Cameron Neylon

A [very interesting
paper](http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0007078)
from [Caroline
Savage](http://www.linkedin.com/pub/caroline-savage/14/375/b0b) and
[Andrew Vickers](http://www.mskcc.org/mskcc/html/3197.cfm) was published
in [PLoS ONE](http://www.plosone.org) last week detailing an empirical
study of data sharing of PLoS journal authors. The results themselves,
that one out ten corresponding authors provided data, are not
particularly surprising, mirroring as they do previous studies, both
[formal](http://users.fmg.uva.nl/jwicherts/datasharing.pdf) \[pdf\] and
[informal](http://www.nytimes.com/2008/01/22/health/views/22essa.html?_r=1)
(also from Vickers, I assume this is a different data set), of data
sharing.

Nor are the reasons why data was not shared particularly new. Two
authors couldn't be tracked down at all. Several did not reply and the
remainder came up with the usual excuses; "too hard", "need more
information", "university policy forbids it". The numbers in the study
are small and it is a shame it wasn't possible to do a wider study that
might have teased out discipline, gender, and age differences in
attitude. Such a study really ought to be done but it isn't clear to me
how to do it effectively, properly, or indeed ethically. The reason why
small numbers were chosen was both to focus on PLoS authors, who might
be expected to have more open attitudes, and to make the request from
the authors, that the data was to be used in a Master educational
project, plausible.

So while helpful, the paper itself isn't doesn't provide much that is
new. What will be interesting will be to see how [PLoS](http://plos.org)
responds. These authors are clearly violating stated PLoS policy on data
sharing (see e.g. [PLoS ONE
policy](http://www.plosone.org/static/policies.action)). The papers
should arguably be publicly pulled from the journals. Most journals have
similar policies on data sharing, and most have no corporate interest in
actually enforcing them. I am unaware of any cases where a paper has
been retracted due to the authors unwillingness to share (if there are
examples I'd love to know about them! \[Ed. [Hilary
Spencer](http://network.nature.com/people/hilary/profile) from
[NPG](http://nature.com) pointed us in the direction of some case
studies in [a presentation from Philip
Campbell](http://precedings.nature.com/documents/2176/version/1)).

Is it fair that a small group be used as a scapegoat? Is it really
necessary to go for the nuclear option and pull the papers? As was said
in a [Friendfeed discussion thread on the
paper](http://friendfeed.com/science-2-0/20780650/plos-one-empirical-study-of-data-sharing-by):
"*IME* \[In my experience\] *researchers are reeeeeeeally good at
calling bluffs. I think there's no other way*". I can't see any other
way of raising the profile of this issue. Should PLoS take the risk of
being seen as hardline on this? Risking the consequences of people not
sending papers there because of the need to reveal data?

The PLoS offering has always been about quality, high profile journals
delivering important papers, and at PLoS ONE critical analysis of the
quality of the methodology. The perceived value of that quality is
compromised by authors who do not make data available. My personal view
is that PLoS would win by taking a hard line and the moral high ground.
Your paper might be important enough to get into Journal X, but is the
data of sufficient quality to make it into PLoS ONE? Other journals
would be forced to follow -- at least those that take quality seriously.

There will always be cases where data can not or should not be
available. But these should be carefully delineated exceptions and not
the rule. If you can't be bothered putting your data into a shape worthy
of publication then the conclusions you have based on that data are
worthless. You should not be allowed to publish. End of. We are running
out of excuses. The time to make the data available is now. If it isn't
backed by the data then it shouldn't be published.

*Update: It is clear from this [editorial blog
post](http://speakingofmedicine.plos.org/2009/09/23/data-sharing-after-publication/)
from the PLoS Medicine editors that PLoS do not in fact know which
papers are involved.Â  As was pointed out by Steve Koch in [the
friendfeed
discussion](http://friendfeed.com/cameronneylon/0fbc705d/show-us-data-now-damnit-excuses-are-running-out)
there is an irony that Savage and Vickers have not, in a sense, provided
their own raw data i.e. the emails and names of correspondents. However
I would accept that to do so would be a an unethical breach of presumed
privacy as the correspondents might reasonably have expected these were
private emails and to publish names would effectively be entrapment.
Life is never straightforward and this is precisely the kind of grey
area we need more explicit guidance on.*

