Going Digital
Rod Page
Photo by Keith Marshall http://www.flickr.com/photos/keithmarshall/432924465/

If you are not online you are
invisible
(Web 1.0)

All useful information will be
online
(Web 1.0)

Value is explicit and based on
usage (links)
(Web 1.0)

Reputation is created…
(Web 2.0)

…not conferred by authority
(Web 2.0)

Everything will have a URL
(Web 3.0)

Yes, I’ve drunk the Kool Aid

…but I’m not alone

Social networking

Dinosaurs ban it

Scaremongers say it causes
cancer

Some “get it”

Some do real work with it

#uksnow

@kzelnioCould you do me a favour:
10.1016/j.anbehav.2008.12.017

Where is the
(digital) museum?
Photo by Keith Marshall http://www.flickr.com/photos/keithmarshall/432924465/

www.nhm.ac.uk

Zoology

This dataset is not accessible by the
public. For more information please
contact the Department of Zoology.

Silo
http://www.flickr.com/photos/kenmccown/132990634/

404

GBIF
http://www.flickr.com/photos/chrisfreeland/3306689322/

Top 10 GBIF data providers

League table
Museum GBIF data Open access Staff Social
journal publications Networking
online
Twitter,
yes
3,446,016 Facebook,
Youtube, etc.
(searchable
yes
collections) (Twitter)
412,797 (planned)
(planned)

Why go digital?
Photo by Keith Marshall http://www.flickr.com/photos/keithmarshall/432924465/

Diverse kinds of data

Apomys datae

Apomys specimen

How do we integrate these data?

Why integrate?

Learn stuff we don’t know

• There are knownknowns, things we know that we
know
• There are knownunknowns, things we now know
we don’t know
• But there are also unknownunknowns, things we
do not know we don't know

Unknown knowns

Things we know
…without knowing that we know

Melissotarsus insularis

1
Melissotarsus insularis no hit
Melissotarsus insularis CASENT0107663-D01
CASENT0107663-D01 DQ176312
DQ176312 Melissotarsus sp. BLF m1
=
Melissotarsus sp. BLF m1 Melissotarsus insularis

No one source has all the
answers

Joining the dots

Identifiers

Digital Object Identifier
(DOI)

Identifies a publication

Globally unique

10.1016/j.ympev.2006.04.006

Paper

Why have DOIs?

Link rot

Refs

Cites
2006
2006

Forward Cites
2006 2009

Shoulders of giants

progress is incremental

reuse past results

Forward Cites
2006 2008

Species
Genes

data linking

data citation

http://iphylo.org/~rpage/challenge

demo

Vision

Chromiscircumaurea

What should
museums do?
Photo by Keith Marshall http://www.flickr.com/photos/keithmarshall/432924465/

Do nothing
Photo by Keith Marshall http://www.flickr.com/photos/keithmarshall/432924465/

The new

Don’t try this at home
• Image storage (Flickr)
• Video storage (YouTube, Vimeo)
• Bibliographies (Connotea, Mendeley)
• Social networking (Facebook, Twitter)
• Annotation (CMS, Wikis, Blogs)
• Bulk storage (Amazon S3)
• Bulk computing (Amazon EC2)

Make it easy
Photo by Keith Marshall http://www.flickr.com/photos/keithmarshall/432924465/

http://www.flickr.com/photos/scobleizer/2256358640/

http://taxonomy.zoology.gla.ac.uk/rod/treeview.html

http://abacus.gene.ucl.ac.uk/software/paml.html

http://mrbayes.csit.fsu.edu/

http://www.tree-puzzle.de/

http://atgc.lirmm.fr/phyml/

No branding

No corporate style

No permission needed

Institution provides
infrastructure…

…then gets out of the way

Top five European papers in
evolutionary biology 1996-2006
1,118 – 4,512 citations

Partnerships
(EOL)
Photo by Keith Marshall http://www.flickr.com/photos/keithmarshall/432924465/

“Dance of the initiatives”
Christine Hine

Danger of too much money

Million Dollar Page

EOL in it’s present form

sucks

Can I do science with it?

