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 Science

Publishers 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 Academia Glory+?

$$, MS review

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 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?

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

GIT housekeeps AUTOMATICALLY, eternally

Daily record of commits and Merges. Can backtrack to ANY Previous version

Community involvement

https://github.com/ContentMine/quickscrape/pulls

Contributions from People “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 management Is a success!

Research DATA management Is 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

Computational Chemistry

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 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

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 Science

Open engineered repository

World community

INSTRUMENT

validate

merge

MODEL CODE

DATA

DATA knowledge

calibrate

Problems are solved communally; Nothing is needlessly duplicated; “publication“ is continuous ; data are SEMANTIC

Machines and humans Working 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

COMMUNITY INVOLVEMENT

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 VALIDATION CRITERIA/TOOLS

DATA

PUBLICLY VALIDATED TRUSTABLE SCIENCE

Where to reposit published crystallography?

Proteins -> PDB, Open

BUT

Inorganics -> ICSD Closed

Organics -> Cambridge (CCDC) Closed

SO

The 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

Open Source and Open Data

www.crystallography.net

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

Copyright, Open Access, and Human Rights March 13, 2015 Kevin Smith, J.D. 2 Comments The United Nations Human Rights Council … a report from Farida Shaheed, who is a “Special Rapporteur” in the area of “cultural rights.” … its frank recognition that intellectual property laws are in tension with the fundamental human right of access to science and culture … WIPO is charged, whether effectively or not, to find ways to facilitate open access to science and culture … this is not just a “what’s best for academia and for my interests” issue, but a true human rights issue. Ms. Shaheed’s report makes this case in a concise and compelling way … - See more at: http://blogs.library.duke.edu/scholcomm/2015/03/13/copyright-open-access-and-human-rights/#sthash.6CQiMoiV.dpuf

Many diagrams had author errors

Supertree created from 4300 papers

Copyright, Open Access, and Human Rights March 13, 2015 Kevin Smith, J.D. 2 Comments The United Nations Human Rights Council … a report from Farida Shaheed, who is a “Special Rapporteur” in the area of “cultural rights.” … its frank recognition that intellectual property laws are in tension with the fundamental human right of access to science and culture … WIPO is charged, whether effectively or not, to find ways to facilitate open access to science and culture … this is not just a “what’s best for academia and for my interests” issue, but a true human rights issue. Ms. Shaheed’s report makes this case in a concise and compelling way … - See more at: http://blogs.library.duke.edu/scholcomm/2015/03/13/copyright-open-access-and-human-rights/#sthash.6CQiMoiV.dpuf

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 Phylogeny Cmunity [*]

[*] 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 research Chris 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 data This 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.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

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)