Reasoning over phenotype diversity, character change, and evolutionary descent
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Transcript of Reasoning over phenotype diversity, character change, and evolutionary descent
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Reasoning over phenotype diversity, character change,
and evolutionary descent
Hilmar LappNational Evolutionary Synthesis Center (NESCent)
Seminar at University of Florida, March 1, 2011
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Life has evolved a stunning
diversity of phenotypes
Images: Web Tree of Life (http://tolweb.org)
Parfrey et al (2010, Parfrey & KatzRegier et al (2010
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Large body of evolutionary phenotype documentation
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Sereno (1999)
Mabee (2000)
from: Understanding Evolution
Chen & Mayden (2010)
Phenotype changes inform
phylogenetic reconstruction
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Phenotype observations important to many fields
Kimmel et al, 2003
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Phenotype observations important to many fields
Kimmel et al, 2003
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As complex, free text phenotypes are resistant to computing
(Lundberg and Akama 2005)
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Finding similar information in free-text is difficult
“lacrymal bone...flat’’ Mayden 1989
“lacrimal...small, flat” Grande and Poyato-Ariza 1999
“lacrimal...triangular’’ Royero 1999
“first infraorbital (lachrimal) shape...flattened” Kailola 2004
“fourth infraorbital...anterior and posterior margins...in parallel” Zanata and Vari 2005
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Meaning of words depends on context
• Burrowing insectivorous mammals in the family Talpidae
• A spy buried secretly within an organization or country
• The SI unit used in chemistry for the amount of a substance
• A small, sometimes raised area of skin, usually with darker pigment
• A Mexican sauce made from chili peppers and other spices, including chocolate
• A massive structure, usually of stone, used as a pier, jetty, or breakwater between places separated by water
Mole:
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What is an ontology?
• An ontology is a type of vocabulary with well-defined terms and the logical relationships that hold between them.
• An ontology represents the knowledge about its subject domain.
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Ontologies support reasoning
• Relationships (“assertions”) induce a hierarchical structure.
• Ontologies can be processed by machines to make inferences.
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The same principles apply to anatomy
is_apart_of
is_a
develops_from
part_ofreplacement bone
basihyal bone
ventral hyoid arch
basihyal cartilage
pharyngeal arch
cartilage
is_abasihyal element
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The same principles apply to anatomy
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Integrating across studies?
Fig. 7, Sereno (2009)
Fig. 6, Sereno (2009)
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Computing example: Search by Similarity
Fig. 3, Washington et al (2009)
Fig. 1, Washington et al (2009)
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Computing example: Search by Similarity
Fig. 3, Washington et al (2009)
Fig. 1, Washington et al (2009)
Trogloglanis pattersoni - a blind catfish
http://tolweb.org/Trogloglanis/69910
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Computing over comparative morphology?
Cyprinus carpio Pangio anguillaris Nemacheilus fasciatus
Catostomus commersoni Gyrinocheilus aymonieri Phenacogrammus interruptus
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Knowledge mining & hypothesis generation
Mutagenesis
Model Organism
Laue et al (2008)
Mutant or missing protein at specific developmental stage
Phenotype change(s) to wildtype
Order Siluriformes
Pimelodus maculatus
spinelet middle nuchal plate
anterior
nuchal plate
Order Characiformes
Catoprion mento
abdominal
scutes
predorsal
spine
2 cm
Non-model organisms
Mutation, selection, drift, gene flow
Altered expression or function of protein
Phenotype changes between evolutionary lineages
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Phenoscape• Collaboration between P. Mabee (PI, U. South
Dakota), M. Westerfield (ZFIN), and Todd Vision (UNC, NESCent)
• Aim: Foster devo-evo synthesis by
• Prototyping a database of curated, machine-interpretable evolutionary phenotypes.
• Integrating these with mutant phenotypes from model organisms.
• Enabling data-mining and discovery for candidate genes of evolutionary phenotype transitions.
