'Stories that persuade with data' - talk at CENDI meeting January 9 2014
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Scientific articles tell stories with a structure similar to traditional stories. They introduce a topic, present a hypothesis and methods, and report results. As claims from papers are cited in subsequent work, they become established as facts. Networks of claims and data could improve knowledge by formally representing claims and connecting them to underlying data and other evidence. This would help address issues like reproducibility and data accessibility. Research data management is evolving to better preserve and share data through repositories, standardized workflows, and initiatives to develop sustainable data infrastructures.
![Scientific articles are stories...
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
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
Name
dAtX-1 and hAtx-1 Induce Similar Phenotypes When Overexpressed in File
Goldilocks was hungry.
Subgoal
Subgoal
test the function of the AXH domain
She tasted the porridge from the
first bowl.
Attempt
Method
overexpressed dAtx-1 in flies using the GAL4/UAS system (Brand and
Perrimon, 1993) and compared its effects to those of hAtx-1.
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 a
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
Data
(data not shown),
Results
both genotypes show many large holes and loss of cell integrity at 28 days
So, she tasted the porridge from the Activity
second bowl.
3
This porridge is too cold, she said
Outcome
Theme
Episode 1](https://image.slidesharecdn.com/storiesthatpersuade-140109104650-phpapp02/85/Stories-that-persuade-with-data-talk-at-CENDI-meeting-January-9-2014-3-320.jpg)
'Stories that persuade with data' - talk at CENDI meeting January 9 2014
- 1. Stories, that Persuade With Data: Some Thoughts on Making Networks of Knowledge. Anita de Waard VP Research Data Collaborations [email protected]
- 2. Outline: • Stories, that persuade with data • Networks of claims and data • Research Data Management: some thoughts.
- 3. Scientific articles are stories... 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 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 Name dAtX-1 and hAtx-1 Induce Similar Phenotypes When Overexpressed in File Goldilocks was hungry. Subgoal Subgoal test the function of the AXH domain She tasted the porridge from the first bowl. Attempt Method overexpressed dAtx-1 in flies using the GAL4/UAS system (Brand and Perrimon, 1993) and compared its effects to those of hAtx-1. 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 a 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 Data (data not shown), Results both genotypes show many large holes and loss of cell integrity at 28 days So, she tasted the porridge from the Activity second bowl. 3 This porridge is too cold, she said Outcome Theme Episode 1
- 4. ...that persuade (editors/authors/readers!)… Aristotle Quintilian Scientific Paper prooimion The introduction of a speech, where one announces the Introduction subject and purpose of the discourse, and where one usually / exordium employs the persuasive appeal to ethos in order to establish credibility with the audience. Introduction: positioning prothesis Statement of The speaker here provides a narrative account of what has Facts/narrati happened and generally explains the nature of the case. o 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 Proof/ 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 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. pistis epilogos
- 6. As claims get cited, they become facts: Voorhoeve et al, Cell, 2006: To investigate the possibility that miR-372 and miR-373 suppress the expression of LATS2, we... Hypothesis Therefore, these results point to LATS2 as a mediator of the miR-372 and miR-373 effects on cell proliferation and tumorigenicity, Implication Raver-Shapira et.al, JMolCell 2007 Cited Implication ... 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). Yabuta, JBioChem 2007: miR-372 and miR-373 target the Lats2 tumor suppressor (Voorhoeve et al., 2006) Fact
- 7. There are many problems with this system! • There are too many papers to read – for people. • Papers are not written in a way that makes reading easy – for computers. • Issues with reproducibility. • Hard to access or assess the data. • And how do we know how many data points a claim was based on?
- 8. What might work: networks of claims and data: Claim PHC undergo Paper A: Growth arrest Paper B: implication implication method fact method link method fact goal fact goal fact results results data 1 data 4 data 2 data 3 data 5 data 6
- 9. How do we get there? Find claims: E.g., scientific discourse analysis: In contrast with previous hypotheses compact plaques form before significant deposition of diffuse A beta, suggesting that different mechanisms are involved in the deposition of diffuse amyloid and the aggregation into plaques. Entities Relationships Temporality Connections Status core information (proposition) information extraction discourse structure discourse analysis rhetorical metadiscourse discourse analysis thematic roles Sándor, Àgnes and de Waard, Anita, (2012).
