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Phenoscape
        Knowledgebase
Jim Balhoff, Wasila Dahdul, Hilmar Lapp, Paula Mabee,
    Peter Midford, Todd Vision, Monte Westerfield
Phenoscape
• Collaboration between P. Mabee (U. South Dakota), M.
   Westerfield (ZFIN, U. Oregon), and T.Vision (NESCent,
   UNC)

• Aim: foster semantic integration of phenotype data by
  • Prototyping a database of curated, machine-interpretable
      evolutionary phenotypes.

  • Integrating these with mutant phenotypes from model
      organisms.

  • Providing reasoner-enabled semantic tools which facilitate
      data-mining of phenotypic diversity and discovery of
      candidate genes for evolutionary phenotype transitions.
Phenoscape Knowledgebase
• ~4 million asserted semantic links (+ 7 million inferred)
• 52 fish systematics publications
  • 4700 morphological characters
  • 11,000 states + ontological descriptions (EQ)
  • 2500 referenced taxa
• ZFIN
   • 3900 genes, 6800 genotypes
   • 30000 experimental phenotype annotations
• 13 ontologies
  • ~80,000 terms
Workflow for phenotype annotation
                               3. Character annotation
         2. Students:            by experts: Entry of
   Manual entry of free text      phenotypes using
    character descriptions,           Phenex
      matrix, taxon list,
   specimens and museum
   numbers using Phenex

                                                         4. Phenoscape Knowledgebase:
                                                            OBD, data services, web
                                                                  application




                                       501,862
      1. Students:
gather publications (scan           phenotypes for
  hard copies, produce
      OCR PDFs)                          taxa
                                                                 Dahdul et al., 2010 PLoS ONE Text
Knowledgebase architecture
        Knowledgebase User Inteface             External web sites
   Web Application for Exploration & Mining         and client
         (Ruby on Rails, JavaScript)               applications



               Knowledgebase Data Services API (REST)


          OBD Programming API
                                                 OBD Reasoner
                 (Java)
                                                                                          Teleost Taxonomy
                                                                                           Ontology (TTO)
                        Knowledgebase (OBD)
                            (PostgreSQL)
                                                                                                       Phenotypic
                                                                                     Anatomy         Quality Ontology
                                                                                    Ontologies            (PATO)
                                                                                    (ZFA, TAO)
Genes & genotypes                    Homology assertions

  Mutant EQ phenotypes              Evolutionary EQ Phenotypes   NeXML
                                                                                                      OBO Library
  from Zebrafish Model                 (through annotation)
   Organism Database

                                                                      Phenex                 Skeletal Character Data
                                                                 (Evolutionary EQ              (from phylogenetic
                                                                   annotation)              treatments in literature)
OBD: Ontology-Based Database
 • Stores data and ontologies in combined
   semantic model - triple based
 • Reasoner executes inference rules as SQL
   queries - results iteratively added to database
 • Supports class expressions based on property
   restrictions, intersections, unions; transitive
   properties, property chains, and subsumption
 • Provenance-tracking via reification
Reasoning across logical relationships




Brachyplatystoma   exhibits some                  round that
  capapretum                                   inheres_in some
                                             ethmoid cartilage



                                                   influences some        split that
                           tfap2a   ts213/ts213
                                                                      inheres_in some
                                                                    ethmoid cartilage
Reasoning across logical relationships


                              tfap2a
                                                                  ethmoid
Brachyplatystoma                                                  cartilage
                                                                                     round
                      variant_of
          is_a                                       inheres_in
                                                                                  is_a


   Brachyplatystoma   exhibits some                  round that                inheres_in         split
     capapretum                                   inheres_in some
                                                ethmoid cartilage
                                                                                                  is_a



                                                         influences some            split that
                              tfap2a   ts213/ts213
                                                                                inheres_in some
                                                                              ethmoid cartilage
Reasoning across logical relationships
                      sequence-specific DNA                                            olfactory
                       binding transcription
                          factor activity             chondrocranium                   region
                                                         cartilage
Pimelodidae                                                                                                     shape
                                 has_function                                         part_of
                                                                      is_a
                                                                                                         is_a
     is_a                                                                                                           is_a
                                     tfap2a
                                                                          ethmoid
Brachyplatystoma                                                          cartilage
                                                                                                     round
                            variant_of
            is_a                                             inheres_in
                                                                                                  is_a


