Unknown Unknowns

Reinventing the Research Article -
Seven Questions on
Science Publishing

Anita de Waard
Researcher Disruptive Technologies,
Elsevier Labs
NWO - Casimir Grantee,
Utrecht University

ELPUB 2008

Seven ’known knowns’ in online science publishing:

1. The internet has caused an information overload.

2. Science papers contain facts.

3. The narrative research article is outdated and needs to be
replaced.

replaced.
4. Since words contain meaning,

replaced.
5. And words (and logic) contain scientiﬁc fact,

replaced.
6. We just need to model them with xml + rdf;

replaced.
6. We just need to model them with xml + rdf;
7. And the publishers should stop making all these papers.

1. The internet has caused an information overload

- My own experience (as a researcher):


- Easy: ﬁnd what I know exists



- OK: Finding things I expect hope exist




- Hard: making sure I haven’t missed anything





- However, none of these make me feel overwhelmed.






- Infuriating:






- Infuriating:

- Trying to respond to people who ask me something






- Infuriating:


- Managing three email accounts on 4 computers






- Infuriating:



- Following up on plans and projects






- Infuriating:



- Following up on plans and projects

- However, we can improve the delivery of science content online.

- Pick (carve out) a ﬁrst set of user needs, e.g.:

- Locate

- Locate
- Understand

- Locate
- Understand
- Believe (Be convinced)

- Locate
- Understand
- Explore

- Locate
- Understand
- Explore
- But this does not address WHAT you want to Locate, Understand, ..

- Locate
- Understand
- Explore
- Semantic network in pharmacology: ‘Grey out what I already know’

- Locate
- Understand
- Explore
- Semantic network in pharmacology: ‘Grey out what I already know’
1. How can we model a user’s interest?

2. Science papers contain facts

- With FEBS Letters Editorial Ofﬁce in Heidelberg/
MINT Database in Rome


- Structured Digital Abstract [Gerstein et. al]: ‘machine-readable
XML summary of pertinent facts’



- For FEBS: provide proteins, methods, protein-protein interactions,
as given in MINT:



as given in MINT:

- 2008: authors provide, editors check



as given in MINT:

- 2008: authors provide, editors check

- 2009: Word Plug-in tool suggests, authors (and editors) check

- Issue: authors cannot be curators!

- Fact is not claim, but created by consensus post-hoc

- How do we model the process of consenses-building, of
disagreement, of fact creation, of mistrust and doubt?

- How do we model the process of consenses-building, of
disagreement, of fact creation, of mistrust and doubt?
2. Can we create (tools for) an ontology of doubt?

3. The narrative RA should be replaced

Aristotle Quintilian Cell APA Style Guide

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

The second part of a classical oration, following the introduction or exordium.
The speaker here provides a narrative account of what has happened and
Statement of
prothesis narratio generally explains the nature of the case. Quintilian adds that the narratio is Introduction Introduction
Facts
followed by the propositio, a kind of summary of the issues or a statement of
the charge.

Coming between the narratio and the partitio of a classical oration, the
Summary propostitio propositio provides a brief summary of what one is about to speak on, or Abstract Abstract
concisely puts forth the charges or accusation.

Following the statement of facts, or narratio, comes the partitio or divisio. In
Division/ this section of the oration, the speaker outlines what will follow, in accordance Table of
partitio Article Outline
outline with what's been stated as the status, or point at issue in the case. Quintilian Contents
suggests the partitio is blended with the propositio and also assists memory.

Following the division / outline or partitio comes the main body of the speech
pistis Proof confirmatio where one offers logical arguments as proof. The appeal to logos is Results Methods, Results
emphasized here.

Following the the confirmatio or section on proof in a classical oration, comes
Refutation refutatio the refutation. As the name connotes, this section of a speech was devoted to Discussion Discussion
answering the counterarguments of one's opponent.

Following the refutatio and concluding the classical oration, the peroratio
epilogos peroratio conventionally employed appeals through pathos, and often included a Discussion Discussion
summing up (see the figures of summary, below).

