going digital
DESCRIPTION
Invited talk given at The Natural History Museum, London, 17 March 2009 (I gave a very similar talk at the Department of Zoology, University of Stockholm, 12 March 2009).TRANSCRIPT
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Going Digital
Rod Page
Photo by Keith Marshall http://www.flickr.com/photos/keithmarshall/432924465/
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If you are not online you are invisible
(Web 1.0)
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All useful information will be online
(Web 1.0)
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Value is explicit and based on usage (links)
(Web 1.0)
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Reputation is created…
(Web 2.0)
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…not conferred by authority
(Web 2.0)
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Everything will have a URL
(Web 3.0)
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Yes, I’ve drunk the Kool Aid
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…but I’m not alone
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Social networking
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Dinosaurs ban it
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Scaremongers say it causes cancer
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Some “get it”
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Some do real work with it
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#uksnow
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@kzelnio Could you do me a favour: 10.1016/j.anbehav.2008.12.017
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Where is the (digital) museum?
Photo by Keith Marshall http://www.flickr.com/photos/keithmarshall/432924465/
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www.nhm.ac.uk
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Zoology
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This dataset is not accessible by the public. For more information please contact the
Department of Zoology.
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Silo
http://www.flickr.com/photos/kenmccown/132990634/
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404
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GBIF
http://www.flickr.com/photos/chrisfreeland/3306689322/
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Top 10 GBIF data providers
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League tableMuseum GBIF data Open access
journalStaff publications online
Social Networking
3,446,016 yes Twitter, Facebook,
Youtube, etc.(searchable collections) yes (Twitter)
412,797 (planned)
(planned)
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Why go digital?
Photo by Keith Marshall http://www.flickr.com/photos/keithmarshall/432924465/
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Diverse kinds of data
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Apomys datae
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Apomys specimen
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How do we integrate these data?
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Why integrate?
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Learn stuff we don’t know
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• There are known knowns, things we know that we know
• There are known unknowns, things we now know we don’t know
• But there are also unknown unknowns, things we do not know we don't know
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Unknown knowns
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Things we know …without knowing that we know
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Melissotarsus insularis
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Melissotarsus insularis no hit
CASENT0107663-D01 DQ176312
Melissotarsus sp. BLF m1DQ176312
CASENT0107663-D01Melissotarsus insularis
1
Melissotarsus insularisMelissotarsus sp. BLF m1 =
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No one source has all the answers
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Joining the dots
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Identifiers
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Digital Object Identifier(DOI)
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Identifies a publication
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Globally unique
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10.1016/j.ympev.2006.04.006
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Paper
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Why have DOIs?
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Link rot
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Refs
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2006
Cites
2006
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Forward Cites
2006 2009
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Shoulders of giants
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progress is incremental
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reuse past results
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Forward Cites
2006 2008
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Species
Genes
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data linking
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data citation
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http://iphylo.org/~rpage/challenge
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demo
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Vision
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Chromis circumaurea
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What should museums do?
Photo by Keith Marshall http://www.flickr.com/photos/keithmarshall/432924465/
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Do nothing
Photo by Keith Marshall http://www.flickr.com/photos/keithmarshall/432924465/
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The new hotness!
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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)
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Make it easy
Photo by Keith Marshall http://www.flickr.com/photos/keithmarshall/432924465/
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http://www.flickr.com/photos/scobleizer/2256358640/
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http://taxonomy.zoology.gla.ac.uk/rod/treeview.html
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http://abacus.gene.ucl.ac.uk/software/paml.html
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http://mrbayes.csit.fsu.edu/
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http://www.tree-puzzle.de/
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http://atgc.lirmm.fr/phyml/
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No branding
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No corporate style
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No permission needed
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Institution provides infrastructure…
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…then gets out of the way
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Top five European papers in evolutionary biology 1996-2006
1,118 – 4,512 citations
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Partnerships(EOL)
Photo by Keith Marshall http://www.flickr.com/photos/keithmarshall/432924465/
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“Dance of the initiatives”
Christine Hine
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Danger of too much money
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Million Dollar Page
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EOL in it’s present form
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sucks
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Can I do science with it?
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Not yet…
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IntellectualProperty
Photo by Keith Marshall http://www.flickr.com/photos/keithmarshall/432924465/
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Fear
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Ignorance
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Silo
http://www.flickr.com/photos/kenmccown/132990634/
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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. …
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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.
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Elachistocleis ovalis
http://www.flickr.com/photos/lleonebio/3328398741/
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You know more than the AMNH database does!
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FEATURES Location/Qualifiers source 1..2400 /organism="Elachistocleis ovalis" /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"
DQ283405
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Tens of thousands of copies all around the world
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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. …
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You are going digital whether you like it or not…
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If it is on the web it will be found, and used
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This is a good thing
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Creative Commons
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Why be open?
Photo by Keith Marshall http://www.flickr.com/photos/keithmarshall/432924465/
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Caeciliidae
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Caeciliidae
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Caeciliidae
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Pagellus erythrinus
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Pagellus erythrinus
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Pagellus erythrinus
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Mannophryne trinitatis
MVZ 199828(Aneides flavipunctatus)
MVZ 199838
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Errors in databases
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Errors in publications
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The Carmen Electra argument for Open Access
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treemap
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reuse data
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Electra pilosa
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Carmen Electra versus Electra
(guess who wins…)
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reuse data
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Homo sapiens
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AJ711044
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should be AJ971044
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How do we find and fix these errors?
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Don’t release data until it is “perfect”
(wrong)
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“given enough eyes, all bugs are shallow”
Eric S Raymond
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Credit
Photo by Keith Marshall http://www.flickr.com/photos/keithmarshall/432924465/
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Google Page Rank
1.49
1.58
0.15
0.78
A
B
C
D
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Page rank for web page
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Scientific citation
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H-index for authors
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Impact factor for journals
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What about an impact factor for data?
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Metric of the value of the data
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Incentive to have globally unique, citable identifiers
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What to digitise first?
Photo by Keith Marshall http://www.flickr.com/photos/keithmarshall/432924465/
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First digitise that which has been cited
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W D Lang Nature 139, 191 (1937) doi:10.1038/139191a0
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http://www.flickr.com/photos/mtl_shag/1403957285/
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www.nhm.ac.uk
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V S Smith
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…end
Photo by Keith Marshall http://www.flickr.com/photos/keithmarshall/432924465/