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Linked biology – from phenotypes towards phylogenetic trees

Linked biology – from phenotypes towards phylogenetic trees

MSc Dissertation presented to the Post Graduate Program of the Institute of Computing of the University of Campinas to obtain a Mestre degree in Computer Science.

Eduardo Miranda

November 22, 2013
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  1. Linked biology – from phenotypes towards phylogenetic trees Eduardo de

    Paula Miranda Advisor: Prof. Dr. André Santanchè Institute of Computing Unicamp November 22, 2013
  2. Outline 2 1.  Introduction a.  Motivation b.  Goal 2.  Related

    work 3.  Our approach 4.  Conclusion and Future work
  3. Motivation 3 A large number of studies in biology result

    in the production of a huge amount of data, for example: •  Phenotype descriptions •  Trees of species •  Trees of genes •  DNA sequence •  RNA sequence •  etc.
  4. Motivation 4 A large number of studies in biology result

    in the production of a huge amount of data, for example: •  Phenotype descriptions •  Trees of species •  Trees of genes •  DNA sequence •  RNA sequence •  etc.
  5. Motivation 5 Phenotype are: •  A set of observable physical

    characteristics and behavior of an individual, resulting from the interaction of its genotype (genetic makeup) with the environment.
  6. Motivation 6 Phenotype are: •  A set of observable physical

    characteristics and behavior of an individual, resulting from the interaction of its genotype (genetic makeup) with the environment. •  Eye color •  Hair color •  The sound of your voice
  7. Motivation 8 Phenotype descriptions are •  Traditionally documented in natural

    language. •  Typically produced as independent entities.
  8. Motivation 9 As a consequence, this wealth of information has

    been largely •  Unavailable for computational comparisons across studies. •  Integration with other biological knowledge.
  9. Motivation 10 Ontologies are one of the promising choices to

    link and express explicitly the existing knowledge in biology.
  10. Goal 11 Our challenge lies in How to take advantage

    of the existing patrimony of data collected and develop techniques for support converting it into a new ontology- based representation.
  11. Mapping CCS → EQ 14 Character / character-state (C,CS) dorsal

    fin shape semicircular triangular linear Character States
  12. Mapping CCS → EQ 15 Ontology – Phenotype and Trait

    Ontology (PATO) shape 2D shape 3D shape morphology size structure semicircular triangular quadrangular aliform subClassOf subClassOf subClassOf subClassOf
  13. Mapping CCS → EQ 16 shape 2D shape 3D shape

    morphology size structure semicircular triangular quadrangular aliform subClassOf subClassOf subClassOf subClassOf Ontology – Phenotype and Trait Ontology (PATO) Definition: A 2-D shape quality that have shape or form of half a circle
  14. Mapping CCS → EQ 17 shape 2D shape 3D shape

    morphology size structure semicircular triangular quadrangular aliform subClassOf subClassOf subClassOf subClassOf Ontology – Phenotype and Trait Ontology (PATO) Definition: A 2-D shape quality that have shape or form of half a circle
  15. Mapping CCS → EQ 18 shape 2D shape 3D shape

    morphology size structure semicircular triangular quadrangular aliform subClassOf subClassOf subClassOf subClassOf Ontology – Phenotype and Trait Ontology (PATO) Definition: A 2-D shape quality that have shape or form of half a circle
  16. Mapping CCS → EQ 19 shape 2D shape 3D shape

    morphology size structure semicircular triangular quadrangular aliform subClassOf subClassOf subClassOf subClassOf Ontology – Phenotype and Trait Ontology (PATO) Definition: A 2-D shape quality that have shape or form of half a circle
  17. Mapping CCS → EQ 20 shape 2D shape 3D shape

    morphology size structure semicircular triangular quadrangular aliform subClassOf subClassOf subClassOf subClassOf Ontology – Phenotype and Trait Ontology (PATO) Definition: A 2-D shape quality that have shape or form of half a circle
  18. Mapping CCS → EQ 21 The benefits of using an

    ontology include •  Standardization of terminology •  Explicit definitions of concepts •  The creation of structured representations of information that facilitate computability.
  19. Mapping CCS → EQ 22 Ontology : Entity – Quality

