On semantic annotation for science publications

1. representing scientific discourse, or:
why triples are not enough
Anita de Waard
Disruptive Technologies Director, Elsevier Labs
Casimir Researcher, Utrecht Institute of Linguistics

2. what is your problem?

3. why triples are not enough (1): commercial tool
insulin maintaining 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 may be involved glucose homeostasis
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.
the triples are often wrong.
you cannot check if they are true.

4. why triples are not enough (2): biocreative challenge
compare:
- In Xenopus oocyte maturation, cytoplasmic polyadenylation
mediated by cytoplasmic polyadenylation element binding protein
(CPEB) induces the translation of maternal mRNA [5].
- In mouse testis, another novel member of the CPEB protein
family (CPEB2) and a homolog of xGLD-2 (mGLD-2) have been
identified [7] and [8]
to:
- TPAP was present in GSG1 immunoprecipitates (Fig. 2B).
The in vivo data suggest that TPAP–GSG1 interactions occur in
mammalian cells.
how do you know this is true?
what is new?

5. why triples are not enough (3): medie
how do you know this is true?
what is new?
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.

6. why is this so difficult?

7. issue # 1: science is rhetoric
Aristotle Quintilian Scientific Paper
The introduction of a speech, where one announces the subject
Introduction and purpose of the discourse, and where one usually employs Introduction:
prooimion / exordium the persuasive appeal to ethos in order to establish positioning
credibility with the audience.
Statement of The speaker here provides a narrative account of what has Introduction: research
prothesis Facts/narratio happened and generally explains the nature of the case.
question
Summary/ The propositio provides a brief summary of what one is about
propostitio to speak on, or concisely puts forth the charges or accusation. Summary of contents
Proof/ The main body of the speech where one offers logical
pistis confirmatio arguments as proof. The appeal to logos is emphasized here. Results
Refutation/ As the name connotes, this section of a speech was devoted to
refutatio answering the counterarguments of one's opponent. Related Work
Following the refutatio and concluding the classical oration, the Discussion: summary,
epilogos peroratio peroratio conventionally employed appeals through
pathos, and often included a summing up. implications.
- goal of the paper is to be published; it uses us as a host system
- format has co-evolved as predator-prey system with reviewers

8. issue # 2: science is a story
Story Grammar The Story of Goldilocks Paper The AXH Domain of Ataxin-1 Mediates
and the Three Bears Grammar Neurodegeneration through Its Interaction with
Gfi-1/Senseless Proteins
Setting Time Once upon a time Background The mechanisms mediating SCA1 pathogenesis are still not fully
understood, but some general principles have emerged.
Character a little girl named Goldilocks Objects of the Drosophila Atx-1 homolog (dAtx-1) which lacks a polyQ tract,
study
Location She went for a walk in the forest.
Pretty soon, she came upon a Experimental studied and compared in vivo effects and interactions to those of
house. setup the human protein
Theme Goal She knocked and, when no one Research Gain insight into how Atx-1's function contributes to SCA1
answered, goal pathogenesis. How these interactions might contribute to the
disease process and how they might cause toxicity in only a subset
Attempt she walked right in. Hypothesis Atx-1 may play a role in the regulation of gene expression
of neurons in SCA1 is not fully understood.
Episode Name At the table in the kitchen, there Name dAtX-1 and hAtx-1 Induce Similar Phenotypes When
were three bowls of porridge. Overexpressed in Files
Subgoal Goldilocks was hungry. Subgoal test the function of the AXH domain
Attempt She tasted the porridge from the Method overexpressed dAtx-1 in flies using the GAL4/UAS system (Brand
first bowl. and Perrimon, 1993) and compared its effects to those of hAtx-1.
Outcome This porridge is too hot! she Results Overexpression of dAtx-1 by Rhodopsin1(Rh1)-GAL4, which drives
exclaimed. expression in the differentiated R1-R6 photoreceptor cells
(Mollereau et al., 2000 and O'Tousa et al., 1985), results in
neurodegeneration in the eye, as does overexpression of hAtx-1
[82Q]. Although at 2 days after eclosion, overexpression of either
So, she tasted the porridge from Atx-1not shown),
(data does not show obvious morphological changes in the
Attempt Data
the second bowl. photoreceptor cells
Outcome This porridge is too cold, she said Results both genotypes show many large holes and loss of cell integrity at
28 days
Attempt So, she tasted the last bowl of Data (Figures 1B-1D).
porridge.
Outcome Ahhh, this porridge is just right, Results Overexpression of dAtx-1 using the GMR-GAL4 driver also induces

9. issue #3: science happens in language
(and language happens in our heads)
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.
a. Figure 4a shows that Intratextual
b. following RASV12 stimulation Method
c. p53 was stabilized and activated Result
d. and the target gene, p21cip1, was induced in all cases, Result
e. indicating an intact p53 pathway in these cells. Implication

10. language happens in our head:
tense use in biology
Conceptual Realm: State Pre s e n t
Argumentational Realm:
Instantaneous Presen t
Discourse Progression Axi s :
Instantaneous Present
Research Progression Axis: Experimental Realm:
Present Per f e c t Event Past