Savage CJ, Vickers AJ (2009) Empirical Study of Data Sharing by Authors
Publishing in PLoS Journals. PLoS ONE 4(9): e7078.
doi:10.1371/journal.pone.0007078

*Full disclosure: I am an academic editor for PLoS ONE and have raised
the issue of insisting on supporting data for all charts and graphs in
PLoS ONE papers in the editors' forum. There is also a [recent paper
with my name
on](http://www.nature.com/nphys/journal/vaop/ncurrent/abs/nphys1371.html)
in which the words "data not shown" appear. If anyone wants that data I
will make sure they get it, and as soon as Nature enable article
commenting we'll try to get something up there. The usual excuses apply,
and don't really cut the mustard.*


A very interesting paper from Caroline Savage and Andrew Vickers was published in PLoS ONE last week detailing an empirical study of data sharing of PLoS journal authors. The results themselves, that one out ten corresponding authors provided data, are not particularly surprising, mirroring as they do previous studies, both formal [pdf] and informal (also from Vickers, I assume this is a different data set), of data sharing.

Show us the data now damnit! Excuses are running out.

An update on the [Workshop that I announced
previously](http://blog.openwetware.org/scienceintheopen/2008/06/25/open-science-workshop-at-southampton-31-august-and-1-september/).
We have a number of people confirmed to come down and I need to start
firming up numbers. I will be emailing a few people over the weekend so
sorry if you get this via more than one route. The plan of attack
remains as follows:

Meet on evening of Sunday 31 August in Southampton, most likely at a
bar/restaurant near the University to coordinate/organise the details of
sessions.

Commence on Monday at \~9:30 and finish around 4:30pm (with the option
of discussion going into the evening) with three or four sessions over
the course of the day broadly divided into the areas of tools, social
issues, and policy. We have people interested and expert in all of these
areas coming so we should be able to to have a good discussion. The
object is to keep it very informal but to keep the discussion
productive. Numbers are likely to be around 15-20 people. For those not
lucky enough to be in the area we will aim to record and stream the
sessions, probably using a combination of [dimdim](http://dimdim.com),
[mogulus](http://mogulus.com), and [slideshare](http://slideshare.com).
Some of these may require you to be signed into our session so if you
are interested drop me a line at the account below.

To register for the meeting please send me an email to my gmail account
(cameronneylon). To avoid any potential confusion, even if you have
emailed me in the past week or so about this please email again so that
I have a comprehensive list in one place. I will get back to you with a
request via PayPal for Â£15 to cover coffees and lunch for the day (so
if you have a PayPal account you want to use please send the email from
that address). If there is a problem with the cost please state so in
your email and we will see what we can do. We can suggest options for
accomodation but will ask you to sort it out for yourself.

I have set up a [wiki](http://sotonopensciworkshop.wikispaces.com/) to
discuss the workshop which is currently completely open access. If I see
spam or hacking problems I will close it down to members only (so it
would be helpful if you could create an account) but hopefully it might
last a few weeks in the open form. Please add your name and any relevant
details you are happy to give out to the [Attendees
page](http://sotonopensciworkshop.wikispaces.com/Attendees) and add any
presentations or demos you would be interested in giving, or would be
interested in hearing about, on the [Programme
suggestion](http://sotonopensciworkshop.wikispaces.com/Programme+suggestions)
page.


An update on the Workshop that I announced previously. We have a number of people confirmed to come down and I need to start firming up numbers. I will be emailing a few people over the weekend so sorry if you get this via more than one route. The plan of attack remains as follows:  Meet on evening of Sunday 31 August in Southampton, most likely at a bar/restaurant near the University to coordinate/organise the details of sessions.

Southampton Open Science Workshop 31 August and 1 September

So [BioBarCamp](https://barcamp.pbwiki.com/BioBarCamp) started yesterday
with a bang and a great kick off. Not only did we somehow manage to
start early we were consistently running ahead of schedule. With several
hours initially scheduled for introductions this actually went pretty
quick, although it was quite comprehensive. During the introduction many
people expressed an interest in 'Open Science', 'Open Data', or some
other open stuff, yet it was already pretty clear that many people meant
many different things by this. It was suggested that with the time
available we have a discussion session on what 'Open Science' might
mean. Pedro and mysey [live blogged this at
Friendfeed](http://friendfeed.com/e/cda930dd-8e36-45ad-9710-c0437138384d/Random-session-on-What-is-open-science/)
and the discussion will continue this morning.