   Brachyplatystoma         exhibits some                    round that                     inheres_in            split
     capapretum                                           inheres_in some
                                                        ethmoid cartilage
                                                                                                                  is_a



                                                                 influences some                split that
                                     tfap2a    ts213/ts213
                                                                                            inheres_in some
                                                                                          ethmoid cartilage
Demo
Phenotype variation
in taxa (left) vs. zebrafish mutants (right)
                                      cardiovascular
                                                                                     digestive

 skeletal
                                        is_a
                                               is_a
                                                                is_a                   endocrine
    sensory                                                            is_a
                        is_a
                                      anatomical                       is_a
                                                                                       hematopoietic
 respiratory           is_a
                                        system                          is_a


                                                                        is_a           immune
                               is_a
                                                         is_a
                                      is_a     is_a
                                                                                      liver and biliary
       reproductive
                       renal                                      musculature
                                         nervous
                >85%   20-30% 15-19% 10-14%           5-9%        1-4%         <1%


    Distributed across anatomical systems
Global view of skeletal data

    4,-62+/0.123"
                                            viewed, summarized,
                                            synthesized, at a scale not
                                            possible otherwise.                  =">03?:.97+9,"9@+9,"3A2,2?07"
;070.57:8+/0.123"


                                                                                 =">9+.2B"C73"
  ;5170</0.123"


                                                                                 =""4.97+-1"
   489.9:+/0.123"




    456.+7+/0.123"




     *+,-.+/0.123"                                                                                               Image from Sabaj-Perez

                     !"   #!"   $!"   %!"   &!"          '!"         (!"   )!"




      Skeletal variation across taxa and regions
Quantify phenotypic similarity
Similarity                         Taxon   Candidate   Gene                            Subsuming
                 Taxon
  (IC)                           phenotype   gene    phenotype                         phenotype

  13.43            Eels          gill rakers, absent    eda     gill rakers, absent   gill rakers count

                                                                   lateral line,
  12.85         Minytrema       lateral line, absent   pcsk5a                         lateral line, size
                                                                     reduced

  12.44        Siluriformes      basihyal, absent      brpf1     basihyal, absent      basihyal, count

                                ceratobranchial 5                ceratobranchial
  11.32        Gyrinocheilus                            eda                             tooth, count
                                  teeth, absent                   teeth, absent
  11.11        Siluriformes       scales, absent        eda       scales, absent       scales, count
                                                                                      dermatocranium,
   9.91        Siluriformes       opercle, shape       edn1      maxilla, shape
                                                                                          shape
   9.19            Mola         caudal fin, absent      yap1     median fin, absent median fin, count

   9.19      Gonorynchiformes   dorsal fin, absent      tf1p2a   median fin, absent median fin, count

   5.17        Siluriformes        eye, reduced        pbx2         eye, small            eye, size
Summary
Semantic framework and reasoning tools provide:

  • Powerful queries not previously possible
     for evolutionary phenotype data
  • Meaningful integration with model
     organism phenotypic and genetic data
Acknowledgments
                                                            Phenoscape Workshop Participants
National Science Foundation (BDI-0641025)                    & Contributors
                                                            ! Arhat Abzhanov
National Evolutionary Synthesis Center                      !
                                                            !
                                                                Michael Ashburner
                                                                Judith Blake
                                                            !   Stan Blum
                                                            !   Quentin Cronk
 Contributors to Teleost Ontologies       Curators:         !   Mário de Pinna
                                                            !   Andy Deans
 ! Gloria Arratia                       Miles Coburn        !   George Gkoutos
                                                            !   Melissa Haendel
 !   Stan Blum                        ! Jeff Engemen        !   Hopi Hoekstra
 !   Miles Coburn
 !   Kevin Conway                     ! Terry Grande        !   Hans Hofmann
                                                            !   Elizabeth Jockusch
 !   Wasila Dahdul                    ! Eric Hilton         !   Elizabeth Kellogg
 !   Mário de Pinna
 !   Jeff Engemen                     ! John Lundberg       !   Chuck Kimmel
                                                            !   Suzanna Lewis
 !   Bill Eschmeyer                   ! Paula Mabee         !   Anne Maglia
 !   Terry Grande
 !   Melissa Haendel                  ! Richard Mayden      !   Austin Mast
 !   Brian Hall                                             !   Chris Mungall
                                      ! Mark Sabaj          !   Martin Ramirez
 !   Eric Hilton
 !   John Lundberg                      Sandrine Tercerie   !   Sue Rhee
 !   Richard Mayden                                         !   Martin Ringwald
 !   Mark Sabaj Pérez                                       !   Nelson Rios
 !   Brian Sidlauskas                                       !   Mark Sabaj Pérez
 !   Richard Vari                                           !   Eric Segerdell
 !   Jacqueline Webb                                        !   Brian Sidlauskas
 !   Edward Wiley                                           !   Barry Smith
                                                            !   David Stern
                                                            !   Peter Vize
                                                            !   Gunter Wagner
                                                            !   Nicole Washington
                                                            !   Edward Wiley

