PLOS Biology is launching a new section focused on meta-research to increase transparency in biosciences research. Meta-research examines issues related to research design, methods, reporting, evaluation and rewards. This will include exploring sources of bias, data sharing standards, and assessment metrics. Registered Reports will also be introduced, which accept studies for publication based on proposed methods rather than results, reducing bias against negative findings. However, most research data is lost within 10-15 years, highlighting the need for improved data sharing policies to maximize the value of research findings.
Talk at the University of Tokyo on history of Retraction Watch, our database, and current trends. Includes titles in Japanese, courtesy of Iekuni Ichikawa.
Talk at the University of Tokyo on history of Retraction Watch, our database, and current trends. Includes titles in Japanese, courtesy of Iekuni Ichikawa.
This presentation gives a quick insight into how Scopus can benefit the scientific community and which value it adds to research institutions.
Increasing the speed to discovery and making resources more visible are just a few key drivers for the world wide success of www.scopus.com.
Read more on at http://info.scopus.com
Prof. sp singh.ph d.course work.2020-21.citation index, journal impact factor...Saurashtra University
Citation index, Journal Impact Factors , H – Index and Impact Factor
-------
RESEARCH, PUBLICATIONS AND QUALITY ASSESSMENT
WIDE VARIATION IN THE ASSESSMENT AND QUALITY JUDGMENT
DIFFRENTIAL LEVEL OF RESEARCH OUTPUT- Reflected by number/frequency/quality of the publication
LACK OF INTEREST
DIFFERNCES IN OVER ALL OBJECTIVES
TYPES OF PUBLICATIONS
TYPES AND QUALITY OF THE JOURNALS
Traditional metrics, such as the h-index and journal impact factors, are used to measure the scholarly impact of research. However, in the current climate of accountability by funding providers, fund recipients would benefit from a more comprehensive impact management system (IMS) to facilitate the capture and reporting of narratives (including metrics) about research impact in the academy, on social policy, in industry, and ultimately with the public.
Librarians have always been good at telling and facilitating stories. Research support librarians can use their storytelling skills to contribute to the implementation and administration of an impact management system. Being able to translate research impact into harvestable and reportable metadata is the key.
Unearthing open access resource evaluationNina Collins
Explores types of unethical publishing tactics among false publishers claiming to be Open Access Scholarly Publishers. Presented at "Discovery to Delivery 5: Better Together", in Indianapolis, on April 25, 2014.
Given at the NIH stock center directors meeting, August 8, 2016. Author: Anita Bandrowski
Project: Resource Identification Initiative http://scicrunch.org/resources
Topic: How is model organism data being used in literature
Presented by Dom Mitchell, Community Manager for DOAJ to 35th Conference of International Association of Scientific and Technological University Libraries (IATUL).
A presentation exploring how DOAJ is using crowdsourcing to evaluate the ~9700 journals currently in DOAJ. Using a network of volunteers, every journals will be reassessed and evaluated based on the new criteria.
This version contains a handful of extra slides that were originally removed due to time restrictions.
Annotation examples. This is an overview of some of the software I have used for annotation (and a few extra features some of this software has.) This was presented in the SwissUniversities Doctoral Programme, Language & Cognition, in the Module: Linguistic and corpus perspectives on argumentative discourse.
Screenshots are given of GATE, UAM Corpus Tool, Excel, BRAT, EPPI Reviewer, and a custom tool. In most cases there are references to one of my papers for further details.
I briefly describe a typical annotation process:
Find text of interest
Find phenomena of interest
Draft an annotation manual
Iteratively test annotation & revise manual
Find questionable annotations, check disagreements.
Revise the manual.
Iterate.
Annotate
Brace for Impact: New Means for Measuring Research MetricsMary Ellen Sloane
As open access journals and repositories gain a foothold in scholarly communication, researchers are finding that the traditional impact factor and citation count metrics only reflect a portion of the dissemination of scholarly works.
New technology, research, and citation tools aid our ability to measure the influence of research. A matrix of tools and initiatives, like PLoS Article-Level Metrics, BePress’ Author Dashboard, Mendeley, Altmetrics, and ImpactStory are providing a more robust picture of scholarly communication today.
This presentation provides an overview of the impact factor system and new tools for gathering metrics and their relevance for librarians and researchers.
Presentation given at the Library Information Technology Association (LITA) Forum in Louisville, KY, in November 2013.
Peer Review is the Process used to judge the quality of articles submitted for publication in a scholarly journal. Peer Reviewed articles are considered the best source to use when writing a research paper.
Haustein, S. (2017). The evolution of scholarly communication and the reward ...Stefanie Haustein
Haustein, S. (2017, February). The evolution of scholarly communication and the reward system of science. Fourth Annual KnoweScape Conference 2017, 22–24 February 2017, Sofia (Bulgaria). keynote
http://knowescape.org/knowescape2017/
This presentation gives a quick insight into how Scopus can benefit the scientific community and which value it adds to research institutions.
