Download to read offline
![WE pay for scholarly
publications that WE
can’t read
[1] The Military-Industrial-Academic complex (1961)
(Dwight D Eisenhower, US President)
Publishers Academia
Glory+?
$$, MS
review
Taxpayer
Student
Researcher
$$ $$
in-kind
The Publisher-Academic complex[1]](https://image.slidesharecdn.com/reasearchdata-160129185840-160131204747/75/The-culture-of-researchData-6-2048.jpg)
![Elsevier wants to control Open Data
[asked by Michelle Brook]](https://image.slidesharecdn.com/reasearchdata-160129185840-160131204747/75/The-culture-of-researchData-7-2048.jpg)
![How NOT to publish data
HT Henry Rzepa
From Henry Rzepa:
this article http://doi.org/10.1126/science.aad6252
which provides a 22 Mbyte PDF of data (mostly bitmaps of NMR
spectra) and comes in at 404 pages long. [1]
But this one http://doi.org/10.1021/jacs.5b05902 [comp chem]
is 505 pages long (the current record holder?)
[1] DATA Behind paywall](https://image.slidesharecdn.com/reasearchdata-160129185840-160131204747/75/The-culture-of-researchData-17-2048.jpg)
![Can we mine for
animals?
YesWith the
Phylogeny
Cmunity [*]
[*] overlaps with “Tree of Life”, “Evolutionary Biology” , “Taxonomy”, “Species”](https://image.slidesharecdn.com/reasearchdata-160129185840-160131204747/75/The-culture-of-researchData-68-2048.jpg)
![The John S. and James L. Knight Foundation is an American private, non-profit foundation
dedicated to supporting "transformational ideas that promote quality journalism, advance
media innovation, engage communities and foster the arts."[2]
DAT supports public data](https://image.slidesharecdn.com/reasearchdata-160129185840-160131204747/75/The-culture-of-researchData-73-2048.jpg)
![I am a statistician interested in detecting potentially problematic research such as data fabrication,
which results in unreliable findings and can harm policy-making, confound funding decisions, and
hampers research progress.
To this end, I am content mining results reported in the psychology literature. Content mining the
literature is a valuable avenue of investigating research questions with innovative methods. For
example, our research group has written an automated program to mine research papers for errors in
the reported results and found that 1/8 papers (of 30,000) contains at least one result that could
directly influence the substantive conclusion [1].
In new research, I am trying to extract test results, figures, tables, and other information reported in
papers throughout the majority of the psychology literature. As such, I need the research papers
published in psychology that I can mine for these data. To this end, I started ‘bulk’ downloading research
papers from, for instance, Sciencedirect. I was doing this for scholarly purposes and took into account
potential server load by limiting the amount of papers I downloaded per minute to 9. I had no intention
to redistribute the downloaded materials, had legal access to them because my university pays a
subscription, and I only wanted to extract facts from these papers.
Full disclosure, I downloaded approximately 30GB of data from Sciencedirect in approximately 10 days.
This boils down to a server load of 0.0021GB/[min], 0.125GB/h, 3GB/day.
Approximately two weeks after I started downloading psychology research papers, Elsevier notified my
university that this was a violation of the access contract, that this could be considered stealing of
content, and that they wanted it to stop. My librarian explicitly instructed me to stop downloading
(which I did immediately), otherwise Elsevier would cut all access to Sciencedirect for my university.
I am now not able to mine a substantial part of the literature, and because of this Elsevier is directly
hampering me in my research.
[1] Nuijten, M. B., Hartgerink, C. H. J., van Assen, M. A. L. M., Epskamp, S., & Wicherts, J. M. (2015). The
prevalence of statistical reporting errors in psychology (1985–2013). Behavior Research Methods, 1–22.
doi: 10.3758/s13428-015-0664-2
Chris Hartgerink’s blog post](https://image.slidesharecdn.com/reasearchdata-160129185840-160131204747/75/The-culture-of-researchData-75-2048.jpg)
![Some Children
of the Digital Enlightenment
• David Carroll & Joe McArthur: OAButton
• Rayna Stamboliyska & Pierre-Carl Langlais
• Jon Tennant
• Ross Mounce
• Jenny Molloy
• Erin McKiernan
• Jack Andraka
• Michelle Brook
• Heather Piwowar
• TheContentMine Team
• Rufus Pollock
• Jonathan Gray
• Sophie Kay
Jean-Claude Bradley [1] a chemist
developed Open notebook science;
making the entire primary record of a
research project publicly available
online as it is recorded. (WP)
J-C promoted these ideas with
UNDERGRADUATE scientists.
