Penev, L., Stoev, P., Komericki, A., Akkari, N., Li, S., Zhou, X., Edmunds, S., Hunter, C., Weigand, A., Porco, D., Zapparoli, M., Georgiev, T., Mietchen, D., Roberts, D., Smith, V. 2013. Next generation sequencing requires next generation publishing: the Biodiversity Data Journal published the first eukaryotic new species with a fully sequenced transcriptome, DNA barcode and microcomputed tomography. TDWG, Biodiversity Information Standards. Grand Hotel Mediterraneo Florence, Italy, 27 Oct - 1 Nov.

1. Next generation sequencing requires
next generation publishing
The first eukaryotic new species described with a
fully sequenced transcriptome, DNA barcode and
microcomputed tomography
ViBRANT

2. Taxonomic descriptions
Not changed much since Linnaeus!

3. The problem?

4. The data deluge
Massive sampling/data gathering

5. High-throughput next
generation sequencing

6. “Only” 13,494 new animal species described
in 2012 (Index of Organism Names)

7. Proportion of dark taxa increase
dramatically!
Rod Page, iPhylo blogspot, 12 April 2011

8. Low uptake of data publishing/sharing

9. Solutions?

10. Turbo-taxonomy:
publish fast and lot!
Pipeline descriptions of
hundreds of new species
 Molecular data
 Concise descriptions
 Digital imaging

11. Jumping into the bug data world:
A holistic description of the ‘new species of the
future’

13. Eupolybothrus cavernocolus

14. Six methods used to describe it






Conventional
morphological study
SEM umages
Barcoding (COI)
Fully sequenced
transcriptomic profile
Micro-CT scanning
Video of living specimen

15. Data repositories
Data have been deposited in:
 GigaDB (all data)
 INSD (COI and transcriptome sequences)
 BOLD (COI)
 Morphbank (morphological images)
 Morphosource (micro CT row data, 3D
model)
 Plazi (original descriptions of all keyed
species

16. Micro-CT scanning
Micro-CT scans
ensure that
morphological
and anatomical
characters can
be examined in
their natural
position
without
damage to the
original
specimen

17. Video of the holotype

18. Why so many methods?
“Big data” management
pilot for taxonomy

19. The first biodiversity paper to join
ISA Commons metadata standard

21. Five data types in GigaDB linked
through ISA-TAB metadata

22. The ‘Cybertype’:
questions and challenges
What data can be used to constitute a cybertype?
Should cybertype be restricted to morphological
data?
Cybertype composite (i.e. consisting of several
data types in one repository) or distributed
(different parts of data residing on different
physical servers)?
Cross-linking molecular and morphological data
through Darwin Core standards?
Global metadata standards for micro-CT data?
Reliable data repositories for micro-CT data?

23. Next generation sequencing
and imaging require
next generation publishing!

26. Novel concepts
Authoring, reviewing and publishing in one
place, for first time!
Upfront markup!
“Small” data imported in and downloadable
from text
Large datasets published as data papers
Text stored and treated as data
Community peer-review and community
ownership of interoperable data
Narrative (text) and data integrated publishing!

27. Taxa and their usages

28. Taxon profile

29. Taxon profile

30. Map localities

31. Download data

33. Imagine how data
(if published in this way) can be reused…
… across different
domains….

34. I
Open Access!
and
….
ViBRANT
PLAZI