• Informatics for the project is developed and hosted at NESCent
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ectopterygoid shape rectangular
Character State
Entity-Quality Model for Evolutionary Phenotypes
Entity Attribute Value
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ectopterygoid shape rectangular
Character
ectopterygoid
Entity (TAO)
rectangular
Quality (PATO)
State
Entity-Quality Model for Evolutionary Phenotypes
Entity Attribute Value
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ectopterygoid shape rectangular
Character
ectopterygoid
Entity (TAO)
rectangular
Quality (PATO)
State
Entity-Quality Model for Evolutionary Phenotypes
Entity Attribute Value
implies
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ectopterygoid shape rectangular
Character
ectopterygoid
Entity (TAO)
rectangular
Quality (PATO)
State
Entity-Quality Model for Evolutionary Phenotypes}
Phenotype
Entity Attribute Value
implies
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some Batrachoglanis
raninus
rectangularinheres_in some
ectopterygoidexhibits some
Taxon phenotype assertion
Taxon ontology term
Anatomy ontology term
Phenotypic Quality ontology term
Links a taxon to a phenotype
Links a quality to the entity that is its bearer
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some Batrachoglanis
raninus
rectangularinheres_in some
ectopterygoidexhibits some
Taxon phenotype assertion
Taxon ontology term
Anatomy ontology term
Phenotypic Quality ontology term
Links a taxon to a phenotype
Links a quality to the entity that is its bearer
Evidence Code Specimen PublicationCurator
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edn1tf216b/tf216b
curvatureinheres_in some
maxillainfluences some
Gene phenotype assertion
Genotype Anatomy ontology term
Phenotypic Quality ontology term
Links a genotype to a phenotype
Links a quality to the entity that is its bearer
Publication
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legacy free-text character data
EQ = body lacks all parts of type scale
EQ = body has fewer parts of type scale
mutant phenotype
Kailola (2004)
Harris et al. (2008)
Here, we describe the phenotypic and molecular characterization of a set of mutants showing loss of adult structures of the dermal skeleton, such as the rays of the fins and the scales, as well as the pharyngeal teeth. The mutations represent adult-viable, loss of function alleles in the ectodysplasin (eda) and ectodysplasin receptor (edar) genes.
is_a
exhibits
exhibits
Siluriformes
is_a
Teleostei
is_a
is_a
edadt3S243X/+
eda
variant_of
body has fewer parts of type scale
influences
towards
towards
towards
is_a
is_ais_a
has number of
is_a
Taxon Anatomical Entity QualityGeneanatomical structure
inheres_in
inheres_in
inheres_in
is_ais_a
Gasterosteiformes
body
body lacks all parts of type scale
body lacks all parts of type scale
lacks all parts of type
scale
is_a
Ictalurus punctatus
Apeltes quadracus
has fewer parts of type
© Jean Ricardo Simões Vitule
Full workflow:free-text → EQ → integrated KB
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legacy free-text character data
EQ = body lacks all parts of type scale
EQ = body has fewer parts of type scale
mutant phenotype
Kailola (2004)
Harris et al. (2008)
Here, we describe the phenotypic and molecular characterization of a set of mutants showing loss of adult structures of the dermal skeleton, such as the rays of the fins and the scales, as well as the pharyngeal teeth. The mutations represent adult-viable, loss of function alleles in the ectodysplasin (eda) and ectodysplasin receptor (edar) genes.