I think for me the most striking outcome of that session was that not
only is this a radically new concept for many people but that many
people don't have any background understanding of open source software
either which can make the discussion totally impenetrable to them. This,
in my view strengthens the need for having some clear brands, or
standards, that are easy to point to and easy to sign up to (or not). I
pitched the idea, basically adapting from [John Wilbank's pitch at the
meeting in
Barcelona](http://blog.openwetware.org/scienceintheopen/2008/07/17/policy-for-open-science-the-wrap-up-session/),
that our first target should that all data and analysis associated with
a published paper should be available. This seems an unarguable basic
standard, but is one that we currently fall far short of. I will pitch
this again in the session I have proposed on 'Building a data commons'.

The [schedule for
today](http://spreadsheets.google.com/ccc?key=phPg75kT_QZbrTeFHhYJWPA&inv=attilacsordas%40gmail.com&t=339609701451780581)
is up as a googledoc spreadsheet with many difficult decisions to make.
My current thinking is;

1.  Kaitlin Thaney â€" Open Science Session
2.  Ricardo Vidal and Vivek Murthy (OpenWetWare and Epernicus).Â  Using
    online communities to share resources efficiently.
3.  Jeremy England & Mark Kaganovich â€" Labmeeting, Keeping Stalin Out
    of Science (though I would also love to do John Cumbers on synthetic
    biology for space colonization, that is just so cool)
4.  Pedro Beltrao & Peter Binfield â€" Dealing with Noise in Science /
    How should scientific articles be measured.
5.  Hard choice: Andrew Hessel â€" building an open source biotech
    company or Nikesh Kotecha + Shirley Wu â€" Motivating annotation
6.  Another doozy: John Cumbers -- Science Worship / Science Marketing
    or Hilary Spencer & Mathias Crawford â€" Interests in Scientific IP
    â€" Who Owns/Controls Scientific Communication and Data?Â  The Major
    Players.
7.  Better turn up to mine I guess :)
8.  Â Joseph Perla â€" Cloud computing, Robotics and the future of
    Science andÂ  Joel Dudley & Charles Parrot â€" Open Access
    Scientific Computing Grids & OpenMac Grid

I am beginning to think I should have brought two laptops and two
webcams. Then I could have recorded one and gone to the other. Whatever
happens I will try to cover as much as I can in the [BioBarCamp room at
FriendFeed](http://friendfeed.com/rooms/biobarcamp), and where possible
and appropriate I will [broadcast and record via
Mogulus](http://www.mogulus.com/cameron_neylon). The wireless was a bit
tenuous yesterday so I am not absolutely sure how well this will work.

Finally, this has been great opportunity to meet up with people I know
and have met before, those who I feel I know well but have never met
face to face, and indeed those whose name I vaguely know (or should
know) but have never connected with before. I'm not going to say who is
in which list because I will forget someone! But if I haven't said hello
yet do come up and harass me because I probably just haven't connected
your online persona with the person in front of me!


So BioBarCamp started yesterday with a bang and a great kick off. Not only did we somehow manage to start early we were consistently running ahead of schedule. With several hours initially scheduled for introductions this actually went pretty quick, although it was quite comprehensive.

BioBarCamp &#8211; Meeting friends old and new and virtual

I'm in Barcelona at a satellite meeting of the EuroScience Open Forum
organised by Science Commons and a number of their partners.Â  Today is
when most of the meeting will be with forums on 'Open Access Today',
'Moving OA to the Scientific Enterprise:Data, materials, software',
'Open access in the the knowledge network', and 'Open society, open
science: Principle and lessons from OA'. There is also a keynote from
Carlos Morais-Pires of the European Commission and the lineup for the
panels is very impressive.

