8. Obstacles to building knowledge graphs
• Need globally unique, persistent identifiers
(how to label the nodes of the graph)
• Need to create and agree on vocabularies
(how to label the edges of the graph)
• Need to agree how to transmit the graph
• Who stores the global graph?
9. A new hope
• The identifier wars are (nearly) over (DOIs FTW)
• Lots of domain-specific vocabularies, but
schema.org is “good enough” for most things
• XML becoming a bedtime story to frighten the
children, JSON is everywhere (JSON-LD FTW).
• Wikidata
19. “Citations for the sum of
human knowledge”
WikiCite @WikiCite
Goal 1: Every citation in the Wikipedias should be in Wikidata
Goal 2: Every citation should be in Wikidata (!?)
24. Hexastore
• A triple is [s, p, o]
• Find all statements [s, ?, ?] is simple array lookup (all elements with key “s”)
• Find all statements [?, ?, o] is slow (scan all triples)…
• …unless we add array of [o, s, p] triples, then simple array lookup (all elements with
key “o”)
• Six variations cover all queries: [s,p,o], [s,o,p], [p, s, o], [p, o, s], [o, s, p], [o, p, s]
(hence “hexastore”)
• In-memory graph database in Javascript (think offline apps)
http://crubier.github.io/Hexastore/
33. 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
BioStor @biostor_org
Biodiversity Heritage Library @biodivlibrary
34. Flora Malesiana. Series I - Seed Plants,
Volume 14. Myristicaceae
https://doi.org/10.3897/ab.e1141
36. Embedded markup (bad)…
Crocidura absconditus, new species
<i>Crocidura absconditus</i>, new species
0 20
{ [0,20], “italics” }
…versus annotation (good)
(think NLM JATS XML markup
versus Substance JSON used
by Lens viewer
https://lens.elifesciences.org/
about/)
Crocidura absconditus, new species
48. specimen plant name
What Sandy really wants
collected type for
publication
person
“What specimens that I collected that have been
described as new species by other people?”
Published in
author
other person
not the same person