Open Palaeontology

http://svpow.wordpress.com/2009/04/23/mydd/

Published Data

Original data format

(Authors)

(Publishers)

My Frustrations

http://en.wikipedia.org/wiki/Nexus_file

My Frustrations

A bit about myself...

Open Palaeontology

the

Data Obfuscation

• reformatted codings

it was formerly {01}

metadata

putting data on the web for all to see and use

{

When data IS 'shared' in a publication

it's often significantly obfuscated

Some scientists won't share data

data wrapper

an example

publishing

• NO metadata

Ross Mounce

Birds

evolved from

Dinosaurs

Table 1: The Data Matrix

Aus 00100 10101 01010 101

Bus 01010 10101 0101A 013

Cus 03254 43504 58423 232

... etc

#NEXUS

Begin data;

Dimensions ntax=7 nchar=99

Format datatype=standard missing=? gap=-;

Matrix

Aus 001001010101010101

Bus 01010101010101{01}013

Cus 032544350458423232

...

end;

the

...even if you explain why

...even post-publication

...even if you ask them face-to-face

...even if they're publicly funded

• printed sideways

(harder to re-extract)

publishing

process

Non-standard formatting

(requires reformatting)

+

in a .pdf or .html

(which programs can't use)

Standardly-formatted data

(information)

+

in a usable digital file

(digital container)

NEXUS -formated information

(phylogenetic info)

+

in a plain-text .nex file

(digital container)

Tabulated information

(phylogenetic info)

+

in an unusable .pdf file

(digital container)

process

slides here: http://bit.ly/openpal

process

2nd year PhD student | Research: Fossils & Phylogeny

(rage!)

• in a .pdf

their data stays private (potentially forever!)

#OpenScience #OpenData

@rmounce

Ubuntu user, occasional FOSS zealot, Internet addict...

the actual data

charge: $800 per research article

The Open Paleontology Journal

(Bentham Science Publishers)

ISSN: 1874-4257

3 of which are self-citations

6 articles -> 4 citations

2008 + 2009

(in 2010)

2010 Impact Factor: 0.66

~34th out of 42

*unofficial

The GenBank model

• sideways

• non-standard coding

• in a pdf

• no metadata

Morpho-Databases

already exist

Paper-based

thinking in 2011

Jo Wolfe (Yale), Graeme Lloyd (NHM)

Katie Davis (NHM), Rachel Warnock (Bristol)

an image of a glass of water

But hardly anyone uses them: it's not mandatory

Homo AGTCGGTC

Pan AGTGGATC

Molecular sequence data is treated appropriately

Why not morphological data too? Similar

Why?

Maxwell, E. E. Generic reassignment of an ichthyosaur from the queen elizabeth islands, northwest territories, canada. Journal of Vertebrate Paleontology 30, 403-415 (2010). URL

http://dx.doi.org/10.1080/02724631003617944

e.g.

or

We can see it but we can't drink (use) it!

Homo 01021011121

Pan 01010100010

"Erm... let's do something about this!"

from: O’Meara, Brian, Whitacre, Jamie, Mounce, Ross, Rosauer, Dan, Vos, Rutger, and Stoltzfus, Arlin.

Publishing re-usable phylogenetic trees, in theory and practice. Presented at iEvoBio, June, 2011

Why not have a rich-content digital version, and a separate paper-friendly version?

in contrast GenBank is mandatory for publishing molecular sequence analyses

Michael Pittman (UCL), Aodhán Butler (Uppsala), Alex Dunhill (Bristol), Russell Garwood (Imperial), James Lamsdell (Kansas), David Legg (Imperial)

http://precedings.nature.com/documents/6048/version/1

also from

a paper

published

in 2010

But the reaction wasn't 100% positive

Getting the message out

Other criticisms (too long to quote)

Over 120 signatures in the 1st week

A website + petition form

A draft Open Letter using:

(criticism is however, good and welcome)

(aka 'leveraging the social networks')

http://supportpalaeodataarchiving.co.uk/

(Fear of people

stealing fossils)

Shouldn't laws

prevent this?

David C. Kopaska-Merkel

"Releasing data always jeopardises future research plans as others now have access to the data"

"...lowering citations for everyone

making it harder for us all to compete for funding"

"This could actually slow the rate of publication"

"I will not endorse anything that implies that we need even less public money or that we are wasting public money"

If they're 'undescribed' why mention them? If they're important, describe them to the level needed for your purposes.

Locality data in field-based studies.

Undescribed specimens

Long-term projects

(I can't know everything before I publish)

Jamale Ijouiher

"Complete openness of data facilitates the advancement of knowledge & reduces information loss."

"As a postgraduate trying to establish myself, greater access to data would be a boon"

'Data accessibility and transparency are absolutely necessary to mend the damage done to science by "climategate." '

"I've been trying to get the Paleo Society to sign on with Dryad, but it's been like slamming my head on jello...."

(inspired by)

(Jeopardising)

William K. Halligan

Mailing-Lists

If you publish 'interim' results don't expect people NOT to use that data

kudos to Jon Antcliffe (Bristol) for saying

what others were thinking, but didn't express

special thx to Jon Hill & Katie Davis

Pete Wagner (Smithsonian)

Lucy Muir & Joe Botting (Nanjing)

Most successful

but YMMV

original source: http://mailman.nhm.ac.uk/pipermail/paleonet/2011-March/001933.html

original source: http://mailman.nhm.ac.uk/pipermail/paleonet/2011-March/001934.html

International support from Palaeontologists

Lessons Learned

What next...?

Other Barriers in Palaeontology

#OpenData heroes

in Palaeontology

Encourage/promote/support existing databases

Feel free to:

share

re-use/remix

re-distribute

my research is publicly funded hence I strive to make my works publicly available

Access to physical fossils is a minefield

(politically, legally, socially...)

http://figshare.com/

http://www.morphobank.org/

• Leverage social networks

• All publicity is good publicity

especially criticism and debate

• Act NOW! Change is sloooow

Commercial rights over fossils vary

hugely between countries and museums.

http://www.treebase.org/

http://paleodb.org/

http://www.zoobank.org/

Graeme T. Lloyd

Mike P. Taylor

Certain institutions very overprotective

and assertive of image 'rights'

c.f. "The best time to plant a tree is 20 years ago

The 2nd best time is NOW"

Matt Wedel

Andy A. Farke

awesome

http://svpow.wordpress.com/

John Wilbanks

slides here: http://bit.ly/openpal

http://maps.google.co.uk/maps/ms?msid=218353561524244017339.0004a697ea032baff7843&msa=0

Callaway, E. Fossil data enter the web period : Nature news.

e.g. Mike Taylor on the NHM http://dml.cmnh.org/2011Jun/msg00010.html

http://www.graemetlloyd.com/

http://www.slideshare.net/wilbanks/data-sharing-as-a-means-to-a-revolution-8421942

http://datadryad.org/

http://paleo.esrf.fr/

http://openpaleo.blogspot.com/

http://opendino.wordpress.com/

http://www.nature.com/news/2011/110411/full/472150a.html

@rmounce

or ross.mounce@gmail.com

for comments on slides: Jenny Greenwood, Alex Dunhill, Anne O'Connor, Martin Hughes, David M. Williams

for being an awesome supervisor: Matthew Wills

Team OKFN for inviting me, and organising a great conf

and to everyone who supported the Open Letter...

Palaeontologists: please share MORE content online;

raw data, high-res images, green OA papers, presentations...