lecture presented at Ento.CH, Neuchâtel, Switzerland; March 4, 2016. Developing a scenario for the future of the Mitteilungen der Schweizerischen Entomologischen Gesellschaft into the direction of semantically enhanced publications.

1. DOI and the Mitteilungen: communicating
scientific results in the future
Donat Agosti
Plazi
Entomo.ch, Neuchâtel
March 4, 2016

3. Why do we publish?

4. Communication
Why do we publish?
• Communication
• Documentation: Building up knowledge
• Attribution: getting credit
• Citation: give credit and references
• Ego
• Career

5. Print: 1450
The Origins of the Mitteilungen (1862)
• Print
• Printer produces print
• Ship by mail
• Library
• Bibliographic citation

6. PDF: 1993
The Begin of the Digital Age of the Mitteilungen: 2006
• Print and PDF (Portable Document Format)
• Editor produces print ready PDF
• Ship by mail / email
• Library / online library (digital archive)
• Bibliographic citation

7. DOI and the begin of linking citations: 2000

8. DOI: Definition
Digital Object Identifier
aka
unique, persistent, resolvable identifier for citations in
scholarly materials

9. DOI: 2000

10. DOI provider: ETHZ / Retroseal
DOI: 10.5169/seals-400145

11. DOI: 2015

12. DOI
DOI: 10.5169/seals-402254
DOI: 10.5281/zenodo.27083

13. DOI provider: Zenodo / Biodiversity Literature Repository

14. DOI Anbieter: ETHZ / Retroseal / Zenodo
DOI provider Retro.seals Zenodo/ BLR
For MSEG legacy
publications
yes no (yes)
For prospective
publications
no yes

15. The future
Beyond the PDF:
from unstructured document to structured, linked, open data

16. Taxonomic publication
Material
citation
TreatmentArticleJournal
is part of is part of is part of
citescites cites
Scientific
names
is part of cites

17. Taxonomic publication
FigureTreatmentArticleJournal
has part has part has part
DOI httpURI DOI
Scientific
names
has part
LSID
Bold: unique, persistent identifiers

18. The future: semantic enhanced articles
PDF XML

19. XML
• Print, PDF, XML
• Author/editor produces XML;
PDF conversion automatic
• (Ship by mail / email), online
• Library / online library (digital
archive) / knowledge system
• Extended Journal Production
Workflow
• Bibliographic citation
Examples:
• Zookeys
• Biodiversity Data Journal
The future: semantic enhanced articles

20. Structured journals: Access and visualization

21. Structured articles: Access and visualization

22. Linked data
Structured treatments: Access and visualization

23. Structured treatments: Access and visualization

24. Treatment
Linking to external data
NCBI

25. Ongoing dissemination

26. Observation
record 1
Treatment Article
digital object
BarCode
Data, content (not only
metadata)
Each element is defined by a
vocabulary/ontology
Name (eg
Zoobank)
Cited
Treatments
Cited Articles
Identifiers
Observation
record 2
Treatment
digital object
BarCode
Name (eg
Zoobank)
Cited
Treatments
Observation
record4
TreatmentArticle
digitalobject
BarCode
Name(eg
Zoobank)
Cited
Treatments
Observation
record3
Treatment
digitalobject
BarCode
Name(eg
Zoobank)
Cited
Treatments
Observation
recordn+1
TreatmentArticle
digitalobject
BarCode
Name(eg
Zoobank)
Cited
Treatments
Observation
recordn
Treatment
digitalobject
BarCode
Name(eg
Zoobank)
Cited
Treatments
Observation
record 5
digital object
BarCode
Trait

27. The «Mehlwurm» lives in dry bread... or the potential of LOD
has traits
is part of
refers to
has traits
“The larva of the mealworm lives in dry
bread and can be eaten in Switzerland”
Bridging the gap from name to literature
or text and data mining

28. The near future
Collaboration with ContentMine to extract treatments on a daily
basis
http://www.slideshare.net/petermurrayrust/?
BioDiv

29. The future
How to get there?
from unstructured document to structured, linked, open data

30. Treatment
?
structureed
Treatment
(1)
Journal run
Atrticle
Treatment
vendor
scientist
Scientist / crowd
Vendor - level
General
markup
structured
treatment (2)
and data
markup programs
services
Domain -
level
Domain specific
markup
Publication
legacyprospective
Taxpub (1)
(zookeys)
Taxpub (2) BDJ
scripting scientist
scientist
crowd
Work Data Work OpenAccess
Publication conversion workflows

31. The future
Where is the future of the Mitteilungen?
It is up to the SEG …
To be considered:
• Outreach
• Costs
• Legacy publications

32. Thanks!
Donat Agosti
agosti@plazi.org