is_a
exhibits
exhibits
Siluriformes
is_a
Teleostei
is_a
is_a
edadt3S243X/+
eda
variant_of
body has fewer parts of type scale
influences
towards
towards
towards
is_a
is_ais_a
has number of
is_a
Taxon Anatomical Entity QualityGeneanatomical structure
inheres_in
inheres_in
inheres_in
is_ais_a
Gasterosteiformes
body
body lacks all parts of type scale
body lacks all parts of type scale
lacks all parts of type
scale
is_a
Ictalurus punctatus
Apeltes quadracus
has fewer parts of type
© Jean Ricardo Simões Vitule
Full workflow:free-text → EQ → integrated KB
•501,862 taxon phenotype annotations•Curated from 4,732 characters in 2,474
species from 52 papers•From ZFIN: 21,829 phenotype annotations
about 3,893 genes
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Phenoscape Knowledgebase
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Major taxonomic groups have similar distribution of entities
among phenotypes
25 July 2008
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0 10 20 30 40 50 60 70
Siluriformes
Cypriniformes
Characiformes
Gymno<formes
Gonorynchiformes
Clupeiformes
% Postcranial axial skeleton
% Paired fins
% Cranium
Some notable differences for skeletal characters
Image from Sabaj-Perez
25 July 2008
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Substantial overlap between model organism and
evolutionary phenotypes
0 500 1000 1500 2000 2500
nervous system
sensory system
skeletal system
cardiovascular system
diges7ve system
immune system
endocrine system
renal system
respiratory system
liver and biliary system
musculature system
reproduc7ve system
hematopoie7c system
Evolu7onary characters
Zebrafish phenotypes
•4,217 zebrafish phenotypes•3,405 evolutionary characters
25 July 2008
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Hypothesis generation:Genetic basis for scale loss in
Siluriformes
Harris et al., 2007
Mutation of eda gene in Danio:
Copyright © Jean Ricardo Simões Vitule, All Rights Reserved
Ictalurus punctatus:
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Wet lab test(Work by Richard Edmunds)
eda expression is lacking in the epidermis
Ictalurus punctatus
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Hypothesis generation:Genetic basis for absence of the basihyal bone in Siluriformes
Mutation of brpf1 gene in Danio:
Ictalurus punctatus:
Laue et al (2008)
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Wet lab test(Work by Richard Edmunds)
Ictalurus punctatus
78 hpf 86 hpf
brpf1 lacks expression in the basihyal
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The parts to make this work
• Ontologies that capture the knowledge domains
• Efficient data curation workflow
• Expressive and scalable inference engine
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Dahdul et al (2009), Cover art: K. Luckenbill
• Teleost Anatomy(seeded from Zebrafish)
• Teleost Taxonomy(based on Eschmeyer’s Catalog of Fishes)
• Phenotypic Quality (PATO)
Ontologydevelopment
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Making PATO usable for evolutionary data
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Getting ontologies right is a challenge
• What is the right axis of classification?
• Structure versus function• Relational vs monadic qualities• PATO: shape and size vs natural language
”Interopercle shape: expanded posteroventrally”
• Different ways to observe or generate a phenotypic quality
• Color as color hue (radiation quality) or pigmentation (structural quality)
• Relative sizes don’t have a universal reference
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CurationDahdul et al., 2010 PLoS ONE
2. Students: Manual entry of free
text character descriptions, matrix, taxon list, specimens
and museum numbers using Phenex
3. Character annotation by experts: Entry of phenotypes
and homology assertions using
Phenex
Curators:Wasila DahdulMiles CoburnJeff EngemenTerry GrandeEric HiltonJohn LundbergPaula MabeeRichard MaydenMark Sabaj Pérez