    (EQ) Anatomical Ontology Phenotype and Trait Ontology (PATO) + Entity Quality
  20. Mapping CCS → EQ 24 Vertebrate Skeletal Anatomy Ontology (VSAO)

    http://purl.obolibrary.org/obo/VSAO_??????? Character dorsal fin shape circular dorsal fin (VSAO:0000165) State Entity
  21. Mapping CCS → EQ 25 Vertebrate Skeletal Anatomy Ontology (VSAO)

    http://purl.obolibrary.org/obo/VSAO_??????? Character dorsal fin shape circular dorsal fin (VSAO:0000165) State Entity
  22. Mapping CCS → EQ 26 Vertebrate Skeletal Anatomy Ontology (VSAO)

    http://purl.obolibrary.org/obo/VSAO_??????? Phenotype And Trait Ontology (PATO) http://purl.obolibrary.org/obo/PATO_??????? Character dorsal fin shape circular dorsal fin (VSAO:0000165) circular (PATO:0000411) 2D shape (PATO:0002006) subClassOf State Entity Quality shape (PATO:0000052) subClassOf
  23. Mapping CCS → EQ 27 Vertebrate Skeletal Anatomy Ontology (VSAO)

    http://purl.obolibrary.org/obo/VSAO_??????? Phenotype And Trait Ontology (PATO) http://purl.obolibrary.org/obo/PATO_??????? Character dorsal fin shape circular dorsal fin (VSAO:0000165) circular (PATO:0000411) 2D shape (PATO:0002006) subClassOf State Entity Quality shape (PATO:0000052) subClassOf
  24. Mapping CCS → EQ 28 Vertebrate Skeletal Anatomy Ontology (VSAO)

    http://purl.obolibrary.org/obo/VSAO_??????? Phenotype And Trait Ontology (PATO) http://purl.obolibrary.org/obo/PATO_??????? Character dorsal fin shape circular dorsal fin (VSAO:0000165) circular (PATO:0000411) 2D shape (PATO:0002006) subClassOf State Entity Quality shape (PATO:0000052) subClassOf
  25. Mapping CCS → EQ 29 Vertebrate Skeletal Anatomy Ontology (VSAO)

    http://purl.obolibrary.org/obo/VSAO_??????? Phenotype And Trait Ontology (PATO) http://purl.obolibrary.org/obo/PATO_??????? Character dorsal fin shape circular dorsal fin (VSAO:0000165) circular (PATO:0000411) 2D shape (PATO:0002006) subClassOf State Entity Quality shape (PATO:0000052) subClassOf
  26. Mapping CCS → EQ 30 The mapping of character states

    into EQs makes this difficult in two ways. 1.  The mapping between a character state and an EQ is not necessarily one-to-one.
  27. Mapping CCS → EQ 31 The mapping of character states

    into EQs makes this difficult in two ways. 1.  The mapping between a character state and an EQ is not necessarily one-to-one. Pattern of the end of tail banded or uniformly dark uniform pale yellow or white
  28. Mapping CCS → EQ 32 The mapping of character states

    into EQs makes this difficult in two ways. 1.  The mapping between a character state and an EQ is not necessarily one-to-one. Pattern of the end of tail banded or uniformly dark uniform pale yellow or white
  29. Mapping CCS → EQ 33 The mapping of character states

    into EQs makes this difficult in two ways. 1.  The mapping between a character state and an EQ is not necessarily one-to-one. Pattern of the end of tail banded or uniformly dark uniform pale yellow or white
  30. Mapping CCS → EQ 34 The mapping of character states

    into EQs makes this difficult in two ways. 2.  In the EQ formalism the attribute that forms part of a traditional character description is implicit in the hierarchical structure of the quality ontology.
  31. Mapping CCS → EQ 35 The mapping of character states

    into EQs makes this difficult in two ways. 2.  In the EQ formalism the attribute that forms part of a traditional character description is implicit in the hierarchical structure of the quality ontology. Character dorsal fin shape circular dorsal fin (VSAO:0000165) circular (PATO:0000411) 2D shape (PATO:0002006) subClassOf State Entity Quality shape (PATO:0000052) subClassOf
  32. Our approach 42 We add an intermediate step between semi-

    structured descriptions and ontologies, remodeling them to a graph abstraction. Ontology Dataspace Linked Graph
  33. Our approach 43 We add an intermediate step between semi-

    structured descriptions and ontologies, remodeling them to a graph abstraction. Ontology Dataspace Linked Graph
  34. Our approach 44 Data interaction Heterogeneous data sources Phenotype descriptions,