The Story of Goldilocks Story Grammar Paper The AXH Domain of Ataxin-1 Mediates
and the Three Bears

Once upon a time
Time Setting Background
Neurodegeneration through Its Interaction with Gﬁ-1/
Senseless Proteins
The mechanisms mediating SCA1 pathogenesis are still not fully
Aristotle Quintilian understood, but some general principles have emerged. Guide
Cell APA Style
a little girl named Goldilocks Characters Objects of study the Drosophila Atx-1 homolog (dAtx-1) which lacks a polyQ tract,
The introduction of a speech, where one announces the subject and purpose
She went for a Introduction
prooimion walk in the exordium
Location of the discourse, and where one usually employs the persuasive appeal of effects and interactions to those of
Experimental studied and compared in vivo Introduction Introduction
forest. Pretty soon, she came ethos in order to establish credibility human protein
setup the with the audience.
upon a house.
She knocked and, when no one Goal The second part of a classical oration, following the introduction or exordium.function contributes to SCA1
Theme Research Gain insight into how Atx-1's
answered, Statement of
pathogenesis. How these interactions might contribute to the
The speaker here provides a narrative account of what has happened and
goal
prothesis narratio generally explains the nature of the case. Quintilian process andnarratio is might cause toxicity in only a subs
disease adds that the how they Introduction Introduction
Facts
followed by the propositio, a kind of summary neurons in SCA1 is not fully understood.
of of the issues or a statement of
the charge.
she walked right in. Attempt Hypothesis Atx-1 may play a role in the regulation of gene expression
Coming between the narratio and the partitio of a classical oration, the
Summary propostitio propositio provides a brief summary of what one is about to speak on, or Abstract Abstract
At the table in the kitchen, there Name EpisodeconciselyNameforth the charges or accusation. Induce Similar Phenotypes When
1 puts dAtX-1 and hAtx-1
were three bowls of porridge. Overexpressed in Files
Following the statement of facts, or narratio, comes the partitio or divisio. In
Division/
Goldilocks was hungry. Subgoalthis section of the oration, the speaker outlines what function of the AXH domain
Subgoal test the will follow, in accordance Table of
partitio Article Outline
outline with what's been stated as the status, or point at issue in the case. Quintilian Contents
She tasted the porridge from Attemptsuggests the partitio is blended with the propositio and also assists memory. using the GAL4/UAS system (Brand
Method overexpressed dAtx-1 in flies
the first bowl. and Perrimon, 1993) and compared its effects to those of hAtx-1.
Following the division / outline or partitio comes the main body of the speech
This porridge is too hot! sheconfirmatio
pistis Proof Outcome where one offers logical arguments asOverexpression of logos is by Rhodopsin1(Rh1)-GAL4, which drive
Results proof. The appeal to dAtx-1 Results Methods, Results
exclaimed. emphasized here.expression in the differentiated R1-R6 photoreceptor cells
(Mollereau et al., 2000 and O'Tousa et al., 1985), results in
Following the the confirmatio or section on proof in a classical oration, comes as does overexpression of hAtx-1
neurodegeneration in the eye,
Refutation refutatio the refutation. As the name connotes, this section of a speech at 2 days after eclosion, overexpression of either
[82Q]. Although was devoted to Discussion Discussion
answering the counterarguments of one's opponent. obvious morphological changes in the
Atx-1 does not show
So, she tasted the porridge Data (data not shown),
photoreceptor cells
from the second bowl. Following the refutatio and concluding the classical oration, the peroratio
This porridge is too cold, sheperoratio
epilogos Outcome conventionally employed appeals through pathos, and often included a large Discussion loss ofDiscussion
Results both genotypes show many holes and cell integrity a
said summing up (see the figures of summary, below).
28 days
So, she tasted the last bowl of Data (Figures 1B-1D).
porridge.
Ahhh, this porridge is just right, Outcome Results Overexpression of dAtx-1 using the GMR-GAL4 driver also induce
she said happily and eye abnormalities. The external structures of the eyes that
overexpress dAtx-1 show disorganized ommatidia and loss of

Discourse Segments:

Discourse Segments:

- “A text is made up of Discourse Segments and the relations
between them” - Grosz and Sidner, Mann-Thomson, Marcu,
Swales

Discourse Segments:

Swales

- Discourse Segment Purpose: element that has a consistent
rhetorical/pragmatic goal.