11. tense use in science and mythology
Facts in the Endogenous small RNAs (miRNAs) regulate I sing of golden-throned Hera whom Rhea
eternal gene expression by mechanisms conserved bare. Queen of the immortals is she, surpassing
present across metazoans. all in beauty: she is the sister and the wife of
loud-thundering Zeus, --the glorious one
whom all the blessed throughout high
Olympus reverence and honor.
Events in the Vehicle-treated animals spent equivalent Now the wooers turned to the dance and to
simple past time investigating a juvenile in the first and gladsome song, and made them merry, and
second sessions in experiments waited till evening should come; and as they
conducted in the NAC and the striatum: made merry dark evening came upon them.
T1 values were 122 ± 6 s and 114 ± 5 s.
Events with We also generated BJ/ET cells expressing And she took her mighty spear, tipped with
embedded the RASV12-ERTAM chimera gene, which is sharp bronze, heavy and huge and strong,
facts only active when tamoxifen is added (De wherewith she vanquishes the ranks of men-of
Vita et al, 2005). warriors, with whom she is wroth, she, the
daughter of the mighty sire.
Attribution in miRNAs have emerged as important In this book I have had old stories written
the present regulators of development and control down, as I have heard them told by intelligent
perfect processes such as cell fate determination people, concerning chiefs who have held
and cell death (Abrahante et al., 2003, dominion in the northern countries, and who
Brennecke et al., 2003, Chang et al., 2004, spoke the Danish tongue; and also concerning
Chen et al., 2004, Johnston and Hobert, some of their family branches, according to
2003, Lee et al., 1993, ... what has been told me.
Implications These results indicate that although Now it is said that ever since then
are hedged, miR-372&3 confer complete protection to whenever the camel sees a place where ashes
and in the oncogene-induced senescence in a manner have been scattered, he wants to get revenge
present tense similar to p53 inactivation, the cellular with his enemy the rat and stomps and rolls in
response to DNA damage remains intact the ashes hoping to get the rat

12. #4: ‘A fact is a claim, agreed by a committee’ Yabuta, JBioChem 2007
miR-372 and miR-373 target the
Lats2 tumor suppressor
To investigate the possibility Voorhoeve et al., (Voorhoeve et al., 2006)
that miR-372 and miR-373 suppress
the expression of LATS2, we...
2006
Raver-Shapira et.al, JMolCell 2007
Therefore, these results point to two miRNAs, miRNA-372 and-373, function as
LATS2 as a mediator of the miR-372 and potential novel oncogenes in testicular germ cell
miR-373 effects on cell proliferation and tumors by inhibition of LATS2 expression, which
tumorigenicity, suggests that Lats2 is an important tumor
suppressor (Voorhoeve et al., 2006).
KnownFact KnownFact
Concepts Hypothesis Implication Fact
Goal
Goal
Method Result Method Result
Data Data
Experiment 1 Experiment 2

13. so should we just
keep reading papers?

14. possible representation:
hypotheses, evidence and relationships
PHC undergo Growth arrest
Paper A: Paper B:
implication implication
g
n nin
method method link
fact rpi method
de fact
un
goal fact goal fact
results
results
data 1
data 4
data 2 data 3
data 5 data 6

15. HYPotheses, Evidence and Relationships
- Goal: Align and expand existing efforts on detection and analysis
of Hypotheses, Evidence & Relationships
- Partners:
- Harvard/MGH: SWAN, ARF
Hypothesis 22: Intramembrenous Aβ dimer may be toxic.
- Open University: Cohere
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
- Oxford University: CiTO, eLearning/Rhetoric
generated, but instead exert their toxic effects by competing with and compromising
the functions of intramembranous segments of membrane-bound proteins that serve
- many criticalaTags
DERI: SALT, functions.
- University of Trento: LiquidPub
- Xerox Research: XIP hypothesis identifier
- U Tilburg: ML for Science
- Elsevier, UUtrecht: Discourse analysis of biology

16. W3C HCLS Sig
Rhetorical Document Task
- Part of subgroup on discourse structure
- Goal: come up with a format for authors to explicitly
create rhetorical/argumentational structure
- Make life of annotators easier!
- Please correct our ‘Pharma Use case’!
- http://esw.w3.org/topic/HCLSIG/SWANSIOC/Actions/
RhetoricalStructure/

17. some things
elsevier is doing

18. collection three dimensions of annotation
data
document
claim
triple Automated Copy Editing
entity
author/editor typesetter/EW/SD reader/curator/data mining
manual Reflect
semi-automated
automated

19. .XMP RDF in all our PDFs: Dublin Core + PRISM

20. Linked Data for Elsevier XML
but we all know
she was wrong that day
said @anita
on Feb 25 2010
this section argues that
<ce:section id=#123> ‘the moon is made of
cheese’
immutable, $$, proprietary dynamic, personal, task-driven, - open?

21. some things to mark up: EMTREE

22. ‘Community effort to establish an open,
independent registry of Researcher Identifiers’

23. questions?
a.dewaard@elsevier.com
http://elsatglabs.com/labs/anita
@anitawaard on Twitter