ARE WE FINALLY READY FOR TRANSCLUSION?*

Dr. Paul Groth | @pgroth | pgroth.com

Disruptive Technology Director

Elsevier Labs | @elsevierlabs

The Future of Text Symposium

September 2017

Thanks Anita de Waard

* AT LEAST FOR ACADEMIC TEXT

TRANSCLUSION

Nelson, T. H. (1995). "The Heart of

Connection: Hypermedia Unified by

Transclusion". Communications of

the ACM. 38 (8): 31-33.

doi:10.1145/208344.208353

3

Enabling data-centric science

[[1] Bleecker, J. ‘A Manifesto for Networked Objects — Cohabiting with Pigeons, Arphids and Aibos in the Internet of Things

http://nearfuturelaboratory.com/2006/02/26/a-manifesto-for-networked-objects/

2] Bechhofer, S., De Roure, D., Gamble, M., Goble, C. and Buchan, I. (2010) Research Objects: Towards Exchange and

Reuse of Digital Knowledge. In: The Future of the Web for Collaborative Science (FWCS 2010), April 2010, Raleigh, NC,

USA. http://precedings.nature.com/documents/4626/version/1

[3] Neylon, C. ‘Network Enabled Research: Maximise scale and connectivity, minimise friction’, http://cameronneylon.net/blog/network-enabled-research/ ‘

Internet of things: (Bleecker, [1])

Interact with ‘objects that blog’ or ‘Blogjects’, that:

track where they are and where they’ve been;have

histories of their encounters and experienceshave agency

- an assertive voice on the social web [2]

Research Objects: (Bechofer et al, [2])

Create semantically rich aggregations of resources, that

can possess some scientific intent or support some

research objective

Networked Knowledge: (Neylon, [3])

If we care about taking advantage of the web and

internet for research then we must tackle the building of

scholarly communication networks.

These networks will have two critical characteristics:

scale and a lack of friction. [3]

From Anita de Waard

A. Changing the unit and form of the research paper

1998: Modular papers:

2000: Argumentation networks:

1987 20171997 2007

2015: Lorena Barba, GWU, teaching in Python:

From Anita de Waard

5

Scientific articles are stories that persuade with data

The Story of Goldilocks and the

Three Bears

Story Grammar Paper The AXH Domain of Ataxin-1 Mediates Neurodegeneration

through Its Interaction with Gfi-1/Senseless Proteins

Once upon a time Time Setting Background The mechanisms mediating SCA1 pathogenesis are still not fully

understood, but some general principles have emerged.

a little girl named Goldilocks Characters Objects of study the Drosophila Atx-1 homolog (dAtx-1) which lacks a polyQ tract,

She went for a walk in the forest.

Pretty soon, she came upon a

house.

Location Experimental

setup

studied and compared in vivo effects and interactions to those of the

human protein

She knocked and, when no one

answered,

Goal Theme Research

goal

Gain insight into how Atx-1's function contributes to SCA1

pathogenesis. How these interactions might contribute to the disease

process and how they might cause toxicity in only a subset of neurons

in SCA1 is not fully understood.

she walked right in. Attempt Hypothesis Atx-1 may play a role in the regulation of gene expression

At the table in the kitchen, there

were three bowls of porridge.

Name Episode 1 Name dAtX-1 and hAtx-1 Induce Similar Phenotypes When Overexpressed in

Files

Goldilocks was hungry. Subgoal Subgoal test the function of the AXH domain

Method overexpressed dAtx-1 in flies using the GAL4/UAS system (Brand and

Perrimon, 1993) and compared its effects to those of hAtx-1. She tasted the porridge from the

first bowl.

Attempt

This porridge is too hot! she

exclaimed.

Outcome Results Overexpression of dAtx-1 by Rhodopsin1(Rh1)-GAL4, which drives

expression in the differentiated R1-R6 photoreceptor cells (Mollereau et

al., 2000 and O'Tousa et al., 1985), results in neurodegeneration in the

eye, as does overexpression of hAtx-1[82Q]. Although at 2 days after

eclosion, overexpression of either Atx-1 does not show obvious

morphological changes in the photoreceptor cells

So, she tasted the porridge from

the second bowl.

Activity Data (data not shown),

This porridge is too cold, she said Outcome Results both genotypes show many large holes and loss of cell integrity at 28

days

So, she tasted the last bowl of

porridge.

Activity Data (Figures 1B-1D).

Ahhh, this porridge is just right,

she said happily and

Outcome Results Overexpression of dAtx-1 using the GMR-GAL4 driver also induces

eye abnormalities. The external structures of the eyes that overexpress

dAtx-1 show disorganized ommatidia and loss of interommatidial

bristles

she ate it all up. Data (Figure 1F),

Aristotle Quintilian Scientific Paper

prooimionIntroduction/

exordium

The introduction of a speech, where one announces the subject and

purpose of the discourse, and where one usually employs the

persuasive appeal to ethos in order to establish credibility with the

audience.

Introduction: positioning

prothesisStatement of

Facts/narrati

o

The speaker here provides a narrative account of what has happened

and generally explains the nature of the case.

Introduction: research

question

Summary/

propostitio

The propositio provides a brief summary of what one is about to speak

on, or concisely puts forth the charges or accusation. Summary of contents

pistisProof/

confirmatio

The main body of the speech where one offers logical arguments as

proof. The appeal to logos is emphasized here.Results

Refutation/

refutatio

As the name connotes, this section of a speech was devoted to

answering the counterarguments of one's opponent.Related Work

epilogos peroratio

Following the refutatio and concluding the classical oration, the

peroratio conventionally employed appeals through pathos, and often

included a summing up.

Discussion: summary,

implications.

Anita

de Waard

TREND: THE ATOMINZATION OF SCHOLARY COMMS

ATOMIZATION: PUBLISH RESOURCES

ATOMIZATION: COMMENTARY & ANNOTATIONS

ATOMIZATION: CLAIMS & CONCEPTS

nanopublications

TREND: PERSISTENT IDS EVERYWHERE

We are adding PIDs for Funding

information, Licensing, Versioning

Every paper we publish has a DOI (= PID).

ORCID enables every researcher to

have a PID

Every dataset we publish has a

DOI (= PID)

Knowledge components are identified

through DOIs, e.g.:

• Chemicals

• Physical Samples

• Resource Identifiers

• Organisms

• Materials

We are helping to create Open Linked Data networks of PIDs

TREND: DUPLICATION

“In her first revision, the author

completely replaced the description of

the method with a citation, as shown in

Fig. Fig.2b.2b. This avoids the problem

of self-plagiarism, but the absence of

any detail makes the method section

look a little thin.”

TREND: MACHINE WRITING

Towards Automating Data Narratives.

Gil, Y.; and Garijo, D. In Proceedings of the

Twenty-Second ACM International Conference

on Intelligent User Interfaces (IUI-17),

Limassol, Cyprus, 2017.

AN EXISTING INFRASTRUCTURE FOR TRANSCLUSION?

See also: https://web.hypothes.is/blog/dois/

Machine

Writing

PIDS w/

Metadata

Background Quotation in Context

Assembled w/ Jupyter Notebooks

Open Annotation

Rendered

FUTURE: CONSTRUCTING SCHOLARLY TEXT FROM

DISTRIBUTED RESEARCH OBJECTS?

• Transclude data, methods, background

through the scholarly infrastructure

• Have the machine help generate text that

can be easily included

• Authors can shape their narrative using

blocks within notebooks

• Notebooks support rendering for different

consumption formats