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Scientific papers as open discovery tools

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Information about Scientific papers as open discovery tools
Technology

Published on March 10, 2014

Author: lemberger

Source: slideshare.net

Description

Presentation given at the Advanced Lecture Course on Systems Biology 2014, in Innsbruck.
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EMBO Scientific Publishing Thomas Lemberger Chief Editor, Molecular Systems Biology Deputy Head of Publications, EMBO 1. Editorial Process 2. Scientific integrity 3. Integrating data in papers

Scientific publishing “The publication of scientific information is intended to move science forward. More specifically, the act of publishing is a quid pro quo in which authors receive credit and acknowledgment in exchange for disclosure of their scientific findings.”

disclose findings

credit

move science forward

critical evaluation

critical evaluation

editorial process

editorial process @EMBO

EMBO Scientific Publications • All areas of molecular & cell biology • All areas of molecular & cell biology • First journal launched by • Short-format papers EMBO (1982) • Science & Society section • Systems biology, synthetic biology, systems medicine • At the interface between basic and clinical life sciences • Open Access • Open Access

quality

quality community

OPEN ACCESS R Aebersold GM Church E Liu L Hood Scope & general policies Senior Editors Advisory Board P Bork EMBO Editors: Thomas Lemberger Maria Polychronidou Julie Ahringer Charles Auffray Ewan Birney Tom Blundell Thomas S. Deisboeck Jan Ellenberg Michael Elowitz Alan Fersht Stan Fields Mark Gerstein Frank Holstege Sung Hou Kim Hiroaki Kitano Doron Lancet Andrew J. Link Stephen Oliver Jeremy Nicholson Bernhard Palsson Rama Ranganathan Uwe Sauer Luis Serrano Lucy Shapiro Pamela Silver Michael Snyder Janet Thornton Masaru Tomita Marc Vidal Hans V. Westerhoff Lothar Willmitzer John Yates

The editorial process time review editorial rejection reject revise reject accept

First editorial decision time review editorial rejection reject revise reject accept

First editorial decision time review editorial rejection reject revise reject accept

First editorial decision EMBO editors read the entire manuscript (yes!) Decision on a balance of multiple factors: • • • • • Scope Novelty & conceptual advance Mechanistic, functional, biological insights Utility of methods, dataset, resource Completeness and conclusiveness of the analysis

In case of doubt... R Aebersold GM Church E Liu L Hood Senior Editors Advisory Board P Bork EMBO Editors: Thomas Lemberger Maria Polychronidou Julie Ahringer Charles Auffray Ewan Birney Tom Blundell Thomas S. Deisboeck Jan Ellenberg Michael Elowitz Alan Fersht Stan Fields Mark Gerstein Frank Holstege Sung Hou Kim Hiroaki Kitano Doron Lancet Andrew J. Link Stephen Oliver Jeremy Nicholson Bernhard Palsson Rama Ranganathan Uwe Sauer Luis Serrano Lucy Shapiro Pamela Silver Michael Snyder Janet Thornton Masaru Tomita Marc Vidal Hans V. Westerhoff Lothar Willmitzer John Yates

Initial editorial decision

To review or not to review... time review editorial rejection reject revise reject accept

Peer-review Referees are invited based on: • Balance of expertise • Reputation as researcher • Reputation as reviewer • No conflict of interest (positive or negative) 3 (4) reviewers / manuscript

Transparent peer review

Referee report 1. Summary • Describe your understanding of the story • What are the key conclusions: findings and concepts • What are the methodology and model system 2. General remarks • Are you convinced of the key conclusions? • Place the work in its context. • What is the nature of the advance (conceptual, technical, clinical)? • How important is the advance as compared to previous knowledge? • What audience will be interested in this? 3. Major points • Specific criticisms related to key conclusions • Specify experiments or analyses required to demonstrate the conclusions • Motivate your critique with relevant citations and argumentation 4. Minor points • Easily addressable points • Presentation and style • Trivial mistakes

Referee report: example Editorial decision letter:

Cross-commenting reviewers reports authors

Cross-commenting Ref #3 Ref #2 Ref #1 Ref #2 cross-comments “…[it] settles a controversy in the field which has been going on for more than ten years. In summary, this is a landmark paper. I cannot support publication in your journal strongly enough!” “As written, the paper is focused on the methods, which is fine given that's where it makes its most substantial contribution. But the writing is quite technical and could benefit from more explanation of the high-level logic of their approach.” “After reading through this nicely-executed technical work, one is left with an impression that after all we really have not gained much new mechanistic insights. …in addition to the XXX data that should be generated under their current framework…” …Each reviewer has numerous suggestions about how to do this. It will likely be impossible to incorporate them all while retaining a coherent narrative. […] Reviewer 3 also calls for an additional experiment including XXX stains in the current dataset. To incorporate this into their current analytical framework, the authors would have to find parameters and reagents to allow simultaneous imaging of 5 genes (not just the 4 presented here). Moreover, they would then have to reacquire all images using the 5-stain protocol. While I agree that it would be useful to have XXX data included, I also believe that this is beyond the scope of this paper.

Post-revision review time review editorial rejection reject revise reject accept

Transparent Process • Transparent Anonymous Peer Review: Anonymous referee reports and editorial correspondence are published alongside papers • Single Round of Major Revision: More than 90% of invited revisions are published at Molecular Systems Biology • Referee Discussion before Decision: Referees are invited to comment on each other's reports before the editor makes a decision • Scooping Protection: Findings that are published by others during review or revision are not a criterion for rejection • Source Data for Figures: Authors can archive and make available the data underlying their published figures • Flexible Formatting: No journal-specific formatting required at submission

Scientific publishing “The publication of scientific information is intended to move science forward. More specifically, the act of publishing is a quid pro quo in which authors receive credit and acknowledgment in exchange for disclosure of their scientific findings.”

Scientific publishing The publication of scientific information is intended to move science forward. More specifically, the act of publishing is a quid pro quo in which authors receive credit and acknowledgment in exchange for disclosure of their scientific findings. Implies: • Originality • Integrity • Authenticity Respect of: • Laws and ethics • Safety and security • Societal context

Data integrity Beautification • Clarification • Aesthetics Selective reporting • Misrepresentation of the data • Biasing data to fit a particular hypothesis Fabrication • Deliberate manufacturin of data

38

39

New submission:

Seoul National University's report on Dr. Hwang Woo Suk: The data in the 2005 article including test results from • DNA fingerprinting, • photographs of teratoma, • embryoid bodies, • MHC-HLA isotype matches and • karyotyping have all been fabricated. http://www.useoul.edu/snunews?bm=v&bbsidx=71494&page=63

Figure 2F Figure 6D (F) NT-ESC colony with typical morphology derived from a caffeinetreated SCNT human blastocyst. (D) Human NT-ESCs expressed standard pluripotency markers detected by immunocytochemistry for antibodies against OCT4, NANOG, SOX2, SSEA-4, TRA-1–60, and TRA-1–81. Original magnification, ×200; Ph, phase contrast.

In Figures 2F and S5 (upper-right), we presented two phase-contrast photos of fields of cells, correctly labeled as SCNT-derived hESO-NT1 and IVF-derived hESO-7, respectively. These images are the same fields of cells shown in the top two images of Figure 6D; however, in Figure 6D, we inadvertently switched the labels on the images. This re-use of the images was intentional, but we should have indicated this in the original legend for Figure 6. We have corrected the labeling error in Figure 6D. We would also like to note that the Scientific Integrity Committee at Oregon Health & Science University has carefully assessed the paper and the errors and has concluded that there is no evidence of fabrication, falsification, or plagiarism that would warrant further inquiry or investigation into research misconduct. Figure 2F Figure 6D (F) NT-ESC colony with typical morphology derived from a caffeinetreated SCNT human blastocyst. (D) Human NT-ESCs expressed standard pluripotency markers detected by immunocytochemistry for antibodies against OCT4, NANOG, SOX2, SSEA-4, TRA-1–60, and TRA-1–81. Original magnification, ×200; Ph, phase contrast. Note that the upper-left image for hESO-NT1 is the same shown in Figure 2F.