[1] Unfortunately J-C died in 2014;
we held a memorial meeting in
Cambridge
Sophie
Kay](https://image.slidesharecdn.com/reasearchdata-160129185840-160131204747/75/The-culture-of-researchData-76-2048.jpg)
![Ross Mounce (Bath), Panton Fellow
• Sharing research data:
http://www.slideshare.net/rossmounce
• How-to figures from PLOS/One [link]:
Ross shows how to bring figures to life:
• PLOSOne at http://bit.ly/PLOStrees
• PLOS at http://bit.ly/phylofigs (demo)](https://image.slidesharecdn.com/reasearchdata-160129185840-160131204747/75/The-culture-of-researchData-88-2048.jpg)
Uploaded byTheContentMine
The culture of researchData
The document emphasizes the need for a cultural shift in research data management, advocating for open access and community-driven approaches to scientific data. Highlighting the limitations imposed by traditional publishers, it underscores the value of open notebook science and collaborative platforms like GitHub for sharing and validating research. The discussion includes various examples and principles that illustrate how transparency and accessibility can enhance the research process and foster innovation.
More Related Content
Similar to The culture of researchData
The culture of researchData
- 1. The Culture ofResearch Data Peter Murray-Rust, ContentMine.org and UniversityOfCambridge LEARN, London, UK 2016-01-29 The technology for Managing Research Data is already here… …but we need a change of culture Open Notebook Science Publishers must be forced to serve us, not tyrranize us
- 2. Just read thebig letters He’s got zillions of slides…
- 3. My European Heroes YoungPeople(ContentMine) NEELIE KROES
- 4. The Right toRead is the Right to Mine http://contentmine.org
- 5. Themes • Highly domain-dependent(chem, cryst, phylo) • Requires community and centrality • University repositories are NOT the solution • Openness makes it dramatically easier/better • The publisher-academic complex is a major problem. • Infrastructure must be open and under our control
- 6. WE pay forscholarly publications that WE can’t read [1] The Military-Industrial-Academic complex (1961) (Dwight D Eisenhower, US President) Publishers Academia Glory+? $$, MS review Taxpayer Student Researcher $$ $$ in-kind The Publisher-Academic complex[1]
- 7. Elsevier wants tocontrol Open Data [asked by Michelle Brook]
- 8. Some topics • Github/ software mgt informs data mgt • Open notebook science • Open source malaria + LabTrove • Open phylogenetics • Computational chemistry • Crystallography • Early career researchers can change the world, if we let them. • Are “publishers” tyrants or servants?
- 9. Every Research Data Manager shouldbe using me
- 10. Why I repositsoftware in GitHub I WANT TO!!! BETTER QUICKER SECURE AUDIT, BACKTRACKABLE EASY get collaborators Most early career software creators have repos How many people have USED Git?
- 11. Free/Open Software Development CODE REPOSITORY World community CODE rewrite validate CODE fork CODE Re-use CODE Re-use Github,BitBucket StackOverflow, Apache inspires OSI Example: ContentMine at http://github.com/ContentMine/quickscrape BORN-OPEN-SOURCE NO WALLS
- 12. GIT housekeeps AUTOMATICALLY,eternally Daily record of commits and Merges. Can backtrack to ANY Previous version
- 13.
- 14. Compile Fail Inactive Fail Tests PassTests Continuous Integration (Jenkins) Every time I commit a change 50 projects are recompiled and tested. Impossible to do this manually!
- 15. Software management Is asuccess! Research DATA management Is a mess.
