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3.
What’s in a name?
Chaos!
• Names and Concepts do not
reconcile that easily
• Names are text strings
• Context is lacking or subjec(ve
• Meaning is not computable
4.
Linnean names point to concepts
Antoine Laurent de Jussieu
Genera Plantarum, 1789
5.
Linnean names point to concepts
Antoine Laurent de Jussieu
Genera Plantarum, 1789
6.
Linnean names point to concepts
Antoine Laurent de Jussieu
Genera Plantarum, 1789
I don’t understand any of those concepts
whether in LaDn or English, but I can sDll
link them to their names, as in one object
to one object
7.
Linnean names point to concepts
Antoine Laurent de Jussieu
Genera Plantarum, 1789
…and 200+
…and 400+
15.
From a human perspecDve, we lose track of concepts. Hard to reconcile all of them. We need
help! Can we compute them?
Idiosyncratic Russian dolls syndrome
16.
Linnean names point to concepts
Antoine Laurent de Jussieu
Genera Plantarum, 1789
…and 200+
…and 400+
17.
• We can uncluNer concepts, and thereby
nomenclature
• How do we navigate along the Tree of Life
repurposing Linnean names, which are
linked to tradi(onal concepts?
23.
Tree-thinking
Berberidopsidaceae
Opiliones
Zingiberaceae
Hamamelidaceae
Sarcolaenaceae
Lingulidae
Hymenoptera
Mammalia
Apocynaceae
Galliformes
Rubiaceae
Anarthriaceae
Lineidae
Crocodylidae
Stylosiphonia
Andrenidae Cracidae
Gavialis
Globba
Micrella
Rhodoleia
Phalangiidae Tachyglossa
Lyginia
Mediusella
Chamaeclitandra
These names are not generated in an evoluDonary-based framework
(Groups defined by character similarity vs. common descent)
24.
Both the Encyclopedia of Life (EOL) and the Open Tree of Life suggest that
Campanuloideae is a misspelling of Campaniloidea (marine gastropods!)
GBIF does not currently have Campanuloideae in its backbone taxonomy.
25.
Are you kidding me?
These are the Campanuloideae!
Wang et al. 2014
26.
Life as a street map How to navigate life as a machine
29.
• How do we build a reliable GPS for phylogenies?
• How do we reproducibly find the right nodes?
Mapping data to phylogene(c
knowledge space
30.
FEED
Textual Definition –
The hyoglossus is a muscle that attaches to
the hyoid and tongue and is innervated by
Cranial Nerve XII.
Computable Definition –
('attached to' some 'hyoid bone')
and ('attached to' some tongue)
and ('innervated by' some 'hypoglossal
nerve') and
spatially disjoint with 'intrinsic tongue
muscle'
Druzinsky et al (2015): Logic definiDons of mammalian
feeding muscles by means of necessary and sufficient
condiDons true for all mammals
Nomenclature ≠ Seman(cs
31.
Phyloreference
=
Logic defini(on of a clade,
using the property common to
all of life
32.
Phyloreferences
Statements formally expressing the paaerns we discover
(analogous to map coordinates)
Node-Based Branch-Based Apomorphy-Based
A B C A B C A B C
X
The clade originaDng
with the last common
ancestor of B and C.
The clade originaDng
with the first ancestor of
B that is not an
ancestor of A.
The clade originaDng
with the first ancestor
of C to evolve X.
33.
Phyloreferences yield a
coordinate system for the Tree of Life
• Any node, branch, subtree is referenceable
• References are unambiguous
• References are computable
• References are portable
• Adapts to new and changing knowledge
34.
Many needed technologies already exist
• OWL ontologies designed
for
– PhylogeneDc knowledge:
CDAO
– Phenotypic knowledge:
Uberon, PATO, …
– Efficient and expressive
reasoners: FaCT++, HermiT,
Racer, ELK
38.
Phyloreferences as ontological expressions
Phyloreference expressions
can be:
• Easily generated by
anyone
• Can work on any tree
• Named and registered
– To promote reuse and
consistency
– To improve usability
and accessibility
Class: Campanulaceae
Annota(ons:
rdfs:label “Campanulaceae_aier_1995”
dc:descripDon “the clade that includes
Campanula laDfolia but not Sphenoclea”
EquivalentTo:
cdao:has_Descendant value
taxon:Campanula_laDfolia and
phyloref:excludes_lineage value taxon:Sphenoclea
Class: AGF4-SHRU-3560
EquivalentTo:
cdao:has_Descendant value
taxon:Campanula_laDfolia and
phyloref:excludes_lineage value taxon:Sphenoclea
vs.
39.
Challenges
• OWL-based data model to saDsfy phylogeneDc
taxonomy, reasoning expressivity, scalability
• ConvenDons for data transformaDon, and
consequences of different choices
• Least common ancestor reasoning for OWL
data
• Lack of canonical specimen idenDfier system
• Specifier mapping ontologies
40.
Tree of Life, ontologized:
A universal coordinate system
• The Tree of Life is itself an aggregaDon and
integraDon of our phylogeneDc knowledge.
• Phyloreferencing is addressing into a knowledge
universe.
• Ontologies, reasoning, and other KR techniques
are powerful tools for this.
41.
Acknowledgements
• NaDonal Science FoundaDon (DBI-1458484)
• Ken and Linda McGurn
• Phenoscape
• EvoIO
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