1. Students: gather publications (scan hard copies,
produce OCR PDFs)
4. Consistency checks, upload of
data to public view of Phenoscape KB
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KB is based on OBD(Ontology-Based Database)
(C. Mungall, LBL)
Node
- is_reiflink
- is_obsolete
- is_transitive
- is_anonymous
- metatype
- uri
- label
- uid
Node_ID
source
Link
- object_quantifier_only
- object_quantifier_some
- applies_to_all
- is_metadata
- is_obsolete
- is_negated
- is_instantiation
- is_inferred
- combinator
Link_ID
source
subject
predicate
object
valid during
reified as
Link_Cardinality
- object_min_cardinality
- object_max_cardinality
- object_cardinality
Link_ID
Inference_Evidence
Inference_Evidence_ID
of link
evidence type
Inference_Evidence_Support
Inference_Evidence_Support_ID
inferred from link
for evidence
inference type
TagVal
- val
TagVal_ID
for node
predicate (tag)
data type
source
Alias
- label
- scope
Alias_ID
Description
- label
- scope
Description_ID
Node_Xref
Node_ID
Description_Xref
Description_ID
source
of node
synonym
type
source
of node
description type
context
Xref
context
Xref
for
for
of link
Figure 1
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TTO:taxon
uid = TTO IDPHENO:exhibits
{TAO,ZFA}:entity
uid = {TAO,ZFA} ID
OBO_REL:inheres_in
OBO_REL:towards
{TAO,ZFA}:entity
uid = {TAO,ZFA} ID
CDAO:has_TU
CDAO:CharacterStateDataMatrix
PHENO:has_publication
CDAO:has_Character
CDAO:Character
name = character text
CDAO:CharacterStateDomain
name = state text
CDAO:has_Datum
PHENO:Publication-dc:abstract
-dc:bibliographicCitation-dc:date
OBO_REL:posited_by
OBO_REL:posited_by
has_measurement
Measurement-value/max/min
-unit
has_evidence
ECO:evidence
publication notes (literal text)
PHENO:has_comment
dc:creator
curator(s)
comment (literal text)
PHENO:has_comment
comment (literal text)
PHENO:has_comment
CDAO:CharacterStateDatum CDAO:has_StateCDAO:TU
name = Publication Taxon
PHENO:has_taxon
comments (literal text)
PHENO:has_comment
Specimen
dwc:catalogID dwc:collectionID
COLLECTIONcatalog number
(literal text)
dwc:individualID
PHENO:asserted_for_otu
PATO:quality
OBO_REL:is_a
Genotype
uid = ZFIN IDOBO_REL:influences
Gene
uid = ZFIN ID
OBO_REL:variant_of
ZFIN:Publication
uid = ZFIN ID
OBO_REL:posited_by
Figure 3
Phenotype(class expression)
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How does reasoning work?
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TTO:Batrochoglanis
raninus
ZFIN:
edn1tf216b/tf216binfluencesexhibits
PATO:rectangular^inheres_in
(TAO:ectopterygoid)
PATO:curvature^inheres_in
(ZFA:maxilla)
How does reasoning work?
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How does reasoning work?
TTO:Pseudopimelodidae
TTO:Batrochoglanis
raninus
TAO:dermal bone
TAO:palatoquadrate arch
is_a
ZFIN:
edn1tf216b/tf216b
PATO:shape
TAO:maxilla
TTO:Batrochoglanis
ZFA:maxilla
TAO:ectopterygoid
part_of
PATO:rectangular
TAXRANK:genusTAXRANK:species
TTO:has_rank
TTO:has_rank
is_a
is_a
influences
is_a
part_of
is_a
is_a
exhibits
PATO:curvature
is_a
ZFIN:edn1
variant_of
PATO:rectangular^inheres_in
(TAO:ectopterygoid)
PATO:curvature^inheres_in
(ZFA:maxilla)
TAXRANK:familyTTO:has_rank
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How does reasoning work?
TTO:Pseudopimelodidae
TTO:Batrochoglanis
raninus
TAO:dermal bone
TAO:palatoquadrate arch
is_a
ZFIN:
edn1tf216b/tf216b
PATO:shape
TAO:maxilla
TTO:Batrochoglanis
ZFA:maxilla
TAO:ectopterygoid
part_of
PATO:rectangular
TAXRANK:genusTAXRANK:species
TTO:has_rank
TTO:has_rank
inheres_in
is_a
is_a
influences
is_a
part_of
is_a
is_a
is_ais_a
inheres_in
exhibits
PATO:curvature
is_a
ZFIN:edn1
variant_of
PATO:rectangular^inheres_in
(TAO:ectopterygoid)
PATO:curvature^inheres_in
(ZFA:maxilla)
TAXRANK:familyTTO:has_rank
![Page 54: Reasoning over phenotype diversity, character change, and evolutionary descent](https://reader034.fdocuments.in/reader034/viewer/2022052619/5559fb95d8b42aa8098b4b5b/html5/thumbnails/54.jpg)
How does reasoning work?