Increasing the speed to discovery and making resources more visible are just a few key drivers for the world wide success of www.scopus.com.
Read more on at http://info.scopus.com
Prof. sp singh.ph d.course work.2020-21.citation index, journal impact factor...Saurashtra University
Citation index, Journal Impact Factors , H – Index and Impact Factor
-------
RESEARCH, PUBLICATIONS AND QUALITY ASSESSMENT
WIDE VARIATION IN THE ASSESSMENT AND QUALITY JUDGMENT
DIFFRENTIAL LEVEL OF RESEARCH OUTPUT- Reflected by number/frequency/quality of the publication
LACK OF INTEREST
DIFFERNCES IN OVER ALL OBJECTIVES
TYPES OF PUBLICATIONS
TYPES AND QUALITY OF THE JOURNALS
Traditional metrics, such as the h-index and journal impact factors, are used to measure the scholarly impact of research. However, in the current climate of accountability by funding providers, fund recipients would benefit from a more comprehensive impact management system (IMS) to facilitate the capture and reporting of narratives (including metrics) about research impact in the academy, on social policy, in industry, and ultimately with the public.
Librarians have always been good at telling and facilitating stories. Research support librarians can use their storytelling skills to contribute to the implementation and administration of an impact management system. Being able to translate research impact into harvestable and reportable metadata is the key.
Unearthing open access resource evaluationNina Collins
Explores types of unethical publishing tactics among false publishers claiming to be Open Access Scholarly Publishers. Presented at "Discovery to Delivery 5: Better Together", in Indianapolis, on April 25, 2014.
Given at the NIH stock center directors meeting, August 8, 2016. Author: Anita Bandrowski
Project: Resource Identification Initiative http://scicrunch.org/resources
Topic: How is model organism data being used in literature
Presented by Dom Mitchell, Community Manager for DOAJ to 35th Conference of International Association of Scientific and Technological University Libraries (IATUL).
A presentation exploring how DOAJ is using crowdsourcing to evaluate the ~9700 journals currently in DOAJ. Using a network of volunteers, every journals will be reassessed and evaluated based on the new criteria.
This version contains a handful of extra slides that were originally removed due to time restrictions.
Annotation examples. This is an overview of some of the software I have used for annotation (and a few extra features some of this software has.) This was presented in the SwissUniversities Doctoral Programme, Language & Cognition, in the Module: Linguistic and corpus perspectives on argumentative discourse.
Screenshots are given of GATE, UAM Corpus Tool, Excel, BRAT, EPPI Reviewer, and a custom tool. In most cases there are references to one of my papers for further details.
I briefly describe a typical annotation process:
Find text of interest
Find phenomena of interest
Draft an annotation manual
Iteratively test annotation & revise manual
Find questionable annotations, check disagreements.
Revise the manual.
Iterate.
Annotate
Brace for Impact: New Means for Measuring Research MetricsMary Ellen Sloane
As open access journals and repositories gain a foothold in scholarly communication, researchers are finding that the traditional impact factor and citation count metrics only reflect a portion of the dissemination of scholarly works.
New technology, research, and citation tools aid our ability to measure the influence of research. A matrix of tools and initiatives, like PLoS Article-Level Metrics, BePress’ Author Dashboard, Mendeley, Altmetrics, and ImpactStory are providing a more robust picture of scholarly communication today.
This presentation provides an overview of the impact factor system and new tools for gathering metrics and their relevance for librarians and researchers.
Presentation given at the Library Information Technology Association (LITA) Forum in Louisville, KY, in November 2013.
Peer Review is the Process used to judge the quality of articles submitted for publication in a scholarly journal. Peer Reviewed articles are considered the best source to use when writing a research paper.
Haustein, S. (2017). The evolution of scholarly communication and the reward ...Stefanie Haustein
Haustein, S. (2017, February). The evolution of scholarly communication and the reward system of science. Fourth Annual KnoweScape Conference 2017, 22–24 February 2017, Sofia (Bulgaria). keynote
http://knowescape.org/knowescape2017/
Sbm open science committee report to the boardBradford Hesse
In the spirit of transparency, I am uploading a mid-course presentation I made to the Board of Directors for the Society of Behavioral Medicine on the topic of Open Science. The report embodies the best thinking of some of the greatest thinkers in our field.
How can we ensure research data is re-usable? The role of Publishers in Resea...LEARN Project
How can we ensure research data is re-usable? The role of Publishers in Research Data Management, by Catriona MacCallum. 2nd LEARN Workshop, Vienna, 6th April 2016
JALA Editor-in-Chief Edward Kai-Hua Chow, Ph.D., of National University of Singapore shared step-by-step advice on how to design and write scientific research papers more clearly and effectively to improve their chances for successful publication at the recently held conference in Washington, DC. Learn what editors want, what they don't want and how reviewers evaluate manuscripts by reviewing slides from the session.
Recomendations for infrastructure and incentives for open science, presented to the Research Data Alliance 6th Plenary. Presenter: William Gunn, Director of Scholarly Communications for Mendeley.