- 10. Turn claims into formal representations: Biological statement with BEL/ epistemic markup BEL representation: Epistemic evaluation These miRNAs neutralize p53-mediated CDK inhibition, possibly through direct inhibition of the expression of the tumor-suppressor LATS2. r(MIR:miR-372) |(tscript(p(HUGO:Trp53)) -| kin(p(PFH:”CDK Family”))) Increased abundance of miR372 decreases abundance of LATS2 r(MIR:miR-372) -| r(HUGO:LATS2) Value = Possible Source = Unknown Basis = Unknown Biological statement with Medscan/epistemic markup MedScan Representation: Epistemic evaluation Furthermore, we present evidence that the secretion of nesfatin-1 into the culture media was dramatically increased during the differentiation of 3T3-L1 preadipocytes into adipocytes (P < 0.001) and after treatments with TNF-alpha, IL-6, insulin, and dexamethasone (P < 0.01). IL-6 NUCB2 (nesfatin-1) Relation: MolTransport Effect: Positive CellType: Adipocytes Cell Line: 3T3-L1 Value = Probable Source = Author Basis = Data
- 11. Use Linked Data to point to claims, and connect them: the xml is fixed, but the structure is open! allows for layers of annotation but we all know she was deluded then said @anitawaard on January 9, 2014 <ce:section id=#123> this says mice like cheese
- 12. What about the data? • • • • Can we see it? How can we evaluate it? Can it be reproduced? Can we combine or compare data points?
- 13. Elsevier Research Data Services • Goals: – – – – Increase data preservation: quantity and quality Improve data use: by and for authors, readers, and lay people Enhance interoperability: between systems, journals, databases Help develop a sustainable data infrastructure. • Guiding principles: – In principle, all data stays open – Work with existing repositories and tools (so URLs, front end etc stay where they are) – 2013/2014: Series of pilots and questionnaires to drive data strategy/data policy and contribute optimally to an integrated data infrastructure, enabling networked knowledge.
- 14. Research data management today: Using antibodies and squishy bits Grad Students experiment and enter details into their lab notebook. The PI then tries to make sense of their slides, and writes a paper. End of story.
- 15. Where research data goes now: > 50 My Papers 2 M scientists 2 My papers/year A small portion of data (1-2%?) stored in small, topic-focused data repositories Majority of data (90%?) is stored on local hard drives PDB: 88,3 k PetDB: 1,5 k MiRB: 25k Some data (8%?) stored in large, generic data repositories Dryad: 7,631 files SedDB: 0.6 k TAIR: 72,1 k Dataverse: 0.6 My Institutional Repositories
- 16. An Urban Legend is born: • How can we make a standard neuroscience wet lab more data-sharing savvy? • Incorporate structured workflows into the daily practice of a typical electrophysiology lab (the Urban Lab at CMU) – What does it take? – Where are points of conflict? • 1-year pilot, funded by Elsevier RDS: – CMU: Shreejoy Tripathy, manage/user test – Elsevier: development, UI, project management
- 18. What does high-quality data curation take? Pilot project with IEDA: – Build a database for lunar geochemistry – Write joint report on building repository, curation, costs and challenges
- 19. Some thoughts about the role of the institute: Funding Agencies Performance reporting Library Institution Research Office Usage/Citation reporting Institutional Repository Indexing Integrated Performance Query Usage/Citation reporting Indexing Research Data Repositories Unified Metadata Layer Curation Deposit / Store Indexing Generic Data Storage (such as Dropbox) Electronic Lab Notebooks Integrated Data Search Data Flow Deposit / Store Indexing & Search Researchers Performance Reporting
- 20. Data Initiatives: • Data Citation group: – Synthesize principles of proper data citation – ‘Declaration of Data Citation Principles’, 8 principles of successful data citation -http://www.force11.org/datacitation • Resource Identification Initiative: – Promote research resource identification, discovery, and reuse – Resource Identification Portal http://scicrunch.com/resources – Central location for obtaining research resource identifiers (RRIDs) for materials and software used in biomedical research • Antibody: Abgent Cat# AP7251E, ABR:AB_2140114 • Tool: CellProfiler Image Analysis Software, NIFRegistry:nif-0000-00280 • Organism: MGI:MGI:3840442
- 21. In summary: • Stories, that persuade with data: – We need better ways to communicate science! • Networks of claims and data: – Promising steps towards identifying claims – Entity identification and Linked Data helps – Problem: access to data • Research Data Management: – Key issue: get data in up-front – Evaluate and scale up role of repositories – Codevelop view of role of institutions/libraries
- 22. Questions? Anita de Waard VP Research Data Collaborations [email protected] http://researchdata.elsevier.com/
- 23. Thank you! Collaborations and discussions gratefully acknowledged: • CMU: Nathan Urban, Shreejoy Tripathy, Shawn Burton, Rick Gerkin, Santosh Chandrasekaran, Matthew Geramita, Eduard Hovy • UCSD: Phil Bourne, Brian Shoettlander, David Minor, Declan Fleming, Ilya Zaslavsky • NIF/Force11: Maryann Martone, Anita Bandrowski • OHSU: Melissa Haendel, Nicole Vasilevsky • California Digital Library: Carly Strasser, John Kunze, Stephen Abrams • IEDA: Kerstin Lehnert, Annika • Elsevier: Mark Harviston, Jez Alder, David Marques
Editor's Notes
- #18: Walk through pieces 1 by 1, also mention that this is very much an uncompleted work in progress