Download - The culture of researchData
The Culture of Research 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 SciencePublishers must be forced to serve us, not tyrranize us
Just read the big letters
He’s got zillions of slides…
My European Heroes
Young People(ContentMine)
NEELIE KROES
The Right to Read is the Right to Mine
http://contentmine.org
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
WE pay for scholarly publications that WE
can’t read
[1] The Military-Industrial-Academic complex (1961)(Dwight D Eisenhower, US President)
Publishers AcademiaGlory+?
$$, MSreview
Taxpayer
Student
Researcher
$$ $$
in-kind
The Publisher-Academic complex[1]
Elsevier wants to control Open Data
[asked by Michelle Brook]
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?
Every Research Data Manager
should be using me
Why I reposit software in GitHubI WANT TO!!!
BETTER QUICKERSECUREAUDIT, BACKTRACKABLEEASY
get collaborators
Most early career software creators have repos
How many people have USED Git?
Free/Open Software Development CODE REPOSITORY
Worldcommunity
CODErewrite
validate
CODEfork
CODE
Re-use
CODERe-use
Github, BitBucketStackOverflow,Apache
inspires
OSI
Example: ContentMine athttp://github.com/ContentMine/quickscrape
BORN-OPEN-SOURCE
NO WALLS
GIT housekeeps AUTOMATICALLY, eternally
Daily record of commits andMerges. Can backtrack to ANY Previous version
Community involvement
https://github.com/ContentMine/quickscrape/pulls
Contributions fromPeople “outside project”
Compile Fail
Inactive
Fail Tests
Pass Tests
Continuous Integration (Jenkins)Every time I commit a change 50 projects are recompiled and tested.
Impossible to do this manually!
Software managementIs a success!
Research DATA managementIs a mess.
Traditional Research and Publication
“Lab” work paper/thesis
Write
rewrite
Re-experiment
publish
???
Validation??
DATA
output “belongs” to publisher
Every process is LOSSY
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
505 pages PDF, was a machine-readable log file that could and should have been in a repo
ComputationalChemistry
MORE of the PDF DATA Destruction
Blind humans and Machines cannot read this
ALWAYS put your (computational,
instrumental, observational)
data directly into a repository
Let’s see some visionaries
JD Bernal’s 1965 vision
However large an array of facts, however rapidly theyaccumulate, it is possible to keep them in order and toextract from time to time digests containing the most
generally significant information, while indicating how tofind 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
PMR’s Tribute
Planned Memorial Meeting July 14th 2014 Cambridge
OPEN NOTEBOOK SCIENCE
https://en.wikipedia.org/wiki/Bermuda_Principles
• Automatic release of 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
Open is FASTER, BETTER, MORE EFFICIENT
Open is FASTER, BETTER, MORE, MORE EFFICIENT
Open Notebook Science, ONS
Jean-Claude Bradley 2006
All data immediately available to all. NO
INSIDER INFORMATION.
TOOLS
Open Notebook ScienceOpen engineeredrepository
Worldcommunity
INSTRUMENT
validate
merge
MODELCODE
DATA
DATAknowledge
calibrate
Problems are solved communally; Nothing is needlessly duplicated; “publication“ is continuous ; data are SEMANTIC
Machines and humansWorking together
Here are three examples
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.
Notebook managed on Git.
Interactive OPEN chemical search tool from cheminfo.org
Interactive OPEN molecular display Jmol (Bob Hanson et al)
Interactive OPEN chemical search tool from cheminfo.org
data is associated with 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
Data thrives on Community
Henry Rzepa does Open 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
COMMUNITYINVOLVEMENT
Crystallography – a model 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
IUCr DICTIONARIES
IUCr VALIDATIONCRITERIA/TOOLS
DATA
PUBLICLYVALIDATEDTRUSTABLESCIENCE
Where to reposit published crystallography?