Overview to: BBSRC Oxford Doctoral Training Partnership - Dr Sansone - July 2014Susanna-Assunta Sansone
What to know when planning for your data management strategy and preparing a data management statement for a research proposal for BBSRC DTP first year students
What is the future of scientific communication? Open Science (Claude Pirmez)http://bvsalud.org/
Apresentação da Profª Drª Claude Pirmez na Reunião de Editores Científicos do CRICS10, em 04/12/2018
http://crics10.org/eventos/pt/event/reuniao-de-editores-cientificos/
There is an abundance of free online tools accessible to scientists and others that can be used for online networking, data sharing and measuring research impact. Despite this, few scientists know how these tools can be used or fail to take advantage of using them as an integrated pipeline to raise awareness of their research outputs. In this article, the authors describe their experiences with these tools and how they can make best use of them to make their scientific research generally more accessible, extending its reach beyond their own direct networks, and communicating their ideas to new audiences. These efforts have the potential to drive science by sparking new collaborations and interdisciplinary research projects that may lead to future publications, funding and commercial opportunities. The intent of this article is to: describe some of these freely accessible networking tools and affiliated products; demonstrate from our own experiences how they can be utilized effectively; and, inspire their adoption by new users for the benefit of science.
Open science framework – Jeff Spies, Centre for Open Science
Active research from lab to publication – Simon Coles, University of Southampton
Managing active research in the university – Robin Rice, University of Edinburgh
Making research available: FAIR principles and Force 11 - David De Roure, Oxford e-Research Centre
Jisc and CNI conference, 6 July 2016
Professional air quality monitoring systems provide immediate, on-site data for analysis, compliance, and decision-making.
Monitor common gases, weather parameters, particulates.
Deep Behavioral Phenotyping in Systems Neuroscience for Functional Atlasing a...Ana Luísa Pinho
Functional Magnetic Resonance Imaging (fMRI) provides means to characterize brain activations in response to behavior. However, cognitive neuroscience has been limited to group-level effects referring to the performance of specific tasks. To obtain the functional profile of elementary cognitive mechanisms, the combination of brain responses to many tasks is required. Yet, to date, both structural atlases and parcellation-based activations do not fully account for cognitive function and still present several limitations. Further, they do not adapt overall to individual characteristics. In this talk, I will give an account of deep-behavioral phenotyping strategies, namely data-driven methods in large task-fMRI datasets, to optimize functional brain-data collection and improve inference of effects-of-interest related to mental processes. Key to this approach is the employment of fast multi-functional paradigms rich on features that can be well parametrized and, consequently, facilitate the creation of psycho-physiological constructs to be modelled with imaging data. Particular emphasis will be given to music stimuli when studying high-order cognitive mechanisms, due to their ecological nature and quality to enable complex behavior compounded by discrete entities. I will also discuss how deep-behavioral phenotyping and individualized models applied to neuroimaging data can better account for the subject-specific organization of domain-general cognitive systems in the human brain. Finally, the accumulation of functional brain signatures brings the possibility to clarify relationships among tasks and create a univocal link between brain systems and mental functions through: (1) the development of ontologies proposing an organization of cognitive processes; and (2) brain-network taxonomies describing functional specialization. To this end, tools to improve commensurability in cognitive science are necessary, such as public repositories, ontology-based platforms and automated meta-analysis tools. I will thus discuss some brain-atlasing resources currently under development, and their applicability in cognitive as well as clinical neuroscience.
Comparing Evolved Extractive Text Summary Scores of Bidirectional Encoder Rep...University of Maribor
Slides from:
11th International Conference on Electrical, Electronics and Computer Engineering (IcETRAN), Niš, 3-6 June 2024
Track: Artificial Intelligence
https://www.etran.rs/2024/en/home-english/
(May 29th, 2024) Advancements in Intravital Microscopy- Insights for Preclini...Scintica Instrumentation
Intravital microscopy (IVM) is a powerful tool utilized to study cellular behavior over time and space in vivo. Much of our understanding of cell biology has been accomplished using various in vitro and ex vivo methods; however, these studies do not necessarily reflect the natural dynamics of biological processes. Unlike traditional cell culture or fixed tissue imaging, IVM allows for the ultra-fast high-resolution imaging of cellular processes over time and space and were studied in its natural environment. Real-time visualization of biological processes in the context of an intact organism helps maintain physiological relevance and provide insights into the progression of disease, response to treatments or developmental processes.
In this webinar we give an overview of advanced applications of the IVM system in preclinical research. IVIM technology is a provider of all-in-one intravital microscopy systems and solutions optimized for in vivo imaging of live animal models at sub-micron resolution. The system’s unique features and user-friendly software enables researchers to probe fast dynamic biological processes such as immune cell tracking, cell-cell interaction as well as vascularization and tumor metastasis with exceptional detail. This webinar will also give an overview of IVM being utilized in drug development, offering a view into the intricate interaction between drugs/nanoparticles and tissues in vivo and allows for the evaluation of therapeutic intervention in a variety of tissues and organs. This interdisciplinary collaboration continues to drive the advancements of novel therapeutic strategies.