    morphological data matrices, phylogenetic tree extraction Graph import LSID linking Character association 2   1   3   4   Linked data Ontologies 5   6   7   Data access DataBase TreeBase Dryad etc. Excel XML CSV RDF Book Mashup DBtune DBPedia Jamendo US Census Data Project Guten- berg DBLP FOAF Revyu Music- brainz Geo- names world Fact book
  35. Our approach 45 Data interaction Heterogeneous data sources Phenotype descriptions,

    morphological data matrices, phylogenetic tree extraction Graph import LSID linking Character association 2   1   3   4   Linked data Ontologies 5   6   7   Data access DataBase TreeBase Dryad etc. Excel XML CSV RDF Book Mashup DBtune DBPedia Jamendo US Census Data Project Guten- berg DBLP FOAF Revyu Music- brainz Geo- names world Fact book
  36. Our approach 46 Data interaction Heterogeneous data sources Phenotype descriptions,

    morphological data matrices, phylogenetic tree extraction Graph import LSID linking Character association 2   1   3   4   Linked data Ontologies 5   6   7   Data access DataBase TreeBase Dryad etc. Excel XML CSV RDF Book Mashup DBtune DBPedia Jamendo US Census Data Project Guten- berg DBLP FOAF Revyu Music- brainz Geo- names world Fact book
  37. Our approach 47 Data interaction Heterogeneous data sources Phenotype descriptions,

    morphological data matrices, phylogenetic tree extraction Graph import LSID linking Character association 2   1   3   4   Linked data Ontologies 5   6   7   Data access DataBase TreeBase Dryad etc. Excel XML CSV RDF Book Mashup DBtune DBPedia Jamendo US Census Data Project Guten- berg DBLP FOAF Revyu Music- brainz Geo- names world Fact book
  38. Our approach 48 Data interaction Heterogeneous data sources Phenotype descriptions,

    morphological data matrices, phylogenetic tree extraction Graph import LSID linking Character association 2   1   3   4   Linked data Ontologies 5   6   7   Data access DataBase TreeBase Dryad etc. Excel XML CSV RDF Book Mashup DBtune DBPedia Jamendo US Census Data Project Guten- berg DBLP FOAF Revyu Music- brainz Geo- names world Fact book
  39. Our approach 49 Data interaction Heterogeneous data sources Phenotype descriptions,

    morphological data matrices, phylogenetic tree extraction Graph import LSID linking Character association 2   1   3   4   Linked data Ontologies 5   6   7   Data access DataBase TreeBase Dryad etc. Excel XML CSV RDF Book Mashup DBtune DBPedia Jamendo US Census Data Project Guten- berg DBLP FOAF Revyu Music- brainz Geo- names world Fact book
  40. Our approach 50 Data interaction Heterogeneous data sources Phenotype descriptions,

    morphological data matrices, phylogenetic tree extraction Graph import LSID linking Character association 2   1   3   4   Linked data Ontologies 5   6   7   Data access DataBase TreeBase Dryad etc. Excel XML CSV RDF Book Mashup DBtune DBPedia Jamendo US Census Data Project Guten- berg DBLP FOAF Revyu Music- brainz Geo- names world Fact book
  41. Our approach 51 Data interaction Heterogeneous data sources Phenotype descriptions,

    morphological data matrices, phylogenetic tree extraction Graph import LSID linking Character association 2   1   3   4   Linked data Ontologies 5   6   7   Data access DataBase TreeBase Dryad etc. Excel XML CSV RDF Book Mashup DBtune DBPedia Jamendo US Census Data Project Guten- berg DBLP FOAF Revyu Music- brainz Geo- names world Fact book
  42. Our approach 52 Data interaction Heterogeneous data sources Phenotype descriptions,

    morphological data matrices, phylogenetic tree extraction Graph import LSID linking Character association 2   1   3   4   Linked data Ontologies 5   6   7   Data access DataBase TreeBase Dryad etc. Excel XML CSV RDF Book Mashup DBtune DBPedia Jamendo US Census Data Project Guten- berg DBLP FOAF Revyu Music- brainz Geo- names world Fact book
  43. Our approach 53 nostrils' form transversal section of the tail

    nuchal scales Varanus albiguralis 2 1 2 Varanus brevicauda 1 2 1 Nostrils' form 1 – well round 2 – oval or split-like Transversal section of the tail 1 – laterally compressed 2 – roundish Nuchal scales 1 – same size than head scales 2 – bigger than head scales Morphological data matrices Characters Character-States Taxon Assigned States
  44. Our approach 54 nostrils' form transversal section of the tail