Last night was an introduction and social kickoff as well. James Boyle
(Duke Law School, Chair of board of directors of Creative Commons,
Founder of Science commons) gave a wonderful talk (40 minutes, no
slides, barely taking breath) where his central theme was the
relationship between where we are today with open science and where
international computer networks were in 1992. He likened making the case
for open science today with that of people suggesting in 1992 that the
networks would benefit from being made freely accessible, freely
useable, and based on open standards. The fears that people have today
of good information being lost in a deluge of dross, of their being
large quantities of nonsense, and nonsense from people with an agenda,
can to a certain extent be balanced against the idea that to put it
crudely, that Google works. As James put it (not quite a direct quote)
'You need to reconcile two statements; both true. 1) 99% of all material
on the web is incorrect, badly written, and partial. 2) You probablyÂ 
haven't opened an encylopedia as a reference in ten year.

James gave two further examples, one being the availability of legal
data in the US. Despite the fact that none of this is copyrightable in
the US there are thriving businesses based on it. The second, which I
found compelling, for reasons that Peter Murray-Rust has described in
some detail. Weather data in the US is free. In a recent attempt to get
long term weather data a research effort was charged on the order of
\$1500, the cost of the DVDs that would be needed to ship the data, for
all existing US weather data. By comparison a single German state wanted
millions for theirs. The consequence of this was that the European data
didn't go into the modelling. James made the point that while the
European return on investment for weather data was a respectable
nine-fold, that for the US (where they are giving it away remember) was
32 times. To me though the really compelling part of this argument is if
that data is not made available we run the risk of being underwater in
twenty years with nothing to eat. This particular case is not about
money, it is potentially about survival.

Finally -- and this you will not be surprised was the bit I most liked
-- he went on to issue a call to arms to get on and start building this
thing that we might call the data commons. The time has come to actually
sit down and start to take these things forward, to start solving the
issues of reward structures, of identifying business models, and to
build the tools and standards to make this happen. That, he said was the
job for today. I am looking forward to it.

I will attempt to do some updates via twitter/friendfeed (cameronneylon
on both) but I don't know how well that will work. I don't have a
roaming data tariff and the charges in Europe are a killer so it may be
a bit sparse.


I’m in Barcelona at a satellite meeting of the EuroScience Open Forum organised by Science Commons and a number of their partners.Â

Policy and technology for e-science &#8211; A forum on on open science policy

[![Sign at The Googleplex. Google limited access to Xenu.net, in March
2002.](http://upload.wikimedia.org/wikipedia/en/thumb/e/ee/Googleplex_Welcome_Sign.jpg/202px-Googleplex_Welcome_Sign.jpg){decoding="async"}](http://en.wikipedia.org/wiki/Image:Googleplex_Welcome_Sign.jpg)I
realised the other day that I havenâ€™t written an exciteable blog post
about getting an invitation to
[SciFoo](http://en.wikipedia.org/wiki/Science_Foo_Camp "Science Foo Camp"){rel="wikipedia"}!
The reason for this is that [I got overexcited over on
FriendFeed](http://friendfeed.com/e/0b4e74bd-9513-4c20-7330-3d51868290fb)
instead and havenâ€™t really had time to get my head together to write
something here. But in this post I want to propose a session and think
through what the focus and aspects of that might be.

I am a passionate advocate of two things that I think are intimately
related. I believe strongly in the need and benefits that will arise
from building, using, and enabling the effective search and processing
of a scientific data commons. I
\[[1](http://blog.openwetware.org/scienceintheopen/2008/04/16/the-science-exchange/),[2](http://blog.openwetware.org/scienceintheopen/2008/05/11/more-on-the-science-exchance-or-building-and-capitalising-a-data-commons/)\]
and others (including
[John](http://network.nature.com/blogs/user/wilbanks/2008/05/10/on-the-erosion-of-the-public-domain)
[Wilbanks](http://network.nature.com/blogs/user/wilbanks/2008/05/11/on-a-data-commons),
[Deepak Singh](http://feeds.feedburner.com/~r/mndoci/~3/288151920/), and
[Plausible
Accuracy](http://www.plausibleaccuracy.com/2008/05/12/data-should-be-public-domain-and-more-esoteric-blog-based-rasslin/))
have written on this quite a lot recently. The second aspect is that I
believe strongly in the need for effective useable and generic tools to
record science as it happens and to process that record so that others
can use it effectively. To me these two things are intimately related.
By providing the tools that enable the record to be created and
integrating them with the systems that will store and process the data
commons we can enable scientists to record their work better,
communicate it better, and make it available *as a matter of course* to
other scientists (not necessarily immediately I should add, but when
they are comfortable with it).