TTO:Pseudopimelodidae
TTO:Batrochoglanis
raninus
TAO:dermal bone
TAO:palatoquadrate arch
is_a
ZFIN:
edn1tf216b/tf216b
PATO:shape
TAO:maxilla
TTO:Batrochoglanis
ZFA:maxilla
TAO:ectopterygoid
part_of
PATO:rectangular
TAXRANK:genusTAXRANK:species
TTO:has_rank
TTO:has_rank
inheres_in
is_a
is_a
influences
is_a
part_of
is_a
is_a
is_ais_a
is_a
inheres_in
exhibits
is_a
part_of
PATO:curvature
is_a
ZFIN:edn1
variant_of
PATO:rectangular^inheres_in
(TAO:ectopterygoid)
PATO:curvature^inheres_in
(ZFA:maxilla)
TAXRANK:familyTTO:has_rank
![Page 55: Reasoning over phenotype diversity, character change, and evolutionary descent](https://reader034.fdocuments.in/reader034/viewer/2022052619/5559fb95d8b42aa8098b4b5b/html5/thumbnails/55.jpg)
How does reasoning work?
TTO:Pseudopimelodidae
TTO:Batrochoglanis
raninus
TAO:dermal bone
TAO:palatoquadrate arch
is_a
ZFIN:
edn1tf216b/tf216b
PATO:shape
TAO:maxilla
TTO:Batrochoglanis
ZFA:maxilla
TAO:ectopterygoid
part_of
PATO:rectangular
TAXRANK:genusTAXRANK:species
TTO:has_rank
TTO:has_rank
inheres_in
is_a
is_a
inheres_in
influences
is_a
part_of
is_a
inheres_in
inheres_in_part_of
is_a
is_ais_a
is_a
inheres_in
is_a
inheres_in
exhibits
is_a
part_of
inheres_in_part_of
PATO:curvature
is_a
is_a
ZFIN:edn1
variant_of
PATO:rectangular^inheres_in
(TAO:ectopterygoid)
PATO:curvature^inheres_in
(ZFA:maxilla)
TAXRANK:familyTTO:has_rank
![Page 56: Reasoning over phenotype diversity, character change, and evolutionary descent](https://reader034.fdocuments.in/reader034/viewer/2022052619/5559fb95d8b42aa8098b4b5b/html5/thumbnails/56.jpg)
How does reasoning work?
TTO:Pseudopimelodidae
TTO:Batrochoglanis
raninus
TAO:dermal bone
TAO:palatoquadrate arch
is_a
ZFIN:
edn1tf216b/tf216b
PATO:shape
TAO:maxilla
TTO:Batrochoglanis
ZFA:maxilla
TAO:ectopterygoid
part_of
PATO:rectangular
TAXRANK:genusTAXRANK:species
TTO:has_rank
TTO:has_rank
inheres_in
is_a
is_a
inheres_in
influences
is_a
part_of
is_a
inheres_in
inheres_in_part_of
is_a
is_ais_a
is_a
inheres_in
is_a
inheres_in
exhibits
is_a
part_of
inhere
s_in_part_of
PATO:curvature
is_a
is_a
ZFIN:edn1
variant_of
PATO:shape^inheres_in
(TAO:dermal bone)
PATO:shape^inheres_in_part_of
(TAO:palatoquadrate arch)
PATO:rectangular^inheres_in
(TAO:ectopterygoid)
PATO:curvature^inheres_in
(ZFA:maxilla)
TAXRANK:familyTTO:has_rank
![Page 57: Reasoning over phenotype diversity, character change, and evolutionary descent](https://reader034.fdocuments.in/reader034/viewer/2022052619/5559fb95d8b42aa8098b4b5b/html5/thumbnails/57.jpg)
How does reasoning work?
TTO:Pseudopimelodidae
TTO:Batrochoglanis
raninus
TAO:dermal bone
TAO:palatoquadrate arch
is_a
ZFIN:
edn1tf216b/tf216b
PATO:shape
TAO:maxilla
TTO:Batrochoglanis
ZFA:maxilla
TAO:ectopterygoid
part_of
PATO:rectangular
TAXRANK:genusTAXRANK:species
TTO:has_rank
TTO:has_rank
inheres_in
is_a
is_a
inheres_in
influences
is_a
part_of
is_a
inheres_in
inheres_in_part_of
is_a
is_ais_a
is_a
inheres_in
is_a
inheres_in
exhibits
is_a
part_of
is_a
is_a
inheres_in
inheres_in_p
art_of
inhere
s_in_part_of
PATO:curvature
is_a
is_a
ZFIN:edn1
variant_of
PATO:shape^inheres_in
(TAO:dermal bone)
PATO:shape^inheres_in_part_of
(TAO:palatoquadrate arch)
PATO:rectangular^inheres_in
(TAO:ectopterygoid)
PATO:curvature^inheres_in
(ZFA:maxilla)
TAXRANK:familyTTO:has_rank
![Page 58: Reasoning over phenotype diversity, character change, and evolutionary descent](https://reader034.fdocuments.in/reader034/viewer/2022052619/5559fb95d8b42aa8098b4b5b/html5/thumbnails/58.jpg)
How does reasoning work?