    nuchal scales Varanus albiguralis 2 1 2 Varanus brevicauda 1 2 1 Nostrils' form 1 – well round 2 – oval or split-like Transversal section of the tail 1 – laterally compressed 2 – roundish Nuchal scales 1 – same size than head scales 2 – bigger than head scales Morphological data matrices Characters Character-States Taxon Assigned States
  45. Our approach 55 nostrils' form transversal section of the tail

    nuchal scales Varanus albiguralis 2 1 2 Varanus brevicauda 1 2 1 Nostrils' form 1 – well round 2 – oval or split-like Transversal section of the tail 1 – laterally compressed 2 – roundish Nuchal scales 1 – same size than head scales 2 – bigger than head scales Morphological data matrices Characters Character-States Taxon Assigned States
  46. Our approach 56 nostrils' form transversal section of the tail

    nuchal scales Varanus albiguralis 2 1 2 Varanus brevicauda 1 2 1 Nostrils' form 1 – well round 2 – oval or split-like Transversal section of the tail 1 – laterally compressed 2 – roundish Nuchal scales 1 – same size than head scales 2 – bigger than head scales Morphological data matrices Characters Character-States Taxon Assigned States
  47. Our approach 57 nostrils' form transversal section of the tail

    nuchal scales Varanus albiguralis 2 1 2 Varanus brevicauda 1 2 1 Nostrils' form 1 – well round 2 – oval or split-like Transversal section of the tail 1 – laterally compressed 2 – roundish Nuchal scales 1 – same size than head scales 2 – bigger than head scales Morphological data matrices Characters Character-States Taxon Assigned States
  48. Our approach 58 Structure Descriptive Data (SDD) CategoricalCharacter   id=“c6”

      States   StateDefini9on   id=“s12”   “well  round”   “Nostrils  look  like  a  quite  per...”   Label   Detail   StateDefini9on   id=“s13”   “oval  or  split-­‐like”   “Nostrils  are  not  perfectly  rou...”   Label   Detail   “nostrils'  form”   “Monitors'  nostrils  may  have  different  forms...”   Label   Detail   Representa9on   Dataset   Datasets   “V.  albiguralis”   “White-­‐throated  monitor.  DistribuIon:  Africa  (West...”   Label   Detail   Representa9on   CodedDescrip9on   id=“D1”   SummaryData   Categorical   ref=“c6”   State   ref=“s13”   Characters Character-States Taxon Assigned States
  49. Our approach 59 Structure Descriptive Data (SDD) CategoricalCharacter   id=“c6”

      States   StateDefini9on   id=“s12”   “well  round”   “Nostrils  look  like  a  quite  per...”   Label   Detail   StateDefini9on   id=“s13”   “oval  or  split-­‐like”   “Nostrils  are  not  perfectly  rou...”   Label   Detail   “nostrils'  form”   “Monitors'  nostrils  may  have  different  forms...”   Label   Detail   Representa9on   Dataset   Datasets   “V.  albiguralis”   “White-­‐throated  monitor.  DistribuIon:  Africa  (West...”   Label   Detail   Representa9on   CodedDescrip9on   id=“D1”   SummaryData   Categorical   ref=“c6”   State   ref=“s13”   Characters Character-States Taxon Assigned States
  50. Our approach 60 Structure Descriptive Data (SDD) CategoricalCharacter   id=“c6”

      States   StateDefini9on   id=“s12”   “well  round”   “Nostrils  look  like  a  quite  per...”   Label   Detail   StateDefini9on   id=“s13”   “oval  or  split-­‐like”   “Nostrils  are  not  perfectly  rou...”   Label   Detail   “nostrils'  form”   “Monitors'  nostrils  may  have  different  forms...”   Label   Detail   Representa9on   Dataset   Datasets   “V.  albiguralis”   “White-­‐throated  monitor.  DistribuIon:  Africa  (West...”   Label   Detail   Representa9on   CodedDescrip9on   id=“D1”   SummaryData   Categorical   ref=“c6”   State   ref=“s13”   Characters Character-States Taxon Assigned States
  51. Our approach 61 Structure Descriptive Data (SDD) CategoricalCharacter   id=“c6”