Richard's entangled aventures in wonderlandRichard Gill
Since the loophole-free Bell experiments of 2020 and the Nobel prizes in physics of 2022, critics of Bell's work have retreated to the fortress of super-determinism. Now, super-determinism is a derogatory word - it just means "determinism". Palmer, Hance and Hossenfelder argue that quantum mechanics and determinism are not incompatible, using a sophisticated mathematical construction based on a subtle thinning of allowed states and measurements in quantum mechanics, such that what is left appears to make Bell's argument fail, without altering the empirical predictions of quantum mechanics. I think however that it is a smoke screen, and the slogan "lost in math" comes to my mind. I will discuss some other recent disproofs of Bell's theorem using the language of causality based on causal graphs. Causal thinking is also central to law and justice. I will mention surprising connections to my work on serial killer nurse cases, in particular the Dutch case of Lucia de Berk and the current UK case of Lucy Letby.
This presentation explores a brief idea about the structural and functional attributes of nucleotides, the structure and function of genetic materials along with the impact of UV rays and pH upon them.
Slide 1: Title Slide
Extrachromosomal Inheritance
Slide 2: Introduction to Extrachromosomal Inheritance
Definition: Extrachromosomal inheritance refers to the transmission of genetic material that is not found within the nucleus.
Key Components: Involves genes located in mitochondria, chloroplasts, and plasmids.
Slide 3: Mitochondrial Inheritance
Mitochondria: Organelles responsible for energy production.
Mitochondrial DNA (mtDNA): Circular DNA molecule found in mitochondria.
Inheritance Pattern: Maternally inherited, meaning it is passed from mothers to all their offspring.
Diseases: Examples include Leber’s hereditary optic neuropathy (LHON) and mitochondrial myopathy.
Slide 4: Chloroplast Inheritance
Chloroplasts: Organelles responsible for photosynthesis in plants.
Chloroplast DNA (cpDNA): Circular DNA molecule found in chloroplasts.
Inheritance Pattern: Often maternally inherited in most plants, but can vary in some species.
Examples: Variegation in plants, where leaf color patterns are determined by chloroplast DNA.
Slide 5: Plasmid Inheritance
Plasmids: Small, circular DNA molecules found in bacteria and some eukaryotes.
Features: Can carry antibiotic resistance genes and can be transferred between cells through processes like conjugation.
Significance: Important in biotechnology for gene cloning and genetic engineering.
Slide 6: Mechanisms of Extrachromosomal Inheritance
Non-Mendelian Patterns: Do not follow Mendel’s laws of inheritance.
Cytoplasmic Segregation: During cell division, organelles like mitochondria and chloroplasts are randomly distributed to daughter cells.
Heteroplasmy: Presence of more than one type of organellar genome within a cell, leading to variation in expression.
Slide 7: Examples of Extrachromosomal Inheritance
Four O’clock Plant (Mirabilis jalapa): Shows variegated leaves due to different cpDNA in leaf cells.
Petite Mutants in Yeast: Result from mutations in mitochondrial DNA affecting respiration.
Slide 8: Importance of Extrachromosomal Inheritance
Evolution: Provides insight into the evolution of eukaryotic cells.
Medicine: Understanding mitochondrial inheritance helps in diagnosing and treating mitochondrial diseases.
Agriculture: Chloroplast inheritance can be used in plant breeding and genetic modification.
Slide 9: Recent Research and Advances
Gene Editing: Techniques like CRISPR-Cas9 are being used to edit mitochondrial and chloroplast DNA.
Therapies: Development of mitochondrial replacement therapy (MRT) for preventing mitochondrial diseases.
Slide 10: Conclusion
Summary: Extrachromosomal inheritance involves the transmission of genetic material outside the nucleus and plays a crucial role in genetics, medicine, and biotechnology.
Future Directions: Continued research and technological advancements hold promise for new treatments and applications.
Slide 11: Questions and Discussion
Invite Audience: Open the floor for any questions or further discussion on the topic.
Nutraceutical market, scope and growth: Herbal drug technologyLokesh Patil
As consumer awareness of health and wellness rises, the nutraceutical market—which includes goods like functional meals, drinks, and dietary supplements that provide health advantages beyond basic nutrition—is growing significantly. As healthcare expenses rise, the population ages, and people want natural and preventative health solutions more and more, this industry is increasing quickly. Further driving market expansion are product formulation innovations and the use of cutting-edge technology for customized nutrition. With its worldwide reach, the nutraceutical industry is expected to keep growing and provide significant chances for research and investment in a number of categories, including vitamins, minerals, probiotics, and herbal supplements.
