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Open Palaeontology

http://okcon.org/2011/programme/open-palaeontology-putting-fossil-data-on-the-web-for-all-to-see-and-use an invited talk, given on Friday 1st July 2011 at the Open Knowledge Conference (Berlin) by Ross Mounce
by Ross Mounce on 1 July 2011

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Transcript of Open Palaeontology

Open Palaeontology putting data on the web for all to see and use Ross Mounce The Open Paleontology Journal
(Bentham Science Publishers)
ISSN: 1874-4257 6 articles -> 4 citations 2008 + 2009 charge: $800 per research article 2010 Impact Factor: 0.66 *unofficial ~34th out of 42 3 of which are self-citations (in 2010) @rmounce #OpenScience #OpenData 2nd year PhD student | Research: Fossils & Phylogeny A bit about myself... Ubuntu user, occasional FOSS zealot, Internet addict... Birds
evolved from
Dinosaurs My Frustrations Some scientists won't share data ...even if you explain why
...even post-publication
...even if you ask them face-to-face
...even if they're publicly funded their data stays private (potentially forever!) My Frustrations When data IS 'shared' in a publication
it's often significantly obfuscated (rage!) Standardly-formatted data
(information)
+
in a usable digital file
(digital container) (Authors) (Publishers) Non-standard formatting
(requires reformatting)
+
in a .pdf or .html
(which programs can't use) publishing process the Data Obfuscation an example publishing process the NEXUS -formated information
(phylogenetic info)
+
in a plain-text .nex file
(digital container) Tabulated information
(phylogenetic info)
+
in an unusable .pdf file
(digital container) Original data format #NEXUS
Begin data;
Dimensions ntax=7 nchar=99
Format datatype=standard missing=? gap=-;
Matrix
Aus 001001010101010101
Bus 01010101010101{01}013
Cus 032544350458423232
...
end; metadata the actual data { data wrapper publishing process the Published Data Aus 00100 10101 01010 101
Bus 01010 10101 0101A 013
Cus 03254 43504 58423 232
... etc NO metadata reformatted codings
it was formerly {01} printed sideways
(harder to re-extract) Table 1: The Data Matrix in a .pdf Paper-based
thinking in 2011 Why not have a rich-content digital version, and a separate paper-friendly version? Why? sideways

non-standard coding

in a pdf

no metadata also from
a paper
published
in 2010 The GenBank model Molecular sequence data is treated appropriately



Why not morphological data too? Similar Homo AGTCGGTC
Pan AGTGGATC Homo 01021011121
Pan 01010100010 http://precedings.nature.com/documents/6048/version/1 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 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 Morpho-Databases
already exist But hardly anyone uses them: it's not mandatory e.g. or in contrast GenBank is mandatory for publishing molecular sequence analyses "Erm... let's do something about this!" Michael Pittman (UCL), Aodhán Butler (Uppsala), Alex Dunhill (Bristol), Russell Garwood (Imperial), James Lamsdell (Kansas), David Legg (Imperial) Jo Wolfe (Yale), Graeme Lloyd (NHM)
Katie Davis (NHM), Rachel Warnock (Bristol) (inspired by) A draft Open Letter using: A website + petition form special thx to Jon Hill & Katie Davis Getting the message out Mailing-Lists (aka 'leveraging the social networks') Over 120 signatures in the 1st week "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...." But the reaction wasn't 100% positive "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" kudos to Jon Antcliffe (Bristol) for saying
what others were thinking, but didn't express Callaway, E. Fossil data enter the web period : Nature news. http://www.nature.com/news/2011/110411/full/472150a.html Lessons Learned Leverage social networks

All publicity is good publicity
especially criticism and debate

Act NOW! Change is sloooow What next...? Encourage/promote/support existing databases awesome Most successful
but YMMV http://supportpalaeodataarchiving.co.uk/ http://maps.google.co.uk/maps/ms?msid=218353561524244017339.0004a697ea032baff7843&msa=0 http://paleodb.org/ http://www.morphobank.org/ http://datadryad.org/ http://opendino.wordpress.com/ http://www.zoobank.org/ http://www.treebase.org/ http://figshare.com/ http://paleo.esrf.fr/ #OpenData heroes
in Palaeontology Andy A. Farke Mike P. Taylor Matt Wedel Graeme T. Lloyd http://openpaleo.blogspot.com/ http://svpow.wordpress.com/ http://www.graemetlloyd.com/ (criticism is however, good and welcome) original source: http://mailman.nhm.ac.uk/pipermail/paleonet/2011-March/001933.html International support from Palaeontologists Pete Wagner (Smithsonian) William K. Halligan Jamale Ijouiher David C. Kopaska-Merkel slides here: http://bit.ly/openpal http://en.wikipedia.org/wiki/Nexus_file c.f. "The best time to plant a tree is 20 years ago
The 2nd best time is NOW" http://www.slideshare.net/wilbanks/data-sharing-as-a-means-to-a-revolution-8421942 John Wilbanks 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... Other Barriers in Palaeontology Access to physical fossils is a minefield
(politically, legally, socially...) e.g. Mike Taylor on the NHM http://dml.cmnh.org/2011Jun/msg00010.html Commercial rights over fossils vary
hugely between countries and museums. Certain institutions very overprotective
and assertive of image 'rights' http://svpow.wordpress.com/2009/04/23/mydd/ If they're 'undescribed' why mention them? If they're important, describe them to the level needed for your purposes. Shouldn't laws
prevent this? (Fear of people
stealing fossils) Locality data in field-based studies.


Undescribed specimens



Long-term projects (Jeopardising) If you publish 'interim' results don't expect people NOT to use that data Other criticisms (too long to quote) (I can't know everything before I publish) Lucy Muir & Joe Botting (Nanjing) original source: http://mailman.nhm.ac.uk/pipermail/paleonet/2011-March/001934.html Feel free to:
share
re-use/remix
re-distribute slides here: http://bit.ly/openpal @rmounce or ross.mounce@gmail.com an image of a glass of water We can see it but we can't drink (use) it! my research is publicly funded hence I strive to make my works publicly available
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