      States   StateDefini9on   id=“s12”   “well  round”   “Nostrils  look  like  a  quite  per...”   Label   Detail   StateDefini9on   id=“s13”   “oval  or  split-­‐like”   “Nostrils  are  not  perfectly  rou...”   Label   Detail   “nostrils'  form”   “Monitors'  nostrils  may  have  different  forms...”   Label   Detail   Representa9on   Dataset   Datasets   “V.  albiguralis”   “White-­‐throated  monitor.  DistribuIon:  Africa  (West...”   Label   Detail   Representa9on   CodedDescrip9on   id=“D1”   SummaryData   Categorical   ref=“c6”   State   ref=“s13”   Characters Character-States Taxon Assigned States
  52. Our approach 62 Structure Descriptive Data (SDD) CategoricalCharacter   id=“c6”

      States   StateDefini9on   id=“s12”   “well  round”   “Nostrils  look  like  a  quite  per...”   Label   Detail   StateDefini9on   id=“s13”   “oval  or  split-­‐like”   “Nostrils  are  not  perfectly  rou...”   Label   Detail   “nostrils'  form”   “Monitors'  nostrils  may  have  different  forms...”   Label   Detail   Representa9on   Dataset   Datasets   “V.  albiguralis”   “White-­‐throated  monitor.  DistribuIon:  Africa  (West...”   Label   Detail   Representa9on   CodedDescrip9on   id=“D1”   SummaryData   Categorical   ref=“c6”   State   ref=“s13”   Characters Character-States Taxon Assigned States
  53. Our approach Morphological data matrices Structure Descriptive Data (SDD) 63

    OTU Type OTU Label Detail Character-State Type State Label Detail Type Character Detail Character Characters Character-States Taxon Assigned States CategoricalCharacter, id=“c6”( States, StateDefini2on, id=“s12”( “well(round”( “Nostrils(look(like(a(quite(per...”( Label, Detail, StateDefini2on, id=“s13”( “oval(or(split<like”( “Nostrils(are(not(perfectly(rou...”( Label, Detail, “nostrils'(form”( “Monitors'(nostrils(may(have(different(forms...”( Label, Detail, Representa2on, Dataset, Datasets, “V.(albiguralis”( “White<throated(monitor.(DistribuIon:(Africa((West...”( Label, Detail, Representa2on, CodedDescrip2on, id=“D1”( SummaryData, Categorical, ref=“c6”( State, ref=“s13”( nostrils' form transversal section of the tail nuchal scales Varanus albiguralis 2 1 2 Varanus brevicauda 1 2 1 Nostrils' form 1 – well round 2 – oval or split-like Transversal section of the tail 1 – laterally compressed 2 – roundish Nuchal scales 1 – same size than head scales 2 – bigger than head scales 1st Conceptual graph based model
  54. Our approach Morphological data matrices Structure Descriptive Data (SDD) 64

    OTU Type OTU Label Detail Character-State Type State Label Detail Type Character Detail Character Characters Character-States Taxon Assigned States CategoricalCharacter, id=“c6”( States, StateDefini2on, id=“s12”( “well(round”( “Nostrils(look(like(a(quite(per...”( Label, Detail, StateDefini2on, id=“s13”( “oval(or(split<like”( “Nostrils(are(not(perfectly(rou...”( Label, Detail, “nostrils'(form”( “Monitors'(nostrils(may(have(different(forms...”( Label, Detail, Representa2on, Dataset, Datasets, “V.(albiguralis”( “White<throated(monitor.(DistribuIon:(Africa((West...”( Label, Detail, Representa2on, CodedDescrip2on, id=“D1”( SummaryData, Categorical, ref=“c6”( State, ref=“s13”( nostrils' form transversal section of the tail nuchal scales Varanus albiguralis 2 1 2 Varanus brevicauda 1 2 1 Nostrils' form 1 – well round 2 – oval or split-like Transversal section of the tail 1 – laterally compressed 2 – roundish Nuchal scales 1 – same size than head scales 2 – bigger than head scales 1st Conceptual graph based model
  55. Our approach Morphological data matrices Structure Descriptive Data (SDD) 65

