bringing reason to phenotype diversity, character change, and common descent
DESCRIPTION
Talk I gave in the National Center for BioOntologies (NCBO) Webinar series, on Nov 17, 2010. Abstract, bio, and video recording are at the NCBO website: http://www.bioontology.org/phenoscapeTRANSCRIPT
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Bringing reason to phenotype diversity,
character change, and common descent
Hilmar LappNational Evolutionary Synthesis Center (NESCent)
NCBO Webinar, Nov 17, 2010
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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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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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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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Integrating across studies?
Fig. 7, Sereno (2009)
Fig. 6, Sereno (2009)
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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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supraorbital bone
supraorbital bone shape
Entity (TAO)
bent
Character
bent
Quality (PATO)
State
Entity-Quality Model for Evolutionary Phenotypes
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supraorbital bone
supraorbital bone shape
Entity (TAO)
bent
Character
bent
Quality (PATO)
State
Entity-Quality Model for Evolutionary Phenotypes
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supraorbital bone
supraorbital bone shape
Entity (TAO)
bent
Character
bent
Quality (PATO)
State
Entity-Quality Model for Evolutionary Phenotypes}
Phenotype
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Brycinus brevis
bentinheres_insupraorbital
bone
exhibits some
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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Brycinus brevis
bentinheres_insupraorbital
bone
exhibits some
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 Publication
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Ontology development
Cover art: K. LuckenbillDahdul et al (2009)
Ontologies for
• Teleost Anatomy
• Teleost Taxonomy
• Phenotypic Quality (PATO)
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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
~ 5 person years
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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• Curated 4,208 characters in 2,310 species from 51 papers
• 333,987 evolutionary phenotype assertions
• 11,267 phenotype statements about 2,953 genes
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Phenoscape Knowledgebase
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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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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)
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KB is based on OBD(Ontology-Based Database)
(C. Mungall, LBL)
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TAO:taxon Phenotype(class expression)
PHENO:exhibits
TAO:entity
OBO_REL:inheres_in
OBO_REL:towards
TAO:entity
CDAO:has_TU
CDAO:CharacterStateDataMatrix
PHENO:has_publication
CDAO:has_CharacterCDAO: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_State
CDAO:TU
name = Publication Taxon
PHENO:has_taxon
comments (literal text)
PHENO:has_comment
Specimen
dwc:catalogID
dwc:collectionIDCOLLECTION
catalog number (literal text)
dwc:individualID
PHENO:asserted_for_otu
PATO:quality
OBO_REL:is_a
GenotypeOBO_REL:influences
Gene
OBO_REL:variant_of
ZFIN:Publication
uid = ZFIN ID
OBO_REL:posited_by
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Phenoscape OBD reasoner• All OBD built-in rules:
• is_transitive(R), X R Y, Y R Z → X R Z• is_reflexive(R) → X R X• X is_a Y, Y R some Z → X R some Z• Y is_a Z, X R some Y → X R some Z• X R Y, Y S Z, transitive_over(R,S) → X
R Z• X R1 Y, Y R2 Z,
holds_over_chain(R,R1,R2) → X R Z
• Additional Phenoscape rule:
• T exhibits P, T is_a T’ → T’ exhibits P• Consistent with OWL due to instance
quantification
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Major taxonomic groups have similar distribution of entities
among phenotypes
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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
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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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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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Attribute Example Qualities
Color black, colorless
Composition cartilaginous, ossified
Count present, absent
Position horizontal, vertical
Quality open, closed, flexible
Relational Shape protruding into
Making PATO usable for evolutionary data
Attribute Example Qualities
Relational Spatial anterior to, lateral to
Relational Structural fused with, overlap with, separated from
Shape concave, interdigitated, lobed, triangular
Size increased length, decreased length
Texture wrinkled, smooth
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Getting PATO right is a challenge • PATO is “single-inheritance” - what is the right
axis of classification?
• relational shape vs monadic shape• relational spatial vs position• 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
• Negation (“not round”, “unelongated”): means complement under attribute ‘(shape and not(round))’
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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.
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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
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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}
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Phenotypic profile: Phenotypic profile tree
Phenotype match
Taxon color indicates the greatest level of match of specified phenotype(s) found within a species in the clade.Phenotypes
including parts
including parts
including parts
X
X
Xopercle triangular
adipose fin absent
dorsal fin absent
Include inferred phenotypes
100%
75%
50%
<50%
Query taxa with these phenotypes.
Visualizing phenotype profiles on a tree
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triangular 1 1
Y-shaped 1 1
shape 8 3
Taxa Phenotype Profiles
Phenotype
Taxonomic distribution ofentity term: basihyal bone
for basihyal bone
Show taxa with unspecified shape phenotypes
Show taxa without phenotype data
Limit tree to Cypriniformes X
or Sets of taxa with matching Phenotype Profiles
Cypriniformes
Cyprinidae
Balitoridae
Psilorhynchidae
Catostomidae
Botiidae
Vaillantellidae
Cobitidae
Gyrinocheilidae
Osariophysii
Navigating phenotype variation on a tree
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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)
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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
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Option 1: Asserting homology at higher-level taxa
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Option 2: Asserting homology at species level
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Validation through standard OWL-DL reasoning
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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
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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)