TTO:Pseudopimelodidae
TTO:Batrochoglanis
raninus
TAO:dermal bone
TAO:palatoquadrate arch
is_a
ZFIN:
edn1tf216b/tf216b
PATO:shape
TAO:maxilla
TTO:Batrochoglanis
ZFA:maxilla
TAO:ectopterygoid
part_of
PATO:rectangular
TAXRANK:genusTAXRANK:species
TTO:has_rank
TTO:has_rank
inheres_in
is_a
is_a
inheres_in
influences
is_a
part_of
is_a
inheres_in
inheres_in_part_of
is_a
is_ais_a
is_a
inheres_in
is_a
inheres_in
exhibits
is_a
part_of
is_a
is_a
inheres_in
inheres_in_pa
rt_of
inhere
s_in_part_of
is_a
is_a is_a
is_a
PATO:curvature
is_a
is_a
ZFIN:edn1
variant_of
PATO:shape^inheres_in
(TAO:dermal bone)
PATO:shape^inheres_in_part_of
(TAO:palatoquadrate arch)
PATO:rectangular^inheres_in
(TAO:ectopterygoid)
PATO:curvature^inheres_in
(ZFA:maxilla)
TAXRANK:familyTTO:has_rank
![Page 59: Reasoning over phenotype diversity, character change, and evolutionary descent](https://reader034.fdocuments.in/reader034/viewer/2022052619/5559fb95d8b42aa8098b4b5b/html5/thumbnails/59.jpg)
How does reasoning work?
TTO:Pseudopimelodidae
TTO:Batrochoglanis
raninus
TAO:dermal bone
TAO:palatoquadrate arch
is_a
ZFIN:
edn1tf216b/tf216b
PATO:shape
TAO:maxilla
TTO:Batrochoglanis
ZFA:maxilla
TAO:ectopterygoid
part_of
PATO:rectangular
TAXRANK:genusTAXRANK:species
TTO:has_rank
TTO:has_rank
inheres_in
is_a
is_a
inheres_in
influences
is_a
part_of
is_a
inheres_in
inheres_in_part_of
is_a
is_ais_a
is_a
inheres_in
is_a
inheres_in
exhibits
is_a
part_of
is_a
is_a
inheres_in
inheres_in_pa
rt_of
inhere
s_in_part_of
is_a
is_a is_a
is_a
PATO:curvature
is_a
is_a
ZFIN:edn1
variant_of
PATO:shape^inheres_in
(TAO:dermal bone)
PATO:shape^inheres_in_part_of
(TAO:palatoquadrate arch)
PATO:rectangular^inheres_in
(TAO:ectopterygoid)
PATO:curvature^inheres_in
(ZFA:maxilla)
TAXRANK:familyTTO:has_rank
![Page 60: Reasoning over phenotype diversity, character change, and evolutionary descent](https://reader034.fdocuments.in/reader034/viewer/2022052619/5559fb95d8b42aa8098b4b5b/html5/thumbnails/60.jpg)
Future Directions:
1. Reasoning
over homology
image by Kyle Luckenbill, ANSP
Entity 1 Taxon 1 Relationship Entity 2 Taxon 2 Evidence Reference(s)
scaphium Otophysi homologous_to neural arch 1 Teleostei IDS, IMS, IPS
(Fink and Fink,
1981; Rosen and
Greenwood,
1970)
intercalarium Otophysi homologous_to
neural arch 2
(ventral
portion)
Teleostei IDS, IMS, IPS
(Rosen and
Greenwood,
1970)
intercalarium Otophysi homologous_to neural arch 2 Teleostei NAS (Fink and Fink,
1981)
intercalarium Otophysi homologous_to neural arch 2 Teleostei IMS (Hora, 1922)
intercalarium Otophysi homologous_to rib of vertebra 2 Teleostei TAS (Hora 1922)
tripus Otophysi homologous_to parapophysis +
rib of vertebra 3 Teleostei IDS, IMS, IPS
(Fink and Fink,
1981; Rosen and
Greenwood,
1970)
![Page 61: Reasoning over phenotype diversity, character change, and evolutionary descent](https://reader034.fdocuments.in/reader034/viewer/2022052619/5559fb95d8b42aa8098b4b5b/html5/thumbnails/61.jpg)
What next?
