, generally without explicit citation
mature miR-373 is a homolog of miR-372
Hypothesis a proposed idea, not supported by evidence This could for instance be a result of high mdm2 levels
Problem unresolved, contradictory, or unclear issue
However, further investigation is required to demonstrate the exact mechanism of LATS2 action
Goal research goal To identify novel functions of miRNAs,
Method experimental method Using fluorescence microscopy and luciferase assays,
Result a restatement of the outcome of an experiment
all constructs yielded high expression levels of mature miRNAs
Implication an interpretation of the results, in light of earlier
hypotheses and facts
our procedure is sensitive enough to detect mild growth differences
Two Types of Derived Segment Types
Two Types of Derived Segment Types
‘Other-segments’, related to (referenced) other work:
Two Types of Derived Segment Types
‘Other-segments’, related to (referenced) other work:
- other-result: ‘they are also found in the FCX and other cortical structures ([Sokoloff et al., 1990]’
Two Types of Derived Segment Types
‘Other-segments’, related to (referenced) other work:
- other-result: ‘they are also found in the FCX and other cortical structures ([Sokoloff et al., 1990]’
- other-goal: ‘the role of D3 receptors in the control of motivation and affect has been intensively studied [Heidbreder et al., 2005]’
Two Types of Derived Segment Types
‘Other-segments’, related to (referenced) other work:
- other-result: ‘they are also found in the FCX and other cortical structures ([Sokoloff et al., 1990]’
- other-goal: ‘the role of D3 receptors in the control of motivation and affect has been intensively studied [Heidbreder et al., 2005]’
- other-implication: ‘D1 or, more likely, D5, receptors have been implicated in mechanisms underlying long-term spatial memory [Hersi et al., 1995]’
Two Types of Derived Segment Types
‘Other-segments’, related to (referenced) other work:
- other-result: ‘they are also found in the FCX and other cortical structures ([Sokoloff et al., 1990]’
- other-goal: ‘the role of D3 receptors in the control of motivation and affect has been intensively studied [Heidbreder et al., 2005]’
- other-implication: ‘D1 or, more likely, D5, receptors have been implicated in mechanisms underlying long-term spatial memory [Hersi et al., 1995]’
Regulatory segments, acting as matrix sentences framing other segments:
Two Types of Derived Segment Types
‘Other-segments’, related to (referenced) other work:
- other-result: ‘they are also found in the FCX and other cortical structures ([Sokoloff et al., 1990]’
- other-goal: ‘the role of D3 receptors in the control of motivation and affect has been intensively studied [Heidbreder et al., 2005]’
- other-implication: ‘D1 or, more likely, D5, receptors have been implicated in mechanisms underlying long-term spatial memory [Hersi et al., 1995]’
Regulatory segments, acting as matrix sentences framing other segments:
- reg-hypothesis: ‘we hypothesized that ’
Two Types of Derived Segment Types
‘Other-segments’, related to (referenced) other work:
- other-result: ‘they are also found in the FCX and other cortical structures ([Sokoloff et al., 1990]’
- other-goal: ‘the role of D3 receptors in the control of motivation and affect has been intensively studied [Heidbreder et al., 2005]’
- other-implication: ‘D1 or, more likely, D5, receptors have been implicated in mechanisms underlying long-term spatial memory [Hersi et al., 1995]’
Regulatory segments, acting as matrix sentences framing other segments:
- reg-hypothesis: ‘we hypothesized that ’
- reg-implication: ‘These observations suggest that’
Two Types of Derived Segment Types
‘Other-segments’, related to (referenced) other work:
- other-result: ‘they are also found in the FCX and other cortical structures ([Sokoloff et al., 1990]’
- other-goal: ‘the role of D3 receptors in the control of motivation and affect has been intensively studied [Heidbreder et al., 2005]’
- other-implication: ‘D1 or, more likely, D5, receptors have been implicated in mechanisms underlying long-term spatial memory [Hersi et al., 1995]’
Regulatory segments, acting as matrix sentences framing other segments:
- reg-hypothesis: ‘we hypothesized that ’
- reg-implication: ‘These observations suggest that’
- intratextual: ‘Fig 4 shows that’
Two Types of Derived Segment Types
‘Other-segments’, related to (referenced) other work:
- other-result: ‘they are also found in the FCX and other cortical structures ([Sokoloff et al., 1990]’
- other-goal: ‘the role of D3 receptors in the control of motivation and affect has been intensively studied [Heidbreder et al., 2005]’
- other-implication: ‘D1 or, more likely, D5, receptors have been implicated in mechanisms underlying long-term spatial memory [Hersi et al., 1995]’
Regulatory segments, acting as matrix sentences framing other segments:
- reg-hypothesis: ‘we hypothesized that ’
- reg-implication: ‘These observations suggest that’
- intratextual: ‘Fig 4 shows that’
- intertextual: ‘reviewed in (Serrano, 1997)’
My categories vs. Latour (1979)
Linguistic and structural properties
Linguistic and structural properties
Linguistic and structural properties1. Position in text
Linguistic and structural properties1. Position in text
- Section of the paper (Introduction, Results, Discussion)
Linguistic and structural properties1. Position in text
- Section of the paper (Introduction, Results, Discussion)
- Beginning/middle/end of section
Linguistic and structural properties1. Position in text
- Section of the paper (Introduction, Results, Discussion)