    OTU Type OTU Label Detail Character-State Type State Label Detail Type Character Detail Character Characters Character-States Taxon Assigned States CategoricalCharacter, id=“c6”( States, StateDefini2on, id=“s12”( “well(round”( “Nostrils(look(like(a(quite(per...”( Label, Detail, StateDefini2on, id=“s13”( “oval(or(split<like”( “Nostrils(are(not(perfectly(rou...”( Label, Detail, “nostrils'(form”( “Monitors'(nostrils(may(have(different(forms...”( Label, Detail, Representa2on, Dataset, Datasets, “V.(albiguralis”( “White<throated(monitor.(DistribuIon:(Africa((West...”( Label, Detail, Representa2on, CodedDescrip2on, id=“D1”( SummaryData, Categorical, ref=“c6”( State, ref=“s13”( nostrils' form transversal section of the tail nuchal scales Varanus albiguralis 2 1 2 Varanus brevicauda 1 2 1 Nostrils' form 1 – well round 2 – oval or split-like Transversal section of the tail 1 – laterally compressed 2 – roundish Nuchal scales 1 – same size than head scales 2 – bigger than head scales 1st Conceptual graph based model
  56. 7 distinct morphological descriptions: •  genus Varanus •  Varanus gouldii

    •  Varanus indicus •  Varanus prasinus •  Varanus salvator •  Varanus spiny •  Varanus timorensis Our approach 66
  57. 7 distinct morphological descriptions: •  genus Varanus •  Varanus gouldii

    •  Varanus indicus •  Varanus prasinus •  Varanus salvator •  Varanus spiny •  Varanus timorensis Our approach 67
  58. 7 distinct morphological descriptions: •  genus Varanus •  Varanus gouldii

    •  Varanus indicus •  Varanus prasinus •  Varanus salvator •  Varanus spiny •  Varanus timorensis Our approach 68
  59. 7 distinct morphological descriptions: •  genus Varanus •  Varanus gouldii

    •  Varanus indicus •  Varanus prasinus •  Varanus salvator •  Varanus spiny •  Varanus timorensis Our approach 69
  60. 7 distinct morphological descriptions: •  genus Varanus •  Varanus gouldii

    •  Varanus indicus •  Varanus prasinus •  Varanus salvator •  Varanus spiny •  Varanus timorensis Our approach 70
  61. 7 distinct morphological descriptions: •  genus Varanus •  Varanus gouldii

    •  Varanus indicus •  Varanus prasinus •  Varanus salvator •  Varanus spiny •  Varanus timorensis Our approach 71
  62. 7 distinct morphological descriptions: •  genus Varanus •  Varanus gouldii

    •  Varanus indicus •  Varanus prasinus •  Varanus salvator •  Varanus spiny •  Varanus timorensis Our approach 72
  63. 7 distinct morphological descriptions: •  genus Varanus •  Varanus gouldii

    •  Varanus indicus •  Varanus prasinus •  Varanus salvator •  Varanus spiny •  Varanus timorensis Our approach 73
  64. 7 distinct morphological descriptions: •  genus Varanus •  Varanus gouldii

    •  Varanus indicus •  Varanus prasinus •  Varanus salvator •  Varanus spiny •  Varanus timorensis Our approach 74
  65. 7 distinct morphological descriptions: •  genus Varanus •  Varanus gouldii

    •  Varanus indicus •  Varanus prasinus •  Varanus salvator •  Varanus spiny •  Varanus timorensis Our approach 75
  66. Our approach 76 Varanus prasinus smooth, unkeeled granular to slightly

    keeled triangular keeled, hull-shaped strongly keeled same size than head scales bigger than head scales Varanus beccarii Varanus bogerti Varanus komodoensis nuchal scales nuchal scales nuchal  scales nuchal  scales nuchal  scales nuchal scales Prasinus.sdd Varanus.sdd OTU Type OTU Label Detail Character-State Type State Label Detail Type Character Detail Character
  67. Our approach 77 Varanus prasinus smooth, unkeeled granular to slightly

    keeled triangular keeled, hull-shaped strongly keeled same size than head scales bigger than head scales Varanus beccarii Varanus bogerti Varanus komodoensis nuchal  scales nuchal  scales nuchal  scales nuchal  scales nuchal  scales nuchal  scales Prasinus.sdd Varanus.sdd OTU Type OTU Label Detail Character-State Type State Label Detail Type Character Detail Character
  68. Our approach 78 Data interaction Heterogeneous data sources Phenotype descriptions,

    morphological data matrices, phylogenetic tree extraction Graph import LSID linking Character association 2   1   3   4   Linked data Ontologies 5   6   7   Data access DataBase TreeBase Dryad etc. Excel XML CSV RDF Book Mashup DBtune DBPedia Jamendo US Census Data Project Guten- berg DBLP FOAF Revyu Music- brainz Geo- names world Fact book
  69. Our approach OTU Type OTU Label Detail Character-State Type State