At last yearâ€™s SciFoo Chris DiBona ran a session called â€˜Give us the
Dataâ€™ \[Ed. As noted below Jon Trowbridge led the session with Chris
DiBona acting as 'session chair'\] Now I wasnâ€™t there but Deepak Singh
[wrote the session up in a blog
post](http://mndoci.com/blog/2007/08/09/scifoo-google-and-large-scientific-datasets/)
which is my main inspiration. The idea here seemed to be to send in big
data sets and that
[Google](http://en.wikipedia.org/wiki/Google "Google"){rel="wikipedia"}
could slurp these up for processing. Now the world has moved on from
last year and I believe we can propose something much more ambitious
*with the tools we have available*. We can build the systems, or at
least the prototypes of systems, that will be so useful for recording
and sharing data that people will want to use them. Google AppEngine,
Amazon Web Services, Freebase,
[CouchDB](http://www.couchdb.com/ "CouchDB"){rel="homepage"}, Twine, and
the growing efforts in actually making controlled vocabularies useful
and useable, as well as a growing web of repositories and services make
this look like an achievable target in a way that it wasnâ€™t twelve
months ago. Once we start building these repositories of data then there
will be a huge incentive both for scientists and big players such as
Google, Microsoft, Yahoo, IBM, and Amazon to look at how to effectively
process, re-process, and present this data. That will be exciting, but
first we need to build the tools and systems that will enable us to put
the data there.

What does this â€˜systemâ€™ look like. Iâ€™m going to suggest a possible
model, based on my non-technical understanding of how these things work.
I will probably get the details wrong (and please comment where I do).
Letâ€™s start at the storage end. We are only interested in open
repositories, where it is explicitly stated that data is in the [public
domain](http://en.wikipedia.org/wiki/Public_domain "Public domain"){rel="wikipedia"}
and therefore freely re-useable. Some of these repositories exist for
specific domains.
[ChemSpider](http://www.chemspider.com/ "ChemSpider"){rel="homepage"} ,
NMRShiftDB and crystallography databases in the chemistry domain,
GenBank,
[PDB](http://en.wikipedia.org/wiki/Protein_Data_Bank "Protein Data Bank"){rel="wikipedia"},
and many others in the biosciences domain. To be honest, for most large
datasets repositories already exist. The problem is not â€˜big
scienceâ€™, the problem is â€˜small scienceâ€™ or â€˜long tailâ€™
science. The vast quantity of data and description that is generated by
small numbers o people in isolated labs. Huge amounts of data
languishing on millions of laptops in non-standard formats. All that
stuff that no-one can really be bothered dealing with.

The storage itself is not really a problem. It can go on [Amazon
S3](http://en.wikipedia.org/wiki/Amazon_S3 "Amazon S3"){rel="wikipedia"},
Google servers, or into the various [Institutional
Repositories](http://en.wikipedia.org/wiki/Institutional_repository "Institutional repository"){rel="wikipedia"}
that Universities are rapidly deploying internationally. In fact, it
should go into all three and a few other places besides. Storage is
cheap, redoing the experiment is not. The digital curation people are
also working on the format problem with standards like
[ORE](http://www.ukoln.ac.uk/repositories/digirep/index/OAI-ORE)
providing a means of wrapping collections of data up and describing the
format internally. Combine this with an open repository of data formats
and the problem of storing and understanding data goes away, or rather
it is still a large technical problem but one that is reasonably soluble
with sufficient effort. One thing that is needed is standards for
describing data formats; both standards in terms of the description and
quality standards for what are the minimal requirements for describing
data (MiSDaFD anyone?). A lot of work is required in the area of
controlled vocabularies and ontologies, particularly in science domains
where they havenâ€™t yet got much traction. These donâ€™t need to be
perfect, they just need to be descriptive. But once again, how to go
about doing this is reasonably clear (devil is in the details I know).

The fundamental problem is how to capture the data, associated metadata,
and do the wrapping in a way that is an easy and convenient enough that
scientists will actually do it. It will come as no suprise to the
regularn readers of this blog that I would advocate the development of
tools to enable scientists to do this effectively at the stage at which
they already record their experiments; when they are done. Not only is
this the point where the scientist already has the task of planning,
executing, and recording their experiment. It is also the point at which
embedding good metadata and recording practice will be the most benefit
to them.