- 16. Traditional Research andPublication “Lab” work paper/th esis Write rewrite Re-experiment publish ??? Validation?? DATA output “belongs” to publisher Every process is LOSSY
- 17. How NOT topublish data HT Henry Rzepa From Henry Rzepa: this article http://doi.org/10.1126/science.aad6252 which provides a 22 Mbyte PDF of data (mostly bitmaps of NMR spectra) and comes in at 404 pages long. [1] But this one http://doi.org/10.1021/jacs.5b05902 [comp chem] is 505 pages long (the current record holder?) [1] DATA Behind paywall
- 18. 505 pages PDF,was a machine-readable log file that could and should have been in a repo Computational Chemistry
- 19. MORE of thePDF DATA Destruction Blind humans and Machines cannot read this
- 20. ALWAYS put your (computational, instrumental, observational) datadirectly into a repository
- 21.
- 22. JD Bernal’s 1965vision However large an array of facts, however rapidly they accumulate, it is possible to keep them in order and to extract from time to time digests containing the most generally significant information, while indicating how to find those items of specialized interest. To do so, however, requires the will and the means. (Bernal, 1965) Quoted by PMR in http://journals.iucr.org/d/issues/1998/06/01/ba0011/ba0011.pdf
- 23. PMR’s Tribute Planned MemorialMeeting July 14th 2014 Cambridge OPEN NOTEBOOK SCIENCE
- 24. https://en.wikipedia.org/wiki/Bermuda_Principles • Automatic releaseof sequence assemblies larger than 1 kb (preferably within 24 hours). • Immediate publication of finished annotated sequences. • Aim to make the entire sequence freely available in the public domain for both research and development in order to maximise benefits to society. HUMAN GENOME project used Open Notebooks
- 25. Open is FASTER,BETTER, MORE EFFICIENT
- 26. Open is FASTER,BETTER, MORE, MORE EFFICIENT
- 27. Open Notebook Science,ONS Jean-Claude Bradley 2006 All data immediately available to all. NO INSIDER INFORMATION.
- 28. TOOLS Open Notebook Science Open engineered repository World community INSTRUMENT validate merge MODEL CODE DATA DATA knowledge calibrate Problemsare solved communally; Nothing is needlessly duplicated; “publication“ is continuous ; data are SEMANTIC Machines and humans Working together
- 29.
- 30. Mat Todd (Sydney)and MANY collaborators http://opensourcemalaria.org/ (Chrome for interactivity) Mat Todd, Univ Sydney, runs an Open Notebook community to create new antimalarials.
- 31.
- 32. Interactive OPEN chemicalsearch tool from cheminfo.org
- 33. Interactive OPEN moleculardisplay Jmol (Bob Hanson et al)
- 35. Interactive OPEN chemicalsearch tool from cheminfo.org
- 36. data is associatedwith the proposed scientific endeavour prior to or at the point of creation rather than by annotating the data with commentary after the experiment has taken place University of Southampton
- 37. Data thrives onCommunity
- 38. Henry Rzepa doesOpen Notebook Computational Chemistry… http://www.rzepa.net/blog/?p=14272 This is a current open notebook discussion, http://www.ch.imperial.ac.uk/rzepa/blog/?p=15552 (see comments, currently 67). … on his blog
- 41.
- 42. Crystallography – amodel for Data Management • Pro-active, friendly international community • Committed active International Union(IUCr) • Data publication valued (1960-present) • Community develops semantics/dictionaries • Committed volunteer software innovators • Heavily Open approach • Massive and valuable re-use of data • Culture of validation/reproducibility • Respect and credit for tool development
- 43.
- 44.
- 45.
- 46.
