Phenoscape: Connectin g evolutionary phenotypes to genes Paula Mabee Hilmar Lapp, Todd Vision, Monte Westerfield Jim Balhoff, Wasila Dahdul, Peter Midford kb.phenoscape.org

Difficult to synthesize morphology across studies

Difficult to relate to genetics & development Cyprinus carpio Pangio anguillaris Nemacheilus fasciatus Catostomus commersoni Gyrinocheilus aymonieri Phenacogrammus interruptus

have their basis in changes in genetic control over development Phenotypic differences

Development understood from study of model organisms Chen & Mayden, 2010

Zebrafish ntla Model for vertebrate development Mutagenesis/gene knock-down Mutant phenotypes genes ZFIN resource

Problem: photo J. Lundberg, ANSP 2002 Pimelodus maculatus Species phenotypes genes at evolutionary scale

slc24a5 involved in pigmentation similarity between fish and humans (Lamason et al., 2005) Zebrafish -- Human Conservation of gene sequence & function and phenotype

Fig. 1, Washington et al., 2010 Translational medicine

Ameiurus nebulosus Fig. 1, Washington et al., 2010 Catfish Trogloglanis pattersoni gene? EQ: eye absent Translational biodiversity?

Phenoscape kb.phenoscape.org 2007 Goal: To prototype a curated, ontology-based evolutionary phenotype database that maps to genetic databases Devo-evo synthesis; candidate gene discovery Enable data-mining and discovery for broad scale evolutionary patterns 25 July 2009; ToL web Ostariophysan fishes

User needs drove KB development: Search for candidate genes underlying evolutionary morphology Search for taxa with particular morphologies Aggregate morphological data across studies

Requirements (generic): 1. Ontologies 2. Curation 3. Database

1. Ontology: terms and relationships is_a part_of is_a develops_from part_of replacement bone basihyal bone ventral hyoid arch basihyal cartilage pharyngeal arch cartilage is_a basihyal element

Teleost Anatomy Ontology Dahdul, W. M., J. G. Lundberg, P. E. Midford, J. P. Balhoff, H. Lapp, T. J. Vision, M. A. Haendel, M. Westerfield, and P. M. Mabee. The Teleost Anatomy Ontology: Anatomical representation for the genomics age. Systematic Biology (Cover art: Kyle Luckenbill)

Ontologies used by Phenoscape Zebrafish Anatomy Ontology (2196 terms; 310 skeletal) Zebrafish Anatomy Ontology (2196 terms; 310 skeletal) Teleost Taxonomy Ontology (36,060 terms; 38,000 synonyms) Teleost Taxonomy Ontology (36,060 terms; 38,000 synonyms) Taxonomic Rank Ontology (8->31 terms) Taxonomic Rank Ontology (8->31 terms) Teleost Anatomy Ontology (2371 terms; 618 skeletal) Teleost Anatomy Ontology (2371 terms; 618 skeletal) Phenotype and Trait Ontology (PATO) (1,075 terms) Spatial Ontology (106 terms) 6 Jan 2009 EvidenceCodeOntology

Curated 4,732 characters in 2,474 species from 52 papers 501,862 taxon phenotype annotations From ZFIN: 21,829 phenotype annotations about 3,893 genes Curated 4,732 characters in 2,474 species from 52 papers 501,862 taxon phenotype annotations From ZFIN: 21,829 phenotype annotations about 3,893 genes 2. Curation Dahdul et al., 2010 PLoS ONE 2. Students: Manual entry of free text character descriptions, matrix, taxon list, specimens and museum numbers using Phenex 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 using Phenex Curators: Wasila Dahdul Miles Coburn Jeff Engemen Terry Grande Eric Hilton John Lundberg Paula Mabee Richard Mayden Mark Sabaj Pérez ~ 5 person years 1. Students: gather publications (scan hard copies, produce OCR PDFs) 4. Phenoscape Knowledgebase: OBD, data services, web application

5K Karacter Challenge Ontology boot camp, NESCent 2005 Phenoscape Data Roundup photo: NESCent photo: Monte Westerfield Buffalo Roundup, SD

Entity-Quality Model for Taxon Phenotypes ethmoid cartilage ethmoid plate form Entity (TAO) rounded Character round Quality (PATO) State } Phenotype

Taxon phenotype annotations round that inheres_in some ethmoid cartilage round that inheres_in some ethmoid cartilage exhibits some Taxon ontology term Anatomy ontology term Phenotypic Quality ontology term Links a quality to the entity that is its bearer Brachyplatystoma capapretum

split that inheres_in some ethmoid cartilage split that inheres_in some ethmoid cartilage influences some Gene phenotype annotations Import from ZFIN data in EQ format tfap2a ts213/ts213

Brachyplatystoma capapretum round that inheres_in some ethmoid cartilage round that inheres_in some ethmoid cartilage exhibits some tfap2a ts213/ts213 split that inheres_in some ethmoid cartilage split that inheres_in some ethmoid cartilage influences some round split ethmoid cartilage Brachyplatystoma tfap2a is_a variant_o f inheres_i n is_a shape chondrocraniu m cartilage olfactory region Pimelodidae sequence-specific DNA binding transcription factor activity is_a has_functio n is_a part_of is_a

Knowledgebase architecture

Phenoscape Knowledgebase 501,862 taxon phenotypes 21,829 gene phenotypes for 3,893 genes kb.phenoscape.o rg Interative user testing of interface

KB inferred candidate genes Phenotypic profile for Siluriformes includes: Scales absent; Basihyal absent Phenotypic profile for Siluriformes includes: Scales absent; Basihyal absent

30% <1% position composition 25% 20%15% 10% count shape structure size PATO qualities used in phenotypes

Siluriform synapomorphies: Ictalurus punctatus Copyright © Jean Ricardo Simões Vitule, All Rights Reserved Scales absentBasihyal absent Ictalurus punctatus Photo: Richard Edmunds

Zebrafish mutant phenotypes Harris et al., 2007 eda: scale lossbrpf1: basihyal loss Laue et al., 2008

In silico prediction of candidate genes Ictalurus punctatus Copyright © Jean Ricardo Simões Vitule, All Rights Reserved Scales absent: eda?Basihyal absent: brpf1? Ictalurus punctatus Photo: Richard Edmunds

Wet lab test (Richard Edmunds) Lack of eda expression in the epidermis supports Phenoscape KB hypothesis Ictalurus punctatus eda

Wet lab test (Richard Edmunds) Ictalurus punctatus 78 hpf 86 hpf Lack of brpf1 expression in the basihyal supports Phenoscape KB hypothesis

E.g., distribution of all characters across anatomical systems in taxa 25 July 2008

E.g., distribution of skeletal characters in broad regions across taxa Image from Sabaj-Perez 25 July 2008

Summary Powerful queries not previously possible for evolutionary phenotype data Meaningful integration with model organism phenotypic and genetic data Makes data accessible for broad group of researchers and creates opportunities for new and synthetic research Semantic framework and reasoning tools provide:

Phenoscape as a resource Ontologies (anatomy, quality, taxon) + EQ data for any taxon Reasoning across EQ data types, uniting multiple studies, genes, etc. Your data?

Acknowledgments Phenoscape Personnel & PIs: P. Mabee, M. Westerfield, T. Vision, H. Lapp, C. Kothari, W. Dahdul, P. Midford, R. Edmunds Phenoscape curators & workshop participants Berkeley Bioinformatics & Ontologies Project (BBOP): C.Mungall, S.Lewis National Evolutionary Synthesis Center (NESCent) NSF (DBI )