So we need to build a lab book system, or a virtual research environment
if you prefer, because this will encompass much more than the
traditional paper notebook. It will also encompass much more than the
current crop of electronic lab notebooks. I donâ€™t want to go into the
details of what I think this should look like here; thatâ€™s the subject
for a post in its own right. But to give an outline this system will
consist of a feed aggregator (not unlike
[Friendfeed](http://friendfeed.com)) where the user can subscribe to
various data streams, some from people, some from instruments or
sensors, and some that they have generated themselves, pictures at
[Flickr](http://flickr.com), comments on [Twitter](http://twitter.com).
The lab book component itself will look more or less like a word
processor, or a blog, or a wiki, depending on what the user wants. In
this system the user will generate documents (or pages); some will
describe samples, some procedures, and some ideas. Critically this
authoring system will have an open plugin architecture supported by an
open source community that enables the user to grab extra functionality
automatically.

A simple plugin might recognise a DNA sequence, or an INCHI code, and
provide a functional graphical display, complete with automatically
generated links back to the appropriate databases. Another plugin might
provide access to a range of ontologies or controlled vocabularies which
enable autocompletion of typed text with the appropriate name or easy or
automatically generate the PDB/SBML/MiBBI compliant datafiles required
for deposition. Journal submission templates could also be plugins or
gadgets that assist in pulling all the relevant information together for
submission and wrapping it up in an appropriate format. Semantic
authoring at the journal submission stage is never going to work.
Building it in early on and sucking it through when required just might.
Adding semantic information could be as easy (but probably should be no
easier than) formatting text. Select, right click, add semantics from
drop down menu.

This environment will have a proper versioning system, web integration
to push documents into the wider world, and a WYSIWYG interface. It will
expose human readable and machine readable versions of the files, and
will almost certainly use an underlying XML document format. It will
probably expose both microformats, rdf, and free text tags.

I think there are essentially two routes towards this kind of system.
One is to build into existing word processor and document handling
ecosystems. Essentially building a plugin architecture for Word or
OpenOffice. This would have the advantage of a system that is already
widely used and familiar to scientists. It has the disadvantage (at
least in the Microsoft case) that it would be built on top of a closed
source product and be reliant on the continued existence and support of
a large company. The alternative approach is to bring a completely open
source product through. This will require much more work, particularly
on the user interface side, but may be easier to handle in terms of open
source plugin architecture. It could be entirely web based. Google
AppEngine provides a very interesting environment for building such a
thing. CouchDB may be a good way of maintaining the underlying data.
Google Gadgets may well provide a lot of the desired plugin architecture
and widgets of various, types, javascript, bookmarklets, and all the
various tools on the web may provide a lot of the rest.

The purpose of this system is ultimately to encourage people to place
research results in the public domain in a way that makes them useful.
For it to get traction it has to be a no-brainer for people to adopt as
a central part of the way they run their laboratory. If it doesnâ€™t
make peopleâ€™s life easier; a lot easier; its not going to get any
traction. The User interface will be crucial, reliability will be
crucial, and the availability of added functionality which is currently
simply unavailable will be crucial.

Agreeing an architecture is likely to be a challenge but an open source
project is probably a more effective way of leveraging effort from a
wide community. There are many open standards available that can be used
here and the key is getting them all working together. Ideally the
choice of authoring environment wonâ€™t matter because it can still push
documents to the web in the same format(s), still use the same plugins,
still interface with the databases. Building this will cost money, quite
a lot of money, but the flip side is enabling the availability of the
data, the procedures into the public domain. As I heard Christoph
Steinbeck say yesterday, we can either get on and do this, or wait for
the singularity. I think weâ€™ve got a while to wait for that, so I
think its time to get on with the build. Who wants to be involved?

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I realised the other day that I havenâ€™t written an exciteable blog post about getting an invitation to SciFoo! The reason for this is that I got overexcited over on FriendFeed instead and havenâ€™t really had time to get my head together to write something here.

Postagens de Rogue Scholar

Show us the data now damnit! Excuses are running out.

Southampton Open Science Workshop 31 August and 1 September

BioBarCamp – Meeting friends old and new and virtual

Policy and technology for e-science – A forum on on open science policy

How do we build the science data commons? A proposal for a SciFoo session