Next generation sequencing requires
next generation publishing

The first eukaryotic new species described with a
fully se...
Taxonomic descriptions
Not changed much since Linnaeus!
The problem?
The data deluge
Massive sampling/data gathering
High-throughput next
generation sequencing
“Only” 13,494 new animal species described
in 2012 (Index of Organism Names)
Proportion of dark taxa increase
dramatically!

Rod Page, iPhylo blogspot, 12 April 2011
Low uptake of data publishing/sharing
Solutions?
Turbo-taxonomy:
publish fast and lot!
Pipeline descriptions of
hundreds of new species
 Molecular data
 Concise descript...
Jumping into the bug data world:
A holistic description of the ‘new species of the
future’
Eupolybothrus cavernocolus
Six methods used to describe it









Conventional
morphological study
SEM umages
Barcoding (COI)
Fully sequenced...
Data repositories
Data have been deposited in:
 GigaDB (all data)
 INSD (COI and transcriptome sequences)
 BOLD (COI)
...
Micro-CT scanning
Micro-CT scans
ensure that
morphological
and anatomical
characters can
be examined in
their natural
posi...
Video of the holotype
Why so many methods?
“Big data” management
pilot for taxonomy
The first biodiversity paper to join
ISA Commons metadata standard
Five data types in GigaDB linked
through ISA-TAB metadata
The ‘Cybertype’:
questions and challenges
What data can be used to constitute a cybertype?
Should cybertype be restricted ...
Next generation sequencing
and imaging require
next generation publishing!
Novel concepts
Authoring, reviewing and publishing in one
place, for first time!
Upfront markup!
“Small” data imported in ...
Taxa and their usages
Taxon profile
Taxon profile
Map localities
Download data
Imagine how data
(if published in this way) can be reused…

… across different
domains….
I

Open Access!
and

….

ViBRANT

PLAZI
Next generation sequencing requires next generation publishing: the Biodiversity Data Journal published the first eukaryot...
Next generation sequencing requires next generation publishing: the Biodiversity Data Journal published the first eukaryot...
Next generation sequencing requires next generation publishing: the Biodiversity Data Journal published the first eukaryot...
Next generation sequencing requires next generation publishing: the Biodiversity Data Journal published the first eukaryot...
Next generation sequencing requires next generation publishing: the Biodiversity Data Journal published the first eukaryot...
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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

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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.

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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

  1. 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. 2. Taxonomic descriptions Not changed much since Linnaeus!
  3. 3. The problem?
  4. 4. The data deluge Massive sampling/data gathering
  5. 5. High-throughput next generation sequencing
  6. 6. “Only” 13,494 new animal species described in 2012 (Index of Organism Names)
  7. 7. Proportion of dark taxa increase dramatically! Rod Page, iPhylo blogspot, 12 April 2011
  8. 8. Low uptake of data publishing/sharing
  9. 9. Solutions?
  10. 10. Turbo-taxonomy: publish fast and lot! Pipeline descriptions of hundreds of new species  Molecular data  Concise descriptions  Digital imaging
  11. 11. Jumping into the bug data world: A holistic description of the ‘new species of the future’
  12. 12. Eupolybothrus cavernocolus
  13. 13. Six methods used to describe it       Conventional morphological study SEM umages Barcoding (COI) Fully sequenced transcriptomic profile Micro-CT scanning Video of living specimen
  14. 14. 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
  15. 15. 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
  16. 16. Video of the holotype
  17. 17. Why so many methods? “Big data” management pilot for taxonomy
  18. 18. The first biodiversity paper to join ISA Commons metadata standard
  19. 19. Five data types in GigaDB linked through ISA-TAB metadata
  20. 20. 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?
  21. 21. Next generation sequencing and imaging require next generation publishing!
  22. 22. 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!
  23. 23. Taxa and their usages
  24. 24. Taxon profile
  25. 25. Taxon profile
  26. 26. Map localities
  27. 27. Download data
  28. 28. Imagine how data (if published in this way) can be reused… … across different domains….
  29. 29. I Open Access! and …. ViBRANT PLAZI

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