The document discusses several topics related to taxonomy and biodiversity data. It summarizes that sequencing may be focused more on phylogeny than taxonomy. It also discusses visualizing data using tools like OneZoom and web maps. Another topic is rethinking how publications are linked and referenced, comparing current one-way links to the potential of two-way links. It proposes building a Biodiversity Knowledge Graph by linking data, descriptions, specimens, and publications. Finally, it suggests treating biodiversity data like source code by allowing edits and tracking changes.

1. The Sam Adams talk
@rdmpage
http://iphylo.blogspot.com

2. Numbers of new animal names
1923
WWI WWII

3. Implications
• Taxonomists are working at capacity
• Maybe we are running out of species to
discover…(!)
• Most taxonomic work is in the past (“legacy”)

5. Two graphs

6. Two graphs
taxonomy

7. Focus on sequences
= focus on phylogeny
taxonomy

8. OneZoom.org

10. Visualise all barcodes
http://iphylo.org/~rpage/bold-map

11. Page R. Visualising Geophylogenies in Web Maps Using GeoJSON. PLOS
Currents Tree of Life. 2015 Jun 23 . Edition 1. doi:
10.1371/currents.tol.8f3c6526c49b136b98ec28e00b570a1e

12. Setting taxonomic
information free
taxonomy

13. Digitise the literature
http://biodiversitylibrary.orghttp://biostor.org

14. BioNames
http://bionames.org
• 5 million (animal)
names
• 1.6 million with
publications
• 454,000 publications
with digital identifier
• DOIs, BHL, BioStor,
PDFs, Gallica, etc.

15. Rethinking publications

16. Ted Nelson Hyperlinks and
hypermedia
Two-way links and
“transclusion”
= Xanadu
Tim Berners-Lee
HTTP, URL, HTML
One-way links
= world wide web

17. Web page Other web page
Web linking, one way, document-level, “target”
doesn’t know that it is linked to (“cited”),
link can break (404)

18. text
Work Source
text
Xanadu linking, two way, fragment-level,
“source” knows it is linked to, source content is
embedded, links don’t break

19. Xanadu

20. Wait, WTF has this to do
with floras?!

21. A New Account of the Genus
Horsfieldia (Myristicaceae), Pt 2
W J J O De Wilde
The Gardens' bulletin, Singapore 38(1): 55-144 (1985)
http://biostor.org/reference/175018
Horsfieldia lancifolia

22. Flora Malesiana. Series I - Seed Plants,
Volume 14. Myristicaceae

23. Description
Description
Flora Article

24. van Balgooy 3973
van Balgooy 3973

25. Description
Article Specimen
{
"key": 1139234988,
"scientificName": "Horsfieldia
lancifolia W.J.J.O. de Wilde",
"kingdom": "Plantae",
"phylum": "Tracheophyta",
"order": "Magnoliales",
"family": "Myristicaceae",
"genus": "Horsfieldia",
"species": "Horsfieldia lancifolia",
"genericName": "Horsfieldia",
"specificEpithet": "lancifolia",
"taxonRank": "SPECIES",
"decimalLongitude": 121.75,
"decimalLatitude": -2.25,
"continent": "ASIA",
"stateProvince": "Sulawesi",
"year": 1979,
"month": 7,
"day": 11,
"occurrenceID":
"http://data.biodiversitydata.nl/naturalis/spe
cimen/L.1769594”
}
Data
(GBIF)
Data

26. Xanadu in the 21st century?

27. text
Article Annotations
table
annotation
annotation

28. @hypothes_is

29. Annotating a scientific paper

30. Aggregating annotations (iPhylo)
http://iphylo.blogspot.co.uk/2016/06/aggregating-annotations-on-scientific_30.html

31. Towards a biodiversity knowledge graph
Research Ideas and Outcomes 2: e8767 (07 Apr 2016)
doi: 10.3897/rio.2.e8767

32. GBIF and the problem of data

33. Data and feedback flow
Something’s wrong!

34. GBIF and the zika virus
http://iphylo.blogspot.co.uk/2016/04/the-zika-virus-gbif-and-missing.html

35. What if we treat data like source code
Original data
Edited data

36. Summary
• Sequencing versus taxonomy?
• Visualisation as a tool
• Rethinking the nature of publications
• The Biodiversity Knowledge Graph
• Data as source code