Discourse Segments:

Swales


- Deﬁne for Biological Research Article:

Discourse Segments:

Swales


- Deﬁne for Biological Research Article:
<EXPERIMENTS>
<Experiment>
<Header header="h1">p53-Independent Initiation of G1 Arrest Induced by IR</Header>
<Fact fact="fa1" factref="br26">Since the transcriptional response by p53 is a relatively slow process,</Fact>
<Problem problem="p1">we asked whether initiation of a G1 arrest following genotoxic stress requires p53.
<Problem>
<Method method="m1">We generated an MCF-7 derivative </Method>
<Fact fact="fa2" factref="br24">that expresses the HPV16 E6 protein, which mediates degradation of p53
(<Bibref bib="br24">[24]</Bibref>).</Fact>
<Result result="r1">In the presence of E6, p53 stabilization in response to IR was almost completely prevented in
MCF-7 cells (<Figref ﬁgref="agami1.gif">Figure 1A).</Figref></Result>
<Result result="r2">Consistent with this, no induction of p21cip1 by IR was seen in the E6-expressing MCF-7 cells

- Narrative is how stories are told; ‘the truth can only be told in
stories’....

stories’....
- Scientiﬁc rhetoric is contained within the narrative

stories’....
- Main goal of article is to persuade: ‘ The author is a medium that
enables the article to get itself published (a la selﬁsh gene/meme)’

stories’....
- Science happens in language - science is done by creating successful
persuasive texts IN ENGLISH! (empowerment rests on mastery of
this genre)

stories’....
this genre)
- How to disentangle good science from good writing?

stories’....
this genre)
- How to disentangle good science from good writing?
3. How can we better represent online narrative? ...


PHC undergo Growth arrest



Paper A:
implication
method fact
goal fact
results



Paper A:
implication
method fact
goal fact
results

data 1

data 2 data 3



Paper A: Paper B:
implication implication
method fact method fact
goal fact goal fact
results
results

data 1
data 4
data 2 data 3
data 5 data 6



Paper A: Paper B:
g
nnin
method fact rpi method
de fact
un
goal fact goal fact
results
results

data 1
data 4
data 2 data 3
data 5 data 6



Paper A: Paper B:
method method link
fact method fact
goal fact goal fact
results
results

data 1
data 4
data 2 data 3
data 5 data 6

- How to develop systems that ‘reconstruct the salami’


- Claim-evidence networks: identify nr. of experiments supporting a
claim, vs. nr. of papers containing two words in a sentence?


- Claim-evidence networks: identify nr. of experiments supporting a
claim, vs. nr. of papers containing two words in a sentence?
3. How can we better represent collections of online
narratives?

4. Words contain meaning
Sicilian?


- ‘A word is worth a thousand pictures’ (Don Loritz)


- The meaning of words occurs in context and is dependent
on knowledge and experience


- The meaning of words occurs in context and is dependent
on knowledge and experience
- This is even more so in science:
PSA = Prostate-Speciﬁc Antigen or Pot Smokers
Association of America?

- Cognitive linguistics: language and cognition cannot be separated -
language acts are cognitive acts


- Lakoff, metaphor: ‘anger is heat’



- Meaning is created in the mind:
a word is not (only) a ‘particle’ but (also) a ‘wave’:
Hearing/reading is not unpacking a package, but resonating at a
speciﬁc frequency - context is its medium - context-free language
does not exist!



- Meaning is created in the mind:
a word is not (only) a ‘particle’ but (also) a ‘wave’:
Hearing/reading is not unpacking a package, but resonating at a
speciﬁc frequency - context is its medium - context-free language
does not exist!
4. How do we model cognitive context?

5. Words (and logic) contain scientiﬁc fact

• “[Y]ou can transform a fact into fiction or a fiction into fact just by
adding or subtracting references [and data]”
– Bruno Latour, ‘Science in Action’,1987

“We generated an MCF-7
derivative that expresses the
HPV16 E6 protein, which
mediates degradation of p53
([24]).”

24. M. Scheffner, B.A. Werness, J.M. Huibregtse, A.J. Levine and
“We generated an MCF-7 P.M. Howley, The E6 oncoprotein encoded by human
papillomavirus types 16 and 18 promotes the degradation of
derivative that expresses the p53. Cell 63 (1990), pp. 1129–1136. SummaryPlus | Full Text
+ Links | PDF (1728 K) | Abstract + References in Scopus |
HPV16 E6 protein, which Cited By in Scopus

([24]).”


([24]).”
“In the presence of E6, p53
stabilization in response to IR
was almost completely
prevented in MCF-7 cells
(Figure 1A).”