Not yet…

Intellectual
Property
Photo by Keith Marshall http://www.flickr.com/photos/keithmarshall/432924465/

Fear

Ignorance

Silo
http://www.flickr.com/photos/kenmccown/132990634/

AMNH Conditions
1. Except as otherwise expressly stated herein, the information, records, or images
in these databases may not be reproduced, distributed, or publicly displayed, in
whole or in part, without the express written permission of the American
Museum of Natural History (AMNH).
2. AMNH does not grant permission for anyone to use, download, reproduce,
publicly display, distribute, or reprint all or substantially all of the information,
records, or images in the database.
3. Subsets of the information, records, or images in the database may be used,
downloaded, reproduced, publicly displayed, distributed, or reprinted strictly for
educational, scientific, scholarly, and other non-profit uses provided that AMNH
is appropriately cited as the source of the information.
4. Subsets of the records from the database downloaded for use with data from
other data sets must be clearly identified by the attribution “AMNH.”
5. Data are provided to individual users with the understanding that said data will
not be passed on to third parties or redistributed, except with approval from
AMNH.
6. …

2. AMNH does not grant permission
for anyone to use, download,
reproduce, publicly display,
distribute, or reprint all or
substantially all of the
information, records, or images in
the database.

Elachistocleisovalis
http://www.flickr.com/photos/lleonebio/3328398741/

You know more than the AMNH
database does!

DQ283405
FEATURES Location/Qualifiers
source 1..2400
/organism=\"Elachistocleisovalis\"
/organelle=\"mitochondrion\"
/mol_type=\"genomic DNA\"
/specimen_voucher=\"AMNH A141136\"
/db_xref=\"taxon:367647\"
/country=\"Guyana: Dubulay Ranch on
the Berbice River, 200ft,
5'40'55N, 57'51'32W\"
misc_RNA<1..>2400
/note=\"contains 12S ribosomal RNA,
tRNA-Val, and 16S ribosomal RNA\"

Tens of thousands of copies all
around the world

AMNH Conditions
1. Except as otherwise expressly stated herein, the information, records, or images
in these databases may not be reproduced, distributed, or publicly displayed, in
whole or in part, without the express written permission of the American
Museum of Natural History (AMNH).
2. AMNH does not grant permission for anyone to use, download, reproduce,
publicly display, distribute, or reprint all or substantially all of the information,
records, or images in the database.
3. Subsets of the information, records, or images in the database may be used,
downloaded, reproduced, publicly displayed, distributed, or reprinted strictly for
educational, scientific, scholarly, and other non-profit uses provided that AMNH
is appropriately cited as the source of the information.
4. Subsets of the records from the database downloaded for use with data from
other data sets must be clearly identified by the attribution “AMNH.”
5. Data are provided to individual users with the understanding that said data will
not be passed on to third parties or redistributed, except with approval from
AMNH.
6. …

You are going digital whether you
like it or not…

If it is on the web it will be found,
and used

This is a good thing

Creative Commons

Why be open?
Photo by Keith Marshall http://www.flickr.com/photos/keithmarshall/432924465/

Caeciliidae

Caeciliidae

Caeciliidae

Pagelluserythrinus

Pagelluserythrinus

Pagelluserythrinus

Mannophrynetrinitatis
MVZ 199838
MVZ 199828
(Aneidesflavipunctatus)

Errors in databases

Errors in publications

The Carmen Electra argument for
Open Access

treemap

reuse data

Electra pilosa

Carmen Electra versus Electra
(guess who wins…)

reuse data

Homo sapiens

AJ711044

should be AJ971044

How do we find and fix these
errors?

Don’t release data until it is
“perfect”
(wrong)

“given enough eyes, all bugs are
shallow”
Eric S Raymond

Credit
Photo by Keith Marshall http://www.flickr.com/photos/keithmarshall/432924465/

Google Page Rank
1.49
A
0.78
B
C
1.58
0.15 D

Page rank for web page

Scientific citation

H-index for authors

Impact factor for journals

What about an
impact factor for data?

Metric of the value of the data

Incentive to have globally
unique, citable identifiers

What to digitise first?
Photo by Keith Marshall http://www.flickr.com/photos/keithmarshall/432924465/

First digitise that which has been
cited

W D Lang Nature 139, 191 (1937)
doi:10.1038/139191a0

http://www.flickr.com/photos/mtl_shag/1403957285/

www.nhm.ac.uk

V S Smith

…end
Photo by Keith Marshall http://www.flickr.com/photos/keithmarshall/432924465/