Nutraceutical market, scope and growth: Herbal drug technology
2015 12 ebi_ganley_final
1. Emma Ganley, Chief Editor, PLOS Biology
eganley@plos.org @GanleyEmma
Dec 2015
Publishing, Open Data,
& Open Access: How
Open is Open?
2. PLOSis a non-profit publisher and
advocacy organization with a mission to
accelerate progress in science and medicine by
leading a transformation in research
communication.
The Mission…
4. ELIMINATE UNNECESSARY BARRIERS
to immediate availability, access and use of research.
PURSUE A PUBLISHING STRATEGY
that drives openness, quality and integrity.
DEVELOP INNOVATIVE APPROACHES
to the assessment, organization and reuse of ideas and data.
PLOSand its authors choose to make
scientific and medical research articles openly
available for the advancement of science and the
greater public good.
...to enable those uses that we can’t yet imagine
5. What is Open Access ?
Free Availability and Unrestricted Use
Free access – no charge to access
No embargos – immediately available
Reuse – Creative Commons Attribution
License (CC BY) - use with proper
attribution
8. The Journal
“Journals form a core part of the process of scholarly
communication and are an integral part of scientific research
itself. Journals do not just disseminate information, they also
provide a mechanism for the registration of the author’s
precedence; maintain quality through peer review and provide
a fixed archival version for future reference.”
The STM Report, Fourth Edition, 2015
9. • >28, 000 peer-reviewed English language journals (2014)
• 10,900 in Journal Citation Reports
• 2.5 million articles a year
• 500-10,000 journal publishers
• 7-9 million researchers
• Most publishers have >90% content available online
• The annual revenues generated from English-language
STM journal publishing are estimated at about $10 billion in
2013, (up from $8 billion in 2008)
• broader STM information publishing market worth some
$25.2 billion [in 2013].
The STM Report, Fourth Edition, 2015)
10. % of Scholarly journal article that are OA varies from ~20%-50%, depending on
source
(Stephen Pinfield , (2015),"Making Open Access work", Online Information Review, Vol.
39 Iss 5 http://dx.doi.org/10.1108/OIR-05-2015-0167 )
From OASPA: http://oaspa.org/growth-of-oa-only-journals-using-a-cc-by-license/
0
20000
40000
60000
80000
100000
120000
140000
160000
2000 2002 2004 2006 2008 2010 2012 2014
No. of Open Access articles published by OASPA members
(Open Access Scholarly Publishers Association)
11. Dissemination by journals
• Many publishers (including societies) remain resistant to OA
• Few conversions of established journals
• ‘Hybrid’ OA very expensive
• Details of methods and results relegated to supplementary
material
• Numerous rounds of unnecessary rejection and re-review
• Many won’t publish negative or confirmatory results
• Content not reusable or discoverable:
• Many publishers don’t permit text and data mining for research
purposes
17. Science & Publishing today
Corrections, Mega-Corrections & Retractions
“In the early 2000s, only about 30 retraction notices appeared
annually; in the last five years, that number has jumped to around 500
(Nature, 478:26-28, 2011). And since the launch of Retraction Watch in
August 2010, there has been a growing interest among publishers,
editors, authors, and the press in manuscripts that are pulled from the
literature. Previously, retractions had no visibility, as they were published
without any warning. Retraction Watch provides a central location where
researchers can keep track of flawed papers and often learn a little about
the stories underlying their retractions.”
Source: Explaining Retractions
Editors and publishers should use a standardized form to detail why they are
pulling papers from the scientific literature.
By Hervé Maisonneuve,Evelyne Decullier | The Scientist December 1, 2015
18. Reporting / Standards / Reproducibility
• Publication bias (-ve studies not published)
• Selective reporting (p-hacking) 1
• Animal research reporting / Cell line authentication
• Poor Study Design (underpowered - small N, lack of
randomisation, blinding and controls)
• Poorly reported methods and results 2
• Data / Metadata not available to assess
• Lack of reproducibility 3
1Head ML, Holman L, Lanfear R, Kahn AT, Jennions MD (2015) The Extent and Consequences of P-
Hacking in Science. PLoS Biol 13(3): e1002106. doi:10.1371/journal.pbio.1002106
2Landis SC, et al. (2012) A call for transparent reporting to optimize the predictive value of preclinical
research. Nature 490(7419): 187–191.
