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


1. First attempt: allow authors to validate entities

Overview



2. Second attempt: discourse analysis

Overview



2. Second attempt: discourse analysis

3. Third attempt: collaboration to identify hypotheses

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




- 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


Alteration of nm23, P53, and S100A4 expression may contribute to the development of gastric


Previous studies have implicated miR-34a as a tumor suppressor gene whose transcription is activated by p53.





Add this knowledge during authoring?

First attempt: allow authors to validate entities

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




- 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)

http://mint.bio.uniroma2.it/mint/search/interaction.do?interactionAc=MINT-6168263


http://www.ebi.uniprot.org/entry/Q8R1W2


http://www.ebi.uniprot.org/entry/Q9WVP6


http://www.ebi.uniprot.org/entry/P52194


http://www.ebi.ac.uk/ontology-lookup/?termId=MI%3A0403




















http://www.ebi.ac.uk/ontology-lookup/?termId=MI:0218




































































































































































































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




http://sig.ma

http://sig.ma

http://sig.ma

Second attempt:

discourse analysis

What else is wrong with MEDIE?









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


i. How can we model the discourse/suasive moves in a biological paper?



ii. Can this model help enable automated epistemic markup?



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


1. Parse text into discourse segments (edu’s) containing a single rhetorical move (if possible...)

Discourse analysis



2. Determine categories or types of discourse segments that have similar semantic/pragmatic properties

Discourse analysis



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


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.


Segmentation




IntratextualMethod

Result Result

Implication

Segmentation




IntratextualMethod

Result Result

Implication

Segmentation


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













‘Other-segments’, related to (referenced) other work:














Regulatory segments, acting as matrix sentences framing other segments:

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





2. Verb:

- Tense, aspect, voice

- Verb class: Thing (increase), Thing-Thing (inhibit), Person-Thing (examine, observe, operate, implicate), Person: Report

- Lexicon





2. Verb:


- 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


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)





- 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 Past: Result (82%), Method (76%) - 50% Passive, of Method 50% Past Perfect

Results: Verb Tense



- Realm of the Modal: 44% in Hypothesis

Results: Verb Tense



- 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



- Person - Implicate: high in Hypothesis, Implication, Problem

Results: Verb Type




- Person - Operate: high in Methods (90%)

Results: Verb Type




- 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


fact fact fact

problem


goalto


fact fact fact

problem


goalto

wemethod

resultresulting in


fact fact fact

problem


goalto

wemethod

resultresulting in


fact fact fact

problem


goalto

wemethod

resultresulting in

Discourse as a Fact-ory

suggests that

implication

discussion

hypothesis

fact fact fact

problem


goalto

wemethod

resultresulting in


suggests that

implication

discussion

hypothesis

fact fact fact

problem


goalto

wemethod

resultresulting in


suggests that

implication

discussion

hypothesis

fact fact fact

problem

introduction


goalto

wemethod

resultresulting in


suggests that

implication

discussion

hypothesis

fact fact fact

problem

introduction

results


goalto

wemethod

resultresulting in


suggests that

implication

discussion

hypothesis

fact fact fact

problem

introduction

results

discussion


goalto

wemethod

resultresulting in


suggests that

implication

discussion

Own viewShared view

hypothesis

fact fact fact

problem

introduction

results

discussion


goalto

hypothetical realm: (might, would)

realm of activity: (to test, to see)

realm of models: present

realm of experience:

past

wemethod

resultresulting in


suggests that

implication

discussion

Own viewShared view

hypothesis

fact fact fact

problem

introduction

results

discussion


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.



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 :-)!






‣ 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



Concepts

KnownFact KnownFact

Experiment 1

Goal

Result

Data

Method

Hypothesis



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



Implication


Voorhoeve, 2006

Concepts

KnownFact KnownFact

Experiment 1

Goal

Result

Data

Method

Goal

Experiment 2

Data

Method Result

Hypothesis



Implication


Voorhoeve, 2006

Concepts

KnownFact KnownFact

Experiment 1

Goal

Result

Data

Method

Goal

Experiment 2

Data

Method Result

Hypothesis



Implication


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



Implication


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 to scale up with more (types of) texts!

Future research:



I. How is a scientific fact created, as it moves from a hedged claim to a throughout successive citations?

Future research:




II. Can we identify a rhetorically successful text, using these segments and characteristics?

Future research:




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.












may be involved

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.












may be involved

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


30



Paper A:implication

results

method

goal

fact

fact

30



Paper A:implication

results

method

goal

fact

fact

data 1

data 2 data 3

30



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



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



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



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



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



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



- Partners:




- DERI: SALT, aTags







- Partners:




- DERI: SALT, aTags







- Partners:




- DERI: SALT, aTags







- Partners:




- DERI: SALT, aTags







- Partners:




- DERI: SALT, aTags







- Partners:




- DERI: SALT, aTags





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

http://hyper.wik.is

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

http://hyper.wik.is

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?

http://hyper.wik.is

http://hyper.wik.is

Conclusion

Conclusion


Conclusion


1. First attempt: allow authors to validate entities - pursue

Conclusion



2. Second attempt: discourse analysis - any help is great!

Conclusion



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

mailto:[email protected]

mailto:[email protected]

http://elsatglabs.elsevier.com/labs/anita

http://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



Hypothesis a proposed idea, not supported by evidence This could for instance be a result of high mdm2 levels


However, further investigation is required to demonstrate the exact mechanism of LATS2 action

Goal research goal To identify novel functions of miRNAs,




Implication an interpretation of the results, in light of earlier

hypotheses and facts


Two Types of Derived Segment Types





- 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]’













- reg-hypothesis: ‘we hypothesized that ’








- reg-implication: ‘These observations suggest that’









- intratextual: ‘Fig 4 shows that’









- intratextual: ‘Fig 4 shows that’

- intertextual: ‘reviewed in (Serrano, 1997)’

My categories vs. Latour (1979)












- First/second third part of sentence





2. Verb:





2. Verb:






2. Verb:


- Verb class (idiosyncratic)





2. Verb:



- Lexicon





2. Verb:



- Lexicon






2. Verb:



- Lexicon


- Connectives





2. Verb:



- Lexicon


- Connectives






2. Verb:



- Lexicon


- Connectives


- Hedges, Boosters





2. Verb:



- Lexicon


- Connectives


- 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


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).


Experimental realm

Data realm

Conceptual realm


-Galactosidase.






(Figures)

(2a) Indeed,


Tense 1: Concepts vs. Experiment


-Galactosidase.






(Figures)

(2a) Indeed,

Expe

r ime n

t al r

ealm

( p

ers o

nal,

past

) D

a ta

real

m

(non

tver

bal)


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

Technology

Xerox2009