- 47. Where to repositpublished crystallography? Proteins -> PDB, Open BUT Inorganics -> ICSD Closed Organics -> Cambridge (CCDC) Closed SO The community has built a Crystallography Open Database
- 48. Restrictions on Re-useof Crystallographic data NOTE: The CCDC is based on data contributed by scientists as part of publication and validation Crystallographic data from publications now belongs to CCDC
- 49. Open Source andOpen Data www.crystallography.net
- 50. Interactive OPEN crystalsearch tool
- 52. Panton Fellows (EarlyCareer Researchers) Panton Principles of Open Scientific Data 2010 Publish data openly (CC0) and record your wishes
- 53. Sophie Kershaw, PantonFellow : Doctoral Training in Oxford
- 54. Sophie Kershaw, PantonFellow
- 55. Rotation-Based Learning (RBL) Phase1: Initiator • No communication permitted between groups • Attempt to reproduce existing literature • Deliver a coherent research story by the end of Phase 1 Phase 2: Successor • Communication between groups still prohibited • Validate and develop the inherited research story • Critique your predecessors • Role of research producer vs. research user • Can this approach help to foster awareness of reproducibility issues? Throughout Phases 1 & 2: • Daily lectures on open science culture & techniques • First-hand application to own research work • Version control using GitHub • Daily group supervision
- 56. … third-year graduate students Sofirst-year grad students should be trained by…
- 57.
- 58. Authors don’t depositdata (Ross Mounce)
- 59.
- 60. And we didit as Open Notebook Science all data and code on Github Discussion on public Discourse Tool
- 61.
- 62. 4300 images inGithub
- 63.
- 64. Many diagrams hadauthor errors
- 65. Supertree created from4300 papers
- 66.
- 67. Supertree for 924species Tree
- 68. Can we minefor animals? YesWith the Phylogeny Cmunity [*] [*] overlaps with “Tree of Life”, “Evolutionary Biology” , “Taxonomy”, “Species”
- 69. So now wecan legally mine the whole literature in the UK Yes! And we are starting to do it… NORMA
- 70. So why notGit for Data?
- 71. DAT is Gitfor Data!!
- 72. DAT! Queen MaryUL reposits DNA
- 73. The John S.and James L. Knight Foundation is an American private, non-profit foundation dedicated to supporting "transformational ideas that promote quality journalism, advance media innovation, engage communities and foster the arts."[2] DAT supports public data
- 74. @Senficon (Julia Reda):Text & Data mining in times of #copyright maximalism: "Elsevier stopped me doing my research" http://onsnetwork.org/chartgerink/2015/11/16/elsevi er-stopped-me-doing-my-research/ … #opencon #TDM Elsevier stopped me doing my research Chris Hartgerink
- 75. I am astatistician interested in detecting potentially problematic research such as data fabrication, which results in unreliable findings and can harm policy-making, confound funding decisions, and hampers research progress. To this end, I am content mining results reported in the psychology literature. Content mining the literature is a valuable avenue of investigating research questions with innovative methods. For example, our research group has written an automated program to mine research papers for errors in the reported results and found that 1/8 papers (of 30,000) contains at least one result that could directly influence the substantive conclusion [1]. In new research, I am trying to extract test results, figures, tables, and other information reported in papers throughout the majority of the psychology literature. As such, I need the research papers published in psychology that I can mine for these data. To this end, I started ‘bulk’ downloading research papers from, for instance, Sciencedirect. I was doing this for scholarly purposes and took into account potential server load by limiting the amount of papers I downloaded per minute to 9. I had no intention to redistribute the downloaded materials, had legal access to them because my university pays a subscription, and I only wanted to extract facts from these papers. Full disclosure, I downloaded approximately 30GB of data from Sciencedirect in approximately 10 days. This boils down to a server load of 0.0021GB/[min], 0.125GB/h, 3GB/day. Approximately two weeks after I started downloading psychology research