Proteins -> PDB, OpenBUTInorganics -> ICSD ClosedOrganics -> Cambridge (CCDC) ClosedSOThe community has built a Crystallography Open Database
Restrictions on Re-use of 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
Interactive OPEN crystal search tool
Panton Fellows (Early Career Researchers)
Panton Principles of Open Scientific Data 2010
Publish data openly (CC0) and record your wishes
Sophie Kershaw, Panton Fellow : Doctoral Training in Oxford
Sophie Kershaw, Panton Fellow
Rotation-Based Learning (RBL)
Phase 1: 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
… third-year graduate students
So first-year grad students should be
trained by…
https://en.wikipedia.org/wiki/Tree_of_life CC BY-SA
Authors don’t deposit data (Ross Mounce)
http://www.slideshare.net/rossmounce/the-pluto-project-ievobio-2014
And we did it as Open Notebook Science
all data and code on Github
Discussion on public Discourse Tool
https://en.wikipedia.org/wiki/Tree_of_life CC BY-SA
4300 images in Github
“Root”
We analysed every pixel
Many diagrams had author errors
Supertree created from 4300 papers
Aves
Apterygidae
Marsupialia
Monotremata
Mammalia
Reptilia
Amphibia
Arthropoda
Myriapodia
Okapia johnstoni
Pyrus
Stuffed Tree of Life
Supertree for 924 species
Tree
Can we mine for animals?
YesWith the PhylogenyCmunity [*]
[*] overlaps with “Tree of Life”, “Evolutionary Biology” , “Taxonomy”, “Species”
So now we can legally mine the
whole literature in the UK
Yes! And we are starting to do it…
NORMA
So why not Git for Data?
DAT is Git for Data!!
DAT! Queen Mary UL reposits DNA
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
@Senficon (Julia Reda) :Text & Data mining in times of #copyright maximalism:
"Elsevier stopped me doing my research" http://onsnetwork.org/chartgerink/2015/11/16/elsevier-stopped-me-doing-my-research/ …
#opencon #TDM
Elsevier stopped me doing my researchChris Hartgerink
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
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
OPEN CLOSED
Zenodo Figshare
Git
Dat
OpenOffice Word, PPT
LabTrove, cheminfo.org Chemdraw
CrystallographyOpenDB Cambridge Cryst data Centre
WriteLatex / Overleaf
ReadCube, Symplectic,
>>> Henry.> Where and what is your latest repository and can I demonstrate it? This will be better than pointing to some dead Quixote site. And any blog posts would be useful. Happy to talk today if you are free. Chempond is still running eg http://chempound.ch.ic.ac.uk:8090/content/f0705698-39fa-4279-b736-f2fdca571e7b/
Timed out... Is it running?
There have been firewall problems in the past. I thought they were fixed. Will check.
Do you have blog posts which show either (a) how the repository is set up and (b) an Open Notebook approach to a project - where you discuss a problem before it is formally published? Both of these would be very useful.
This is a current 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 dataThis one starts discussion as an open notebook http://www.ch.imperial.ac.uk/rzepa/blog/?p=12115 with the resulting formal publication at 10.1002/jcc.23985This 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.596This 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=15313This shows the principles: http://www.ch.imperial.ac.uk/rzepa/blog/?p=10972This is an introductory tutorial http://www.ch.imperial.ac.uk/rzepa/blog/?p=14454This is a critique http://www.ch.imperial.ac.uk/rzepa/blog/?p=13826This is “convincing case” http://www.ch.imperial.ac.uk/rzepa/blog/?p=13248This is about metadata http://www.ch.imperial.ac.uk/rzepa/blog/?p=12932And its use http://www.ch.imperial.ac.uk/rzepa/blog/?p=12526You have seen this data nightmare before: http://www.ch.imperial.ac.uk/rzepa/blog/?p=12728This is about ORCID http://www.ch.imperial.ac.uk/rzepa/blog/?p=12513
Open Source software inspires Open Science
Jean-Claude Bradley 2006
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)
