13. Carolus Linnaeus (left), the initiator of the ‘Linnean age of taxonomy’, with the
morphological-descriptive assessment of some 23,000 geometrid species,
achieved in 257 years. Paul D. N. Hebert (right), the initiator of the ‘Hebertian age
of taxonomy’, has led to the molecular definition of some 20,000 geometrid BINs
… in just 12 years. https://doi.org/10.1098/rstb.2015.0339
Classical taxonomy versus DNA barcodes
33. Citation patterns in taxonomy
Taxonomy is
“long data”
rather than
“big data”
(every paper is a
classic, every paper
is a review)
Ozymandias: A biodiversity
knowledge graph
https://doi.org/10.1101/485854
34. Need access to digitised literature
for both humans and machines
Will give us access to taxonomic names, descriptions, and traits.
BHL (Australia), scanning
Australian literature from
museums, herbaria, and
scientific societies right
up to present day.
Plazi and Biodiversity
Literature Repository
(Switzerland), extracting
images from free AND
paywall journals.
36. Knowledge graphs are fun,
but we already have ALA…
• Classical aggregators merge together data based on
a couple of key attributes (e.g., species names,
geographical coordinates)
• Doesn’t link to underlying knowledge (e.g., work by
taxonomists, systematists, etc.)
• Doesn’t know everything that it knows (not a
graph)
37.
38. There are known knowns, things we
know that we know
There are known unknowns, things
we now know we don’t know
But there are also unknown
unknowns, things we do not know
we don't know
Donald Rumsfeld
43. Adding linked literature to ALA
https://ozymandias-demo.herokuapp.com/alademo.php?q=Maricoccus+brucei+Poore%2C+1994
DOIs
linking to
taxonomic
work
You can
read for
free!
46. Publications in AFD have images
that ALA doesn’t know about
ALA has no
images for
these
weevils
Plazi has
them from
Zookeys
paper, so
they are in
Ozymandias
49. Originally a database of facts
underlying Wikipedia, fast becoming
a global database of everything…
50. Here comes everybody…
Wikidata has thousands of entries
for researchers (especially
taxonomists) linked to ORCIDs as
well as taxonomic identifiers such
as ZooBank, IPNI, and social
networks such as ResearchGate.
59. Predictions
• Knowledge graphs are coming to a biodiversity
database near you – get ready
• These knowledge graphs will rely heavily on
Wikidata (already has many species, taxonomic
papers, taxonomists, and more)
• The biggest driver for creating knowledge graphs
may be metrics (e.g., Bloodhound) rather than
science (cf. citation metrics and impact factors)