• Modeling and reasoning over homology
• Efficient searching and scoring of semantic similarity
• Reducing the bottlenecks in data curation
![Page 62: Reasoning over phenotype diversity, character change, and evolutionary descent](https://reader034.fdocuments.in/reader034/viewer/2022052619/5559fb95d8b42aa8098b4b5b/html5/thumbnails/62.jpg)
Opening descriptive biological data to computing can enable new science
Descriptive biology
- Phenotypes- Traits
- Function- Behavior- Habitat
- Life Cycle- Reproduction
- Conservation Threats
Biodiversity(Specimens, Occurrence
records)
Taxonomy, Species ID
Conservation Biology
Ecology
Genetics
Genomics, Gene
expression
Genetic variation
Physiology
![Page 63: Reasoning over phenotype diversity, character change, and evolutionary descent](https://reader034.fdocuments.in/reader034/viewer/2022052619/5559fb95d8b42aa8098b4b5b/html5/thumbnails/63.jpg)
Acknowledgements
• PhenoscapePersonnel & PIs:P. Mabee,M. Westerfield, T. Vision,J. Balhoff,C. Kothari,W. Dahdul,P. Midford
• Phenoscape curators & workshop participants
• Berkeley Bioinformatics & Ontologies Project (BBOP):C.Mungall, S.Lewis
• National Evolutionary Synthesis Center (NESCent)
• NSF (DBI 0641025)
![Page 64: Reasoning over phenotype diversity, character change, and evolutionary descent](https://reader034.fdocuments.in/reader034/viewer/2022052619/5559fb95d8b42aa8098b4b5b/html5/thumbnails/64.jpg)
![Page 65: Reasoning over phenotype diversity, character change, and evolutionary descent](https://reader034.fdocuments.in/reader034/viewer/2022052619/5559fb95d8b42aa8098b4b5b/html5/thumbnails/65.jpg)
Similarity (IC)
Taxon (subsuming taxon with variable phenotypes in
subsumed taxa)
Taxon phenotype
(one of two or more subsumed variable taxon
phenotypes)
Candiate Gene(s)
(zebrafish)
Gene phenotype
Subsumingphenotype
15.16 Danio
Danio rerio: epural
separated from urostyle
trpm7epural,
compositionepural,
structure
14.45 OtophysiSiluriformes: scales, absent
eda scales, absent scales, count
13.25 SiluriformesSiluriformes:
basihyal cartilage, absent
brpf1, disc1 and 10 more
basihyal cartilage, absent
basihyal cartilage,
count
10.0 Tachysurus
process of Meckel’s cartilage,
adjacent to coronoid process
edn1, foxd3 and 22 more
Meckel’s cartilage,
mislocalized posteriorly
Meckel’s cartilage, position
Phenotypic similarity matches taxa to candidate genes
![Page 66: Reasoning over phenotype diversity, character change, and evolutionary descent](https://reader034.fdocuments.in/reader034/viewer/2022052619/5559fb95d8b42aa8098b4b5b/html5/thumbnails/66.jpg)
Mapping EQs back to characters is a challenge
• Properties of “good” phylogenetic characters:
• Exclusivity of states
• Distinguishability of states
• Independence of characters
• Finding exclusive states requires incompatible phenotypes. How to determine incompatibility?
• Two phenotypes are incompatible iff they cannot both inhere in the same specimen.
