surfacing the deep data of taxonomy
DESCRIPTION
Talk at Linnean Society London, 20 September 2012TRANSCRIPT
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Surfacing the deep data of taxonomy
@rdmpage
http://iphylo.blogspot.com
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To a first approximation the taxonomy of life is already digital…
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doi:10.1126/science.276.5313.734
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Data – GenBank
Publications – PubMed
Names – Names4Life
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So, we’re done! (aren’t we?)
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doi:10.1126/science.276.5313.734
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Zoology as microbiology
GenBank DNA barcoding➔
PubMed Digital archives (BHL)➔
Names ION, ZooBank, uBio, …➔
Microbiology Zoology
Images from http://phylopic.org
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Why does having a single database of names matter?
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Bacterial names linked to literature
http://dx.doi.org/10.1099/ijs.0.035154-0
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Paenibacillus polymyxa
• http://dx.doi.org/10.1601/nm.5110 (name)• http://dx.doi.org/10.1601/tx.5110 (taxon)
Image from http://dx.doi.org/10.1128/ AEM.71.11.7292-7300.2005
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…still not convinced?
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O Lambert et al. Nature 466, 105-108 (2010) doi:10.1038/nature09067
Skull, mandible and tooth morphology of the holotype of L. melvillei MUSM 1676.
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Leviathan melvillei
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Bugger…
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Livyatan melvillei
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Two kinds of #fail
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We don’t have a list of all names
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Publications containing names often not accessible
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Leviathan melvillei
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Need more convincing?
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Dark taxa
http://iphylo.blogspot.co.uk/2011/04/dark-taxa-genbank-in-post-taxonomic.html
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Mammals in GenBank
Proper Linnaean names
Aus sp.
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Mammals
Proper Linnaean names
Aus sp.
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“Invertebrates”
BOLD
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Is this a problem?
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It’s the norm for Bacteria
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Dark taxa will only increase in number
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Roth v. Wikipeia
http://www.newyorker.com/online/blogs/books/2012/09/an-open-letter-to-wikipedia.html
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Wikipedia says “no”
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“I understand your point that the author is the greatest authority on their own work,” writes the Wikipedia Administrator—“but we require secondary sources.”
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@quominus
http://quominus.org/archives/981
One of Wikipedia’s core principles, along with things like neutrality, is verifiability: a reader must be able to look at a statement in a Wikipedia article and find out where it comes from.
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Taxonomic statements should be verifiable
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Literature is the evidence base for taxonomy
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Literature online
Museums, universities,and scientific societies
Digital archives
Commercialpublishers
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http://iphylo.org/~rpage/itaxon
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Animal names per decade
Data from http://www.organismnames.com
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Names with a DOI
25%
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BioStor (BHL)
©25%
@biostor_org
http://biostor.org
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Online(DOI, BioStor, JSTOR,DSpace,PDF, …)
50%
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Identifiers
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Vast majority of names are in the legacy literature
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Zootaxa and Zookeys
XML
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My wish list…
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Names linked to:
literaturespecimensgeographysequences
phylogeny…
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BioNames
(real soon now…)
Computable Data Challenge