What can PIs do? • • • • • • • Provide guidance to students and postdocs View original data Organize good data management practice Maintain an open lab environment Accept only relevant authorship Cooperate with editors Retract/correct as appropriate

What can journals do? • • • • Rigorous peer review Check by editors before publication Investigation and retraction policy Data transparency

What is a paper? Title Abstract Synopsis Main paper „Expanded view‟ Datasets & code

8/27 What is a figure? A scientific result converted into a collection of pixels…

11/27

12/27

• Data archival service • Data‘transparency‟ • Data reuse • Data-oriented search

15/27 Structured metadata: „perturbation-observation-assay‟ (Level 0:metadata associated to individual panels.) Level 1: „object-oriented‟ representation of experimental variables as a list of chemical and biological components. Level 2: represent the causality of the experimental design: “Measurement of Y as a function of A, B, C, using assay P in biological system S.” Level 3: machine-readable representation with standard identifiers. experimental system perturbed component measured component assayed property

9/27 SourceData Tools to publish figures as structured digital objects that link the human-readable illustrations with machine-readable metadata and „source data‟ in order to •improve data transparency; •make published data useable; •enable data-oriented search.

19/27 drug Z activity kinase Y kinase Y protein X Paper 3 Paper 2 Paper 1 Data-oriented search gene x P tissue T disease D Resulting hypothesis: test drug Z in disease D.

… 1,4 … 2 TGFbeta VE-cdh 1 4 4 Smad3 Tsc2 5 6 2 Hey1 5 Rad51 foci 6 3 AR TGFb, Smad3 Rad51 Nuclear complexes

Scientific publishing • Dominant channel for the dissemination of peer-reviewed data. • Journals function as a proxy for quality in research assessment • The rate of publishing keeps increasing. • Papers are human-readable but poorly machine-readable.

search

The Paper of the Future? Search <!DOCTYPE article PUBLIC "-//NLM//DTD Journal Archiving and Interchange DTD v2.3 20070202//EN" "archivearticle.dtd"> <article article-type="researcharticle"><?properties no_embargo?> <front> <journal-meta> <journal-id journal-id-type="nlm-ta">Mol Syst Biol</journal-id> <journal-title>Molecular Systems Biology</journal-title> <issn pub-type="epub">1744-4292</issn> <publisher> <publisher-name>Nature Publishing Group</publisher-name> </publisher> </journal-meta> <article-meta> <article-id pub-idtype="pmc">2238715</article-id> Data Methods Claims Authors Models

Future directions in systems biology • Genome-wide genetics of human diseases • Translational systems biology or systems medicine • Genome-scale engineering & synthetic biology • Temporal structure of biological processes • ‘In vivo biochemistry’ with single-cell singlemolecule assays • Bridge the gap between ‘omics’ and mechanistic models

“How do we get from the Jimome & Craigome to systems biology?” George M Church, Senior Editor

Multi-omics data integration Global analysis of genome, transcriptome and proteome reveals the response to aneuploidy in human cells. Zuzana Storchova, Mol Syst Biol. 2012 8:608. Integration of clinical data with a genome-scale metabolic model of the human adipocyte. Jens Nielsen and colleagues, Mol Syst Biol. 2013;9:649.

Comparative omics for functional discoveries Human disease locus discovery and mapping to molecular pathways through phylogenetic profiling. Gary Ruvkun and colleagues, Mol Syst Biol. 2013 9:692 19 017 human genes Phylogenetic profiles of across 86 eukaryotic genomes.

Beyond the hairball ? Costanzo et al, Science 2010 Hoog et al, Dev Cell 2007

Spatial patterns Waks et al, 2011 Mol Syst Biol 7:506 Di Vetura and Sourjik , 2011 Mol Syst Biol 7:457

Temporal patterns Promoter decoding of transcription factor dynamics involves a tradeoff between noise and control of gene expression. Hansen AS, O'Shea EK. Mol Syst Biol. 2013 9:704

Cell population & dynamics Digital cell quantification identifies global immune cell dynamics during influenza infection. Ido Amit and colleagues, 2014 Mol Syst Biol. 10:720

Microbiome & metagenomics A top-down systems biology view of microbiomemammalian metabolic interactions in a mouse model. J. Nicholson and colleagues, Mol Syst Biol. 2007 3:112. Toward molecular trait-based ecology through integration of biogeochemical, geographical and metagenomic data. Peer Bork and colleagues, Mol Syst Biol. 2011 7:473

Synthetic biology Synthesizing a novel genetic sequential logic circuit: a push-on push-off switch. Qi Ouyang (Beijing University), Mol Syst Biol. 2010;6:350.

Genome-scale engineering Genome-scale engineering for systems and synthetic biology. Esvelt KM, Wang HH, Mol Syst Biol. 2013 9:641.

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