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The Phenoscape Knowledgebase

  • 1. Phenoscape Knowledgebase Jim Balhoff, Wasila Dahdul, Hilmar Lapp, Paula Mabee, Peter Midford, Todd Vision, Monte Westerfield
  • 2. Phenoscape • Collaboration between P. Mabee (U. South Dakota), M. Westerfield (ZFIN, U. Oregon), and T.Vision (NESCent, UNC) • Aim: foster semantic integration of phenotype data by • Prototyping a database of curated, machine-interpretable evolutionary phenotypes. • Integrating these with mutant phenotypes from model organisms. • Providing reasoner-enabled semantic tools which facilitate data-mining of phenotypic diversity and discovery of candidate genes for evolutionary phenotype transitions.
  • 3. Phenoscape Knowledgebase • ~4 million asserted semantic links (+ 7 million inferred) • 52 fish systematics publications • 4700 morphological characters • 11,000 states + ontological descriptions (EQ) • 2500 referenced taxa • ZFIN • 3900 genes, 6800 genotypes • 30000 experimental phenotype annotations • 13 ontologies • ~80,000 terms
  • 4. Workflow for phenotype annotation 3. Character annotation 2. Students: by experts: Entry of Manual entry of free text phenotypes using character descriptions, Phenex matrix, taxon list, specimens and museum numbers using Phenex 4. Phenoscape Knowledgebase: OBD, data services, web application 501,862 1. Students: gather publications (scan phenotypes for hard copies, produce OCR PDFs) taxa Dahdul et al., 2010 PLoS ONE Text
  • 5. Knowledgebase architecture Knowledgebase User Inteface External web sites Web Application for Exploration & Mining and client (Ruby on Rails, JavaScript) applications Knowledgebase Data Services API (REST) OBD Programming API OBD Reasoner (Java) Teleost Taxonomy Ontology (TTO) Knowledgebase (OBD) (PostgreSQL) Phenotypic Anatomy Quality Ontology Ontologies (PATO) (ZFA, TAO) Genes & genotypes Homology assertions Mutant EQ phenotypes Evolutionary EQ Phenotypes NeXML OBO Library from Zebrafish Model (through annotation) Organism Database Phenex Skeletal Character Data (Evolutionary EQ (from phylogenetic annotation) treatments in literature)
  • 6. OBD: Ontology-Based Database • Stores data and ontologies in combined semantic model - triple based • Reasoner executes inference rules as SQL queries - results iteratively added to database • Supports class expressions based on property restrictions, intersections, unions; transitive properties, property chains, and subsumption • Provenance-tracking via reification
  • 7. Reasoning across logical relationships Brachyplatystoma exhibits some round that capapretum inheres_in some ethmoid cartilage influences some split that tfap2a ts213/ts213 inheres_in some ethmoid cartilage
  • 8. Reasoning across logical relationships tfap2a ethmoid Brachyplatystoma cartilage round variant_of is_a inheres_in is_a Brachyplatystoma exhibits some round that inheres_in split capapretum inheres_in some ethmoid cartilage is_a influences some split that tfap2a ts213/ts213 inheres_in some ethmoid cartilage