- Beginning/middle/end of section
- First/second third part of sentence
Linguistic and structural properties1. Position in text
- Section of the paper (Introduction, Results, Discussion)
- Beginning/middle/end of section
- First/second third part of sentence
2. Verb:
Linguistic and structural properties1. Position in text
- Section of the paper (Introduction, Results, Discussion)
- Beginning/middle/end of section
- First/second third part of sentence
2. Verb:
- Tense, aspect, voice
Linguistic and structural properties1. Position in text
- Section of the paper (Introduction, Results, Discussion)
- Beginning/middle/end of section
- First/second third part of sentence
2. Verb:
- Tense, aspect, voice
- Verb class (idiosyncratic)
Linguistic and structural properties1. Position in text
- Section of the paper (Introduction, Results, Discussion)
- Beginning/middle/end of section
- First/second third part of sentence
2. Verb:
- Tense, aspect, voice
- Verb class (idiosyncratic)
- Lexicon
Linguistic and structural properties1. Position in text
- Section of the paper (Introduction, Results, Discussion)
- Beginning/middle/end of section
- First/second third part of sentence
2. Verb:
- Tense, aspect, voice
- Verb class (idiosyncratic)
- Lexicon
3. Metadiscourse markers [Hyland, 2003]:
Linguistic and structural properties1. Position in text
- Section of the paper (Introduction, Results, Discussion)
- Beginning/middle/end of section
- First/second third part of sentence
2. Verb:
- Tense, aspect, voice
- Verb class (idiosyncratic)
- Lexicon
3. Metadiscourse markers [Hyland, 2003]:
- Connectives
Linguistic and structural properties1. Position in text
- Section of the paper (Introduction, Results, Discussion)
- Beginning/middle/end of section
- First/second third part of sentence
2. Verb:
- Tense, aspect, voice
- Verb class (idiosyncratic)
- Lexicon
3. Metadiscourse markers [Hyland, 2003]:
- Connectives
- Endophorics, Evidentials
Linguistic and structural properties1. Position in text
- Section of the paper (Introduction, Results, Discussion)
- Beginning/middle/end of section
- First/second third part of sentence
2. Verb:
- Tense, aspect, voice
- Verb class (idiosyncratic)
- Lexicon
3. Metadiscourse markers [Hyland, 2003]:
- Connectives
- Endophorics, Evidentials
- Hedges, Boosters
Linguistic and structural properties1. Position in text
- Section of the paper (Introduction, Results, Discussion)
- Beginning/middle/end of section
- First/second third part of sentence
2. Verb:
- Tense, aspect, voice
- Verb class (idiosyncratic)
- Lexicon
3. Metadiscourse markers [Hyland, 2003]:
- Connectives
- Endophorics, Evidentials
- Hedges, Boosters
- Person markers
Verb class
Verb classTwo types of entities interact in biology texts:
- Thing:
- Thing -> Increase, die, etc
- Thing-thing: affect, stimulate etc.
- People:
- People -> Thing:
- Examine (Goal)
- Operate (Method)
- Observe (Result)
- Implicate (Implication)
- People - people: Report
Interpretation: 3 Realms of Science:
Experimental realm
Data realm
Conceptual realm
Interpretation: 3 Realms of Science:
Experimental realm
Data realm
Conceptual realm
(1) Oncogene-induced senescence is characterized by the appearance of cells with a flat morphology that express senescence associated (SA)-
-Galactosidase.
(4b) transduction with either miR-Vec-371&2 or miR-Vec-373 prevents RASV12-induced growth arrest in primary human cells.
(2b) control RASV12-arrested cells showed relatively high abundance of flat cells expressing SA- -Galactosidase
(3b) very few cells showed senescent morphology when transduced with either miR-Vec-371&2, miR-Vec-373, or control p53kd.
(4a) Altogether, these data show that
(3a) Consistent with the cell growth assay,
(Figures)
(2a) Indeed,
(2c) (Figures 2G and 2H).
Interpretation: 3 Realms of Science:
Experimental realm
Data realm
Conceptual realm
(1) Oncogene-induced senescence is characterized by the appearance of cells with a flat morphology that express senescence associated (SA)-
-Galactosidase.
(4b) transduction with either miR-Vec-371&2 or miR-Vec-373 prevents RASV12-induced growth arrest in primary human cells.
(2b) control RASV12-arrested cells showed relatively high abundance of flat cells expressing SA- -Galactosidase
(3b) very few cells showed senescent morphology when transduced with either miR-Vec-371&2, miR-Vec-373, or control p53kd.
(4a) Altogether, these data show that
(3a) Consistent with the cell growth assay,
(Figures)
(2a) Indeed,
(2c) (Figures 2G and 2H).
Tense 1: Concepts vs. Experiment
(1) Oncogene-induced senescence is characterized by the appearance of cells with a flat morphology that express senescence associated (SA)-
-Galactosidase.
(4b) transduction with either miR-Vec-371&2 or miR-Vec-373 prevents RASV12-induced growth arrest in primary human cells.
(2b) control RASV12-arrested cells showed relatively high abundance of flat cells expressing SA- -Galactosidase
(3b) very few cells showed senescent morphology when transduced with either miR-Vec-371&2, miR-Vec-373, or control p53kd.
(4a) Altogether, these data show that
(3a) Consistent with the cell growth assay,
(Figures)
(2a) Indeed,
Expe
r ime n
t al r
ealm
( p
ers o
nal,
past
) D
a ta
real
m
(non
tver
bal)
(2c) (Figures 2G and 2H).
Con
c ep t
real
m
Tense 2: Referral
Introduction
Current work (= Results section)
After current work: past
Before current work: present
Discussion
present past future
othe
r pap
ers
own
pap e
r
Other Work
After other work: past
Tense 1+ 2 = 3:
Reading time
Expe
rient
ial
Con
cept
ual
past present future
Claim, fact
Experiment