3Freedman LP, Cockburn IM, Simcoe TS (2015) The Economics of Reproducibility in Preclinical
Research. PLoS Biol 13(6): e1002165. doi: 10.1371/journal.pbio.1002165
VALUE of the research $£€
19. TOP Guidelines
Transparency & Openness Promotion Guidelines (Center for Open Science)
Transparency, open sharing, and reproducibility are core features of science, but not
always part of daily practice. Journals can increase transparency and reproducibility
of research by adopting the TOP Guidelines. TOP includes eight modular standards,
each with three levels of increasing stringency. Journals select which of the eight
transparency standards they wish to adopt for their journal, and select a level of
implementation for the selected standards. These features provide flexibility for adoption
depending on disciplinary variation, but simultaneously establish community standards.
https://cos.io/top/
20. TOP Guidelines
• Citation standards
• Data Transparency
• Analytic Methods (Code) Transparency
• Research Materials Transparency
• Design & Analysis Transparency
• Preregistration of Studies
• Preregistration of Analysis Plans
• Replication
Science 26 June 2015:
Vol. 348 no. 6242 pp. 1422-1425
DOI: 10.1126/science.aab2374
22. Meta-Research in PLOS Biology
Recognizing the importance of research about research to
increase transparency in the biosciences
23. Will publish /
officially launch
4th Jan, 2016
2 new papers +
collection of
relevant papers
we have already
published
24. Meta-Research in PLOS Biology
The new meta-research section of PLOS Biology will be data-driven and feature experimental,
observational, modelling, and meta-analytic research that addresses issues related to the
design, methods, reporting, verification, and evaluation of research. It will also
encompass research into the systems that evaluate and reward individual scientists
and institutions. We welcome both exploratory and confirmatory research that has the potential to
drive change in research and evaluation practices in the life sciences and beyond. The themes
include, but are not limited to, transparency, established and novel methodological
standards, sources of bias (conflicts of interest, selection, inflation, funding, etc.),
data sharing, evaluation metrics, assessment, reward, and funding structures.
Kousta S, Ferguson C, Ganley E (2016) Meta-Research: Broadening the Scope of PLOS
Biology. PLoS Biol 14(1): e1002334.
DOI:10.1371/journal.pbio.1002334 January 4, 2016
25. Meta-Research in PLOS Biology
New Editorial Board Members:
Lisa Bero (Univerity of Sydney);
Isabelle Boutron (Université Paris Descartes);
Ulrich Dirnagl (Charité—Universitätsmedizin Berlin);
John PA Ioannidis (Stanford University);
Jonathan Kimmelman (McGill University);
Malcolm Macleod (University of Edinburgh);
David Vaux (Walter and Eliza Hall Institute of Medical Research);
Eric-Jan Wagenmakers (University of Amsterdam)
27. Registered Reports in PLOS Biology
Coming in 2016… We’re collaborating with
the Open Science Foundation &
Centre for Open Science to implement Registered
Reports as a new format
See https://osf.io/8mpji/wiki/home/ & https://cos.io/
“Registered Reports eliminates the bias against negative results in publishing because the
results are not known at the time of review” said Daniel Simons, Professor at University of Illinois,
Urbana-Champaign and co-Editor of Registered Replication Reports at Perspectives on Psychological
Science. Chris Chambers, Professor at Cardiff University, section editor at Cortex and Royal Society
Open Science, and chair of the Registered Reports Committee supported by the Center for Open
Science (COS) adds, “Because the study is accepted in advance, the incentives for authors
change from producing the most beautiful story to producing the most accurate one.”
28. Registered Reports in PLOS Biology
What are Registered Reports?
A departure from regular peer review
“scientists state at least part of what they’re going to
do before they do it, registration gently but firmly compels
us to stick to the scientific method.” – Chris Chambers
Not ideal for exploratory science
Very good for well defined protocols e.g. trials/statistical
analysis/animal research trials/field studies/… etc.
http://www.theguardian.com/science/head-quarters/2014/may/20/psychology-registration-revolution
30. Data Availability Declines Over Time
ALMOST ALL DATA LOST
10-15 YRS AFTER
PUBLICATION
Source: How Does the Availability of Research Data Change With
Time Since Publication?
Timothy H. Vines and colleagues, Abstract (podium), Peer
Review Congress, 2013
31. Phylogenetics Data
7500 papers studied from 2000-2012:
• data deposited for only 1/6…
• available on request from the
original authors in a further 1/6…
• 2/3 of trees only available as figure
panels in the original paper.
• potentially irretrievable loss of the
bulk of the data on which this field
rests.
Source: Drew et al., PLOS Biology 2013, DOI: 10.1371/journal.pbio.1001636
32. Challenges and Opportunities
Science 11 February 2011:
vol. 331 no. 6018 692-693
CREDIT: M. TWOMBLY/SCIENCE;
SOURCE: SCIENCE ONLINE SURVEY
2011 Survey in Science
33. Old to New Policy – March 2014
OLD: Authors should make all relevant data immediately
available without restrictions (excl. patient confidentiality)
NEW: Require authors to make all data underlying the
findings described in their manuscript fully available
without restriction, with rare exception.
Authors must provide a Data Availability Statement (DAS)
describing compliance with PLOS’ policy.
*No change to WHAT data needs to be shared, but the focus
was placed on WHERE it is housed, WHEN it is shared, and
HOW authors provide access for those who want it*
VALUE OF DATA
Replication/Validation;
New analysis;
Better interpretation;
Include in meta-studies;
Facilitate reproducibility;
Scrutiny post- publication;
* $$$* Better return on
research investment.
