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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 control 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 support them.
• ContentMining (TDM) as research
• Are “publishers” tyrants or servants?
Every Research
Data Manager
should be using Git
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/th
esis
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
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
Without
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…
So we can now
legally contentmine
the whole literature
in the UK…
NORMA
Ross Mounce and PMR
created a SuperTree of Life
for microorganisms!
…Yes! And in UK
we are starting
to do it…
http://www.slideshare.net/rossmounce/the-pluto-project-ievobio-2014
https://en.wikipedia.org/wiki/Tree_of_life CC BY-SA
Aves
Apterygidae
Marsupialia
Monotremata
Mammalia
Reptilia
Amphibia
Arthropoda
Myriapodia
Okapia johnstoni
Pyrus
Stuffed Tree of Life
Authors don’t deposit data (Ross Mounce)
And we did it as Open Notebook
Science
all data and code on Github
Discussion on public Discourse Tool
NO INSIDER KNOWLEDGE
4300 images in Github
“Root”
We analysed every pixel
Many diagrams had author errors
Supertree created from 4300 papers
Supertree for 924 species
Tree
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/elsevi
er-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
Unused slides…
OPEN CLOSED
Zenodo Figshare
Git
Dat
OpenOffice Word, PPT
LabTrove, cheminfo.org Chemdraw
CrystallographyOpenDB Cambridge Cryst data Centre
WriteLatex / Overleaf
ReadCube, Symplectic,
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=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
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)
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The culture of researchData

  • 1. 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 control us
  • 2. Just read the big letters He’s got zillions of slides…
  • 3. My European Heroes Young People(ContentMine) NEELIE KROES
  • 4. The Right to Read 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 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]
  • 7. Elsevier wants to control 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 support them. • ContentMining (TDM) as research • Are “publishers” tyrants or servants?
  • 10. 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?
  • 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
  • 14. 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!
  • 15. Software management Is a success! Research DATA management Is a mess.
  • 16. Traditional Research and Publication “Lab” work paper/th esis Write rewrite Re-experiment publish ??? Validation?? DATA output “belongs” to publisher Every process is LOSSY
  • 17. 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
  • 18. 505 pages PDF, was a machine-readable log file that could and should have been in a repo Computational Chemistry
  • 19. MORE of the PDF DATA Destruction Blind humans and Machines cannot read this
  • 22. 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
  • 23. PMR’s Tribute Planned Memorial Meeting July 14th 2014 Cambridge OPEN NOTEBOOK SCIENCE
  • 24. 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 Without
  • 25. Open is FASTER, BETTER, MORE, MORE EFFICIENT
  • 26. Open Notebook Science, ONS Jean-Claude Bradley 2006 All data immediately available to all. NO INSIDER INFORMATION.
  • 27. 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
  • 29. 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. Interactive OPEN chemical search tool from cheminfo.org
  • 32. Interactive OPEN molecular display Jmol (Bob Hanson et al)
  • 33.
  • 34. Interactive OPEN chemical search tool from cheminfo.org
  • 35. 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
  • 36. Data thrives on Community
  • 37. 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
  • 38.
  • 39.
  • 41. 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
  • 44. DATA
  • 46. 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
  • 47. 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
  • 48. Open Source and Open Data www.crystallography.net
  • 50.
  • 51. Panton Fellows (Early Career Researchers) Panton Principles of Open Scientific Data 2010 Publish data openly (CC0) and record your wishes
  • 52. Sophie Kershaw, Panton Fellow : Doctoral Training in Oxford
  • 54. 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
  • 55. … third-year graduate students So first-year grad students should be trained by…
  • 56. So we can now legally contentmine the whole literature in the UK… NORMA Ross Mounce and PMR created a SuperTree of Life for microorganisms! …Yes! And in UK we are starting to do it…
  • 60. Authors don’t deposit data (Ross Mounce)
  • 61. And we did it as Open Notebook Science all data and code on Github Discussion on public Discourse Tool NO INSIDER KNOWLEDGE
  • 62. 4300 images in Github
  • 64. Many diagrams had author errors
  • 65. Supertree created from 4300 papers
  • 66. Supertree for 924 species Tree
  • 67. So why not Git for Data?
  • 68. DAT is Git for Data!!
  • 69. DAT! Queen Mary UL reposits DNA
  • 70. 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
  • 71. @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
  • 72. 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
  • 73. 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
  • 75.
  • 76.
  • 77. OPEN CLOSED Zenodo Figshare Git Dat OpenOffice Word, PPT LabTrove, cheminfo.org Chemdraw CrystallographyOpenDB Cambridge Cryst data Centre WriteLatex / Overleaf ReadCube, Symplectic,
  • 78. 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=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
  • 79.
  • 80. Open Source software inspires Open Science Jean-Claude Bradley 2006
  • 81.
  • 82.
  • 83.
  • 84.
  • 85.
  • 86. 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

  1. 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.