([24]).”
“In the presence of E6, p53
stabilization in response to IR
was almost completely
prevented in MCF-7 cells
(Figure 1A).” Figure 1. Initiation and Maintenance of G1 Arrest Induced by
IR(A) Stable MCF-7 clones containing either pCDNA3.1 (Neo)
or pCDNA3.1-E6 were irradiated (20 Gy), and cellular protein
extracts were made 2 hr later, separated on 10% SDS PAGE,
and immunoblotted to detect p53 and cyclin D1 proteins.


- Essential persuasive elements are non-textual



- Open Data, how to incorporate into ‘text mining’?




- Bioimage consortium (Shotton, Oxford): access biology images
across a variety of sources (PLoS, Nature, Elsevier...) and create
common metadata format





- SPIDER: Allowing shared access to epidemiology data (meta-
epidemiology)





epidemiology)

- Tie in to Open Data initiative, generalise, get buy in, sustainability:





epidemiology)

- Tie in to Open Data initiative, generalise, get buy in, sustainability:
5. How do we represent (and access) non-textual
elements?

6. Just model the facts with xml + rdf


- Content in XML - but what about overlapping tags?



- Versioning in DTDs/Schemas? Principle of hierarchical trees - not
always best model of a content set




- First pass at relations in RDF (Resource Description Framework:





- Cohere: Open University - (open!) system of creating and
linking claims





linking claims

- More experiments with RDF:





linking claims


- DOPE: Semantic access to heterogeneous data in pharmacology





linking claims



- OKKAM: Entity-centric web (EU-funded)

1. DOPE (2003) the facts with xml + rdf
6. Just model
deduplicate thesaurus term


always best model of a content set visualise overlap results


select co-occurrence terms
linking claims


see results set + link to full-text

- OKKAM: Entity-centric web (EU-funded)

8

- Yes, but:

- Yes, but:

- In practice: ScienceDirect does not use our XML... (shhh....)

- Yes, but:


- At Elsevier: Project Harpoon: ‘stab’ the document with
metadata, asynchronous, linked in (XPath/XQuery), distributed

- Yes, but:



- Not solved in XML - how to access a phrase inside an article:

- Yes, but:




- access inside a PDF by coordinates? Format, content changes

- Yes, but:





- add IDs to every single element? Format, content, version
changes?

- Yes, but:





changes?

- How to represent relations, even if we know where they link?

- Yes, but:





changes?

- How to represent relations, even if we know where they link?
6. How can we better model discourse elements (and
relations)?

7. And publishers should stop making all those papers.

- 6 uses of a RA:

- 6 uses of a RA:
- job application

- 6 uses of a RA:
- job application
- report card

- 6 uses of a RA:
- job application
- report card
- thesis

- 6 uses of a RA:
- job application
- report card
- thesis
- conference tickets

- 6 uses of a RA:
- job application
- report card
- thesis
- research assessment

- 6 uses of a RA:
- job application
- report card
- thesis
- and yes, by the way, reporting on scientiﬁc work.

- 6 uses of a RA:
- job application
- report card
- thesis
- Scientists are evaluated largely based on publications:
this enables their production to be evaluated by non-specialists

- 6 uses of a RA:
- job application
- report card
- thesis
- Scientists are evaluated largely based on publications:
this enables their production to be evaluated by non-specialists

- This places an undue stress on quantity, conformity (for risk of
being rejected), publishing for its own sake.

The real challenge:

The real challenge:

- in Holland, chemistry departments are dwindling

The real challenge:


- in large companies, nr. of PhDs is inversely proportional to power

The real challenge:



- direction of scientiﬁc research determined by managers for adolescents

The real challenge:



For science to survive, we need:

The real challenge:




- ‘Hanny’, who found a Voorwerp on GalaxyZoo.org

The real challenge:





- Prof. Twalib Ngoma, Professor of Oncology from
Dar-Es-Salaam, Nigeria

The real challenge:






- Prof. Zimitri Erasmus, Sociologist from Cape Town

The real challenge:






How can we access their science?

The real challenge:






How can we access their science?
7. How can we disentangle communication and evaluation
(‘metric of attribution’ - virtual RFID)?

Seven ‘Known Unknowns’ in Online Science Publishing

2. Can we create an ontology of doubt?

3. How can we better represent collections of online narrative?

5. How do we represent and access non-textual elements?

6. How can we better model discourse elements and relations?

6. How can we better model discourse elements and relations?
7. How can we disentangle communication and evaluation?

Unknown Unknowns

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