1.
Integra(ng data with phylogenies,
at scale
Nico Cellinese
University of Florida
&
Hilmar Lapp
Duke University

2.
WHAT’S IN A NAME?

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+

8.
Idiosyncratic Russian dolls syndrome

9.
Idiosyncratic Russian dolls syndrome

10.
Idiosyncratic Russian dolls syndrome

11.
Idiosyncratic Russian dolls syndrome

12.
Idiosyncratic Russian dolls syndrome

13.
Idiosyncratic Russian dolls syndrome

14.
Idiosyncratic Russian dolls syndrome

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?

18.
Dark taxa!

19.
Dark taxa!
How do we integrate data with this tree?

20.
Tree-thinking
Common descent àevoluDon at the center of taxonomy
B C D
Branches
Synapomorphies
A
Clades = taxa
Discovery

21.
Tree-thinking
Common descent àevoluDon at the center of taxonomy
Discovery
CommunicaDon How??
0147
Density
0.07
0.22
0.72
Diversification rate

22.
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

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

27.
Mapping data to phylogene(c
knowledge space

28.
Street signs serve people, not machines

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

35.
0.0
Campanula_rotundifolia
Pseudonemacladus_oppositifolius
Lobelia_cardinalis
Campanula_latifolia
Cyphocarpus_rigescens
Wahlenbergia_linifolia
Nemacladus_ramosissmus
Lobelia_coronopifolia
Cyphia_elata
Pentaphragma
Crysanthemum
Sphenoclea
Platycodon_grandiflorus
Cyphia_bulbosa
5
3
Campanula
1
7
8
9
4
Lobelia
Cyphia
6
1 0
2
Class: Campanulaceae_1889_to_1980
EquivalentTo:
cdao:has_Descendant value taxon:Campanula_laDfolia
and phyloref:excludes_lineage value taxon:Crysanthemum

36.
0.0
Campanula_rotundifolia
Pseudonemacladus_oppositifolius
Lobelia_cardinalis
Campanula_latifolia
Cyphocarpus_rigescens
Wahlenbergia_linifolia
Nemacladus_ramosissmus
Lobelia_coronopifolia
Cyphia_elata
Pentaphragma
Crysanthemum
Sphenoclea
Platycodon_grandiflorus
Cyphia_bulbosa
5
3
Campanula
1
7
8
9
4
Lobelia
Cyphia
6
1 0
2
Class: Campanulaceae_1980
EquivalentTo:
cdao:has_Descendant value taxon:Campanula_laDfolia
and phyloref:excludes_lineage value taxon:Lobelia

37.
0.0
Campanula_rotundifolia
Pseudonemacladus_oppositifolius
Lobelia_cardinalis
Campanula_latifolia
Cyphocarpus_rigescens
Wahlenbergia_linifolia
Nemacladus_ramosissmus
Lobelia_coronopifolia
Cyphia_elata
Pentaphragma
Crysanthemum
Sphenoclea
Platycodon_grandiflorus
Cyphia_bulbosa
5
3
Campanula
1
7
8
9
4
Lobelia
Cyphia
6
1 0
2
Class: Campanulaceae_aier_1995
EquivalentTo:
cdao:has_Descendant value taxon:Campanula_laDfolia
and phyloref:excludes_lineage value taxon:Sphenoclea

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