34. DAS
NB The DAS is openly available, and machine-readable as part of the
PLOS search API
36. New Policy – What Data & How?
The policy applies to the dataset used to reach the conclusions drawn in the manuscript
with related metadata and methods, and any additional data required to replicate the
reported study findings in their entirety. You need not submit your entire dataset, or all raw
data collected during an investigation, but you must provide the portion that is relevant
to the specific study.
DATA-SHARING METHODS
Data deposition (strongly recommended; must include
DOIs or accession numbers/codes).
Data in supporting information files (in a format
from which data can be efficiently extracted e.g. .csv,
excel, NOT .pdf)
EXCEPTIONS
Ethical or legal (e.g. patient privacy). Data access
overseen via ethics oversight committee (Data Access
Committee), anonymized appropriately*
Data from a third party (data must be available from
third party in the same way it was accessed by the
authors.)
* Guidance on confidentiality & anonymity in data about individuals - see BMJ 2010;340:c181; Preparing raw clinical data for
publication: guidance for journal editors, authors, and peer reviewers
37. “… make an honest effort to make the data
accessible and useful to others, and chances are
you’re probably good to go.”
- Matt MacManes, http://genomebio.org/
39. Data Policy – Unknowns
QUESTIONS WE DON’T KNOW ANSWERS TO YET
• How long should people store data? How much data needed to replicate?
• Licensing & attribution;
• Treatment of software/code;
• How should materials sharing differ?
• What to do with big data?
• Do we need better/more aligned consenting for patient studies?
• Best practices for data access committees?
• How to fund data access committees?
• Preservation of obsolete formats?
• How to cite data & credit data reuse?
Very Useful reading: Michael Carroll. PLOS Biology 2015. Sharing Research Data and Intellectual Property Law: A Primer
Also, coming soon: An editorial from the EiCs of PLOS Genetics on the policy & data sharing standards in PLOS Genetics.
40. Compliance? Data on Data @PLOS
Audit on ~11k PLOS articles published post new policy
% papers with full access to data / % restrictions 88% / 12%
% papers with data deposited in repositories 11%
% papers w/ all data in the MS/SI files 66%
% papers w/ data held by 3rd party 2%
% papers with data containing sensitive info 2%
Restrictions by subject area/subfields:
Human & clinical data; fMRI & MRI images; trajectories & simulation
data, human or government data requiring access; fields where data
are too large to submit; geo/satellite; new & emerging
fields/techniques (NTDs)
42. Anecdotes & Interpretation
Source: ‘Confusion over publisher’s pioneering
open-data rules’ Nature 515, 478 (27 November
2014) doi:10.1038/515478a
‘Mandated data archiving greatly improves access
to research data’ T. H Vines et al. Faseb J 27,
1304-1308; Jan 2013
50 fMRI studies in PLOS ONE
38 had shared the data
12 had not shared the data
(completely anecdotal)
An increase in data sharing:
- from 12% to 40%
- even up to as much as 76%
Not seeing full compliance but we are
seeing a MASSIVE improvement
43. Improving & Measuring Reuse?
http://plos.figshare.com/statistics
Analytics on PLOS
Figs, tables, SI files
● usage
○ views
○ downloads
● demographics
○ country
○ Institution
Available by journal or for entire PLOS corpus
44. Publishers in Data Access & Sharing
Lin J, Strasser C (2014) Recommendations for the Role of Publishers in Access to Data.
PLoS Biol 12(10): e1001975. doi:10.1371/journal.pbio.1001975
NSF Funded project:
Make Data Count.
To explore and test
data-level metrics.
Meeting co-organized
by PLOS & California
Digital Library
45. Carrots vs Sticks
Investigating how to:
- Work with Biocurators to assess data & reporting
- Incentivize better reporting standards & scientific practices
- Assess whether we can ‘badge’ good reporting as an incentive
- Improve on Data Citation Standards
- Better recognize Author Contributions
- Implement ORCID id requirement
- Incentivize Openness (for review process, early preprint posting etc.)
- Change an Ingrained Mindset
- Educate the masses…
46. Other Lofty Goals
- Move the World away from Impact Factor as single
metric for evaluation (DORA)
- Individual Article & Data Metrics
- Impact how research assessment is performed
- Experiment with Open Peer Review
- Encouraging Early Online Posting
- Move Towards More Dynamic Publications with
post-publication review and versioning of papers
47. A Changing Currency in Science?
Scientific papers in
physical journals
Scientific papers
online & in print
Online only papers
Online Publication +
data
Data + analysis
(publication?)
O
p
e
n
n
e
s
s
48. A Sea Change
"Tsunami by hokusai 19th century" by Katsushika Hokusai (葛飾北斎) - Metropolitan
Museumphoto of the artwork. Licensed under Public Domain via Commons
ACADEMIC EDITORS:
Making the data available (at least to the editors) at
the time of submission is a logical and reasonable
requirement.
I also think that when the authors of a paper published in
a PLOS journal refuse to provide the data upon request
that the paper should be withdrawn from publication (i.e.,
the journal should retract the paper).