papers, Elsevier notified my university that this was a violation of the access contract, that this could be considered stealing of content, and that they wanted it to stop. My librarian explicitly instructed me to stop downloading (which I did immediately), otherwise Elsevier would cut all access to Sciencedirect for my university. I am now not able to mine a substantial part of the literature, and because of this Elsevier is directly hampering me in my research. [1] Nuijten, M. B., Hartgerink, C. H. J., van Assen, M. A. L. M., Epskamp, S., & Wicherts, J. M. (2015). The prevalence of statistical reporting errors in psychology (1985–2013). Behavior Research Methods, 1–22. doi: 10.3758/s13428-015-0664-2 Chris Hartgerink’s blog post
- 76. Some Children of theDigital Enlightenment • David Carroll & Joe McArthur: OAButton • Rayna Stamboliyska & Pierre-Carl Langlais • Jon Tennant • Ross Mounce • Jenny Molloy • Erin McKiernan • Jack Andraka • Michelle Brook • Heather Piwowar • TheContentMine Team • Rufus Pollock • Jonathan Gray • Sophie Kay Jean-Claude Bradley [1] a chemist developed Open notebook science; making the entire primary record of a research project publicly available online as it is recorded. (WP) J-C promoted these ideas with UNDERGRADUATE scientists. [1] Unfortunately J-C died in 2014; we held a memorial meeting in Cambridge Sophie Kay
- 79. OPEN CLOSED Zenodo Figshare Git Dat OpenOfficeWord, PPT LabTrove, cheminfo.org Chemdraw CrystallographyOpenDB Cambridge Cryst data Centre WriteLatex / Overleaf ReadCube, Symplectic,
- 80. This is acurrent open notebook discussion, http://www.ch.imperial.ac.uk/rzepa/blog/?p=15552 (see comments, currently 67). This is an earlier one, http://www.rzepa.net/blog/?p=14272 (with 86 comments) and also incorporates Jsmol to visualise all the data This one starts discussion as an open notebook http://www.ch.imperial.ac.uk/rzepa/blog/?p=1211 with the resulting formal publication at 10.1002/jcc.23985 This was the original open notebook post http://www.ch.imperial.ac.uk/rzepa/blog/?p=984 with the resulting formal publication at 10.1038/NCHEM.596 This one incorporates open data into its citation list http://www.ch.imperial.ac.uk/rzepa/blog/?p=15505 and is also an open notebook follow up to my PhD thesis work, formally published in 1975 or so, thus operating in reverse to the above. This shows some end outcomes: http://www.ch.imperial.ac.uk/rzepa/blog/?p=15313 This shows the principles: http://www.ch.imperial.ac.uk/rzepa/blog/?p=10972 This is an introductory tutorial http://www.ch.imperial.ac.uk/rzepa/blog/?p=14454 This is a critique http://www.ch.imperial.ac.uk/rzepa/blog/?p=13826 This is “convincing case” http://www.ch.imperial.ac.uk/rzepa/blog/?p=13248 This is about metadata http://www.ch.imperial.ac.uk/rzepa/blog/?p=12932 And its use http://www.ch.imperial.ac.uk/rzepa/blog/?p=12526 You have seen this data nightmare before: http://www.ch.imperial.ac.uk/rzepa/blog/?p=12728 This is about ORCID http://www.ch.imperial.ac.uk/rzepa/blog/?p=12513
- 82. Open Source softwareinspires Open Science Jean-Claude Bradley 2006
- 88. Ross Mounce (Bath),Panton Fellow • Sharing research data: http://www.slideshare.net/rossmounce • How-to figures from PLOS/One [link]: Ross shows how to bring figures to life: • PLOSOne at http://bit.ly/PLOStrees • PLOS at http://bit.ly/phylofigs (demo)
Editor's Notes
- #2 Hi, I’m here to talk about AMI; a data extraction framework and tool. First, I just want highlight some of key contributors to the projects; Andy for his work on the ChemistryVisitor and Peter for the overall architecture. In this talk, I’m going to impress the importance of data in a specific format and its utility to automated machine processing. Then I’m going to demonstrate AMI’s architecture and the transformation of data as it flows through the process. I’m going to dwell a little on a core format used, Scalable Vector Graphics (SVG) before introducing the concept of visitors, which are pluggable context specific data extractors. Next, I’m going to introduce Andy’s ChemVisitor, for extracting semantic chemistry data, along with a few other visitors that can process non-chemistry specific data. Finally, I will demonstrate some uses of the ChemVisitor, within the realm of validation and metabolism.