• Two qualities are incompatible iff an entity cannot bear both.
![Page 67: Reasoning over phenotype diversity, character change, and evolutionary descent](https://reader034.fdocuments.in/reader034/viewer/2022052619/5559fb95d8b42aa8098b4b5b/html5/thumbnails/67.jpg)
Which EQs and qualities are incompatible?
• Incompatible Qs
• present vs. absent• triangular vs.
round• absent vs. any
other quality
• Incompatible EQs
• (Q inheres_in bone E) vs (cartilage E absent)
• Compatible Qs
• present vs. any other quality (except absent)
• serrated vs. round• some colors
![Page 68: Reasoning over phenotype diversity, character change, and evolutionary descent](https://reader034.fdocuments.in/reader034/viewer/2022052619/5559fb95d8b42aa8098b4b5b/html5/thumbnails/68.jpg)
Hemiodus argenteus
Hemiodus unimaculatus
{shape:bent inheres_in supraorbital bone,count:absent inheres_in upper pharyngeal 5 tooth}
{shape:straight inheres_in supraorbital bone,count:present inheres_in upper pharyngeal 5 tooth}
Hemiodus{shape:bent inheres_in supraorbital bone,shape:straight inheres_in supraorbital bone, count:absent inheres_in upper pharyngeal 5 tooth, count:present inheres_in upper pharyngeal 5 tooth}
Detecting phenotype change and variation
{Change in: shape inheres_in supraorbital bone,Change in: count inheres_in upper pharyngeal 5 tooth}
![Page 69: Reasoning over phenotype diversity, character change, and evolutionary descent](https://reader034.fdocuments.in/reader034/viewer/2022052619/5559fb95d8b42aa8098b4b5b/html5/thumbnails/69.jpg)
System architecture
Phenotypic Quality Ontology
(PATO)
Teleost Taxonomy Ontology (TTO)
Knowledgebase (OBD)(PostgreSQL)
Genes & genotypes
OBD Programming API(Java)
Knowledgebase Data Services API (REST)
Knowledgebase User IntefaceWeb Application for Exploration & Mining
(Ruby on Rails, JavaScript)
OBD Reasoner
Phenex(Evolutionary EQ
annotation)
Homology assertions
Mutant EQ phenotypes from Zebrafish Model Organism Database
External web sites and client
applications
Skeletal Character Data(from phylogenetic
treatments in literature)
OBO LibraryNeXMLEvolutionary EQ Phenotypes
(through annotation)
Anatomy Ontologies(ZFA, TAO)
![Page 70: Reasoning over phenotype diversity, character change, and evolutionary descent](https://reader034.fdocuments.in/reader034/viewer/2022052619/5559fb95d8b42aa8098b4b5b/html5/thumbnails/70.jpg)
Formalizing homology relationships
• Formal pattern is ternary:E1 in_taxon T1 homologous_to E2 in_taxon T2 as E3 in_taxon T3
• Classifying homology relationships
• 1-1 homology (phylogenetic homology)
• serial homology
• A iso_homologous_to B as C⇒ all A derived_by_descent_from some (C and has_derived_by_descendent some B) and all B derived_by_descent_from some (C and has_derived_by_descendent some A)
• shares_ancestor_with as a relation chain:derived_by_descent_from o has_derived_by_descendent
![Page 71: Reasoning over phenotype diversity, character change, and evolutionary descent](https://reader034.fdocuments.in/reader034/viewer/2022052619/5559fb95d8b42aa8098b4b5b/html5/thumbnails/71.jpg)
Option 1: Asserting homology at higher-level taxa
![Page 72: Reasoning over phenotype diversity, character change, and evolutionary descent](https://reader034.fdocuments.in/reader034/viewer/2022052619/5559fb95d8b42aa8098b4b5b/html5/thumbnails/72.jpg)
Option 2: Asserting homology at species level
![Page 73: Reasoning over phenotype diversity, character change, and evolutionary descent](https://reader034.fdocuments.in/reader034/viewer/2022052619/5559fb95d8b42aa8098b4b5b/html5/thumbnails/73.jpg)
Validation through standard OWL-DL reasoning