Surfacing the deep data of taxonomy

@rdmpage

http://iphylo.blogspot.com

To a first approximation the taxonomy of life is already digital…

doi:10.1126/science.276.5313.734

Data – GenBank

Publications – PubMed

Names – Names4Life

So, we’re done! (aren’t we?)

doi:10.1126/science.276.5313.734

Zoology as microbiology

GenBank DNA barcoding➔

PubMed Digital archives (BHL)➔

Names ION, ZooBank, uBio, …➔

Microbiology Zoology

Images from http://phylopic.org

Why does having a single database of names matter?

Bacterial names linked to literature

http://dx.doi.org/10.1099/ijs.0.035154-0

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

…still not convinced?

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.

Leviathan melvillei

Bugger…

Livyatan melvillei

Two kinds of #fail

We don’t have a list of all names

Publications containing names often not accessible

Leviathan melvillei

Need more convincing?

Dark taxa

http://iphylo.blogspot.co.uk/2011/04/dark-taxa-genbank-in-post-taxonomic.html

Mammals in GenBank

Proper Linnaean names

Aus sp.

Mammals

Proper Linnaean names

Aus sp.

“Invertebrates”

BOLD

Is this a problem?

It’s the norm for Bacteria

Dark taxa will only increase in number

Roth v. Wikipeia

http://www.newyorker.com/online/blogs/books/2012/09/an-open-letter-to-wikipedia.html

Wikipedia says “no”

“I understand your point that the author is the greatest authority on their own work,” writes the Wikipedia Administrator—“but we require secondary sources.”

@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.

Taxonomic statements should be verifiable

Literature is the evidence base for taxonomy

Literature online

Museums, universities,and scientific societies

Digital archives

Commercialpublishers

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

Animal names per decade

Data from http://www.organismnames.com

Names with a DOI

25%

BioStor (BHL)

©25%

@biostor_org

http://biostor.org

Online(DOI, BioStor, JSTOR,DSpace,PDF, …)

50%

Identifiers

Vast majority of names are in the legacy literature

Zootaxa and Zookeys

XML

My wish list…

Names linked to:

literaturespecimensgeographysequences

phylogeny…

BioNames

(real soon now…)

Computable Data Challenge