  • 9. Reasoning across logical relationships sequence-specific DNA olfactory binding transcription factor activity chondrocranium region cartilage Pimelodidae shape has_function part_of is_a is_a is_a is_a tfap2a ethmoid Brachyplatystoma cartilage round variant_of is_a inheres_in is_a Brachyplatystoma exhibits some round that inheres_in split capapretum inheres_in some ethmoid cartilage is_a influences some split that tfap2a ts213/ts213 inheres_in some ethmoid cartilage
  • 10. Demo
  • 11. Phenotype variation in taxa (left) vs. zebrafish mutants (right) cardiovascular digestive skeletal is_a is_a is_a endocrine sensory is_a is_a anatomical is_a hematopoietic respiratory is_a system is_a is_a immune is_a is_a is_a is_a liver and biliary reproductive renal musculature nervous >85% 20-30% 15-19% 10-14% 5-9% 1-4% <1% Distributed across anatomical systems
  • 12. Global view of skeletal data 4,-62+/0.123" viewed, summarized, synthesized, at a scale not possible otherwise. =">03?:.97+9,"9@+9,"3A2,2?07" ;070.57:8+/0.123" =">9+.2B"C73" ;5170</0.123" =""4.97+-1" 489.9:+/0.123" 456.+7+/0.123" *+,-.+/0.123" Image from Sabaj-Perez !" #!" $!" %!" &!" '!" (!" )!" Skeletal variation across taxa and regions
  • 13. Quantify phenotypic similarity Similarity Taxon Candidate Gene Subsuming Taxon (IC) phenotype gene phenotype phenotype 13.43 Eels gill rakers, absent eda gill rakers, absent gill rakers count lateral line, 12.85 Minytrema lateral line, absent pcsk5a lateral line, size reduced 12.44 Siluriformes basihyal, absent brpf1 basihyal, absent basihyal, count ceratobranchial 5 ceratobranchial 11.32 Gyrinocheilus eda tooth, count teeth, absent teeth, absent 11.11 Siluriformes scales, absent eda scales, absent scales, count dermatocranium, 9.91 Siluriformes opercle, shape edn1 maxilla, shape shape 9.19 Mola caudal fin, absent yap1 median fin, absent median fin, count 9.19 Gonorynchiformes dorsal fin, absent tf1p2a median fin, absent median fin, count 5.17 Siluriformes eye, reduced pbx2 eye, small eye, size
  • 14. Summary Semantic framework and reasoning tools provide: • Powerful queries not previously possible for evolutionary phenotype data • Meaningful integration with model organism phenotypic and genetic data
  • 15. Acknowledgments Phenoscape Workshop Participants National Science Foundation (BDI-0641025) & Contributors ! Arhat Abzhanov National Evolutionary Synthesis Center ! ! Michael Ashburner Judith Blake ! Stan Blum ! Quentin Cronk Contributors to Teleost Ontologies Curators: ! Mário de Pinna ! Andy Deans ! Gloria Arratia Miles Coburn ! George Gkoutos ! Melissa Haendel ! Stan Blum ! Jeff Engemen ! Hopi Hoekstra ! Miles Coburn ! Kevin Conway ! Terry Grande ! Hans Hofmann ! Elizabeth Jockusch ! Wasila Dahdul ! Eric Hilton ! Elizabeth Kellogg ! Mário de Pinna ! Jeff Engemen ! John Lundberg ! Chuck Kimmel ! Suzanna Lewis ! Bill Eschmeyer ! Paula Mabee ! Anne Maglia ! Terry Grande ! Melissa Haendel ! Richard Mayden ! Austin Mast ! Brian Hall ! Chris Mungall ! Mark Sabaj ! Martin Ramirez ! Eric Hilton ! John Lundberg Sandrine Tercerie ! Sue Rhee ! Richard Mayden ! Martin Ringwald ! Mark Sabaj Pérez ! Nelson Rios ! Brian Sidlauskas ! Mark Sabaj Pérez ! Richard Vari ! Eric Segerdell ! Jacqueline Webb ! Brian Sidlauskas ! Edward Wiley ! Barry Smith ! David Stern ! Peter Vize ! Gunter Wagner ! Nicole Washington ! Edward Wiley