Refusing to allow other scientists to evaluate the
data (particularly if there are concerns regarding the
analyses and conclusions) is hardly in the spirit of
the PLOS open access model. in context
AUTHORS:
“I apologise sincerely for the errors that were included in previous versions of the
manuscript.
This is the first time that I have been required to provide a data spreadsheet
alongside a manuscript, and the value of doing this, which meant that I ended
up double-checking the values in our figures, figure legends and
spreadsheets, has been illustrated amply. In the future (whether required to by
the journal or not!) I will prepare a similar file prior to initial submission in
order to prevent this from ever happening again. We appreciate the precision
with which your staff has edited our manuscript, as its quality has improved because
of it.”
Profound & Notable
Transformation
We want speed, we want early online posting, we want post-pub peer review, we want lots of things, but we also want quality & there is an expectation that very rigourous checks will have been performed. And the world is only too happy to point out errors. But there is a tension here in what is wanted and how much this costs…
Why is data availability important?
In a study by Tim Vines and colleagues of morphological data from plants, animals, or other organisms, 37% of the data from papers published in 2011 still existed, but this fell to 18% for 2001 and 7% for 1991
The odds of receiving the data decreased by about 7% per year.
For papers where they heard about the status of the data, the proportion of authors reporting it lost or on inaccessible hardware rose gradually from 0 of 30 in 2011 to 2 of 9 (22%) in 1997, and then increased to 7 of 8 in 1993 (87%) and 4 of 6 (66%) in 1991.
The end result was that almost all research data was lost 10 to 15 years after publication.
Data are not available for replication, reanalysis, meta-analysis or even if a question arises about the veracity of the research.
Science Magazine conducted a survey on the availability and use of data with 1700 responses with representation across research areas and geographic regions. They published their results in the February 2011 issue. Here, we see that 77% of researchers have asked colleagues for data, while they have had difficulty in getting it 50% of the time. What all of these figures attest to is that there is recognized demand for researchers to access others’ data. In fact, I believe this view undercounts the real need. If there is proven “demand” for data, why aren’t they available? Let’s flip to the other hat that researchers wear and examine the situation as one doing the research (generating data as part of my research project). While there are many underlying reasons, which will take all day to enumerate, this one particular figure highlights a piece of the puzzle in stark way. Here we see that data are not stored, stored in labs, on university servers, in a community repository, or “other.” (I think that’s what you mark when it’s in stuffed in a shoebox at home.)
Aside from community repositories, which account for 7.6% of the data, it’s just not available to others.
We actually didn’t change WHAT data needs to be shared, rather the focus was placed on WHERE it is housed, WHEN it is shared, and HOW authors provide access for those who want it
Development of new data access policy over > 1 year
Steering committee included staff plus journal editors who are also active researchers
Data policy committee involving individuals from, and communicating with, all levels of journal review and production
Presentations at conferences and meetings
Consultations with editorial boards
Review of policy iterations and communications before public release
Pre-implementation questions from researchers
What to do with massive datasets?
What if the researcher plans to publish additional studies using the data?
What if competitors take advantage?
In cases of “data available on request,” what if no data access committee exists and the IRB is not willing to take on the responsibility?
Concerns over privacy for human data
EMPHASIS TEXT ON WHITE
PHOTO WITH HEADLINE 1
Pavel Tomancek uses SPIM microscopy – if he ran it on max capacity for 24 hrs, he would produce 138Tb of data (as compared with CERN who produce a paltry 82 Tb/day)
Another researcher noted that he had 8Tb of data that he condensed to produce a single movie for his talk.
What would we do with this???
Need practical solutions at the Institute level too.
NSF funded project – Make Data Count – to explore and test data-level metrics that capture activity surrounding research data
Meeting co-org by PLOS and California Digital Library
Organizers
● Jennifer Lin, Senior Product Manager, PLOS
● Cameron Neylon, Advocacy Director, PLOS
● Carly Strasser, Data Curation Specialist, California Digital Library
Participants
● Stephen Abrams, Associate Director of UC Curation Center, California Digital Library
● Rachel Bruce, Director, Technology Innovation, Jisc
● Eleni Castro, Research Coordinator, IQSS,Harvard University
● John Chodacki, Director of Product Development, PLOS
● Patricia Cruse, Director of UC Curation Center, California Digital Library
● Ingrid Dillo, Head Policy Communication Development, DANS
● Alex Garnett, Data Curation & Digital Preservation Specialist, Simon Fraser University
● Jennifer Green, Director of Research Data Services, University of Michigan
● Simon Hodson, Executive Director, CODATA
● Eric Kansa, Technology Director, Open Context
● Belinda Norman, Research Data Manager, University of Sydney
● Mark Parsons, Secretary General, Research Data Alliance
● Jonathan Tedds, Senior Research Fellow, University of Leicester
● Todd Vision, Principal Investigator, Dryad; Associate Director for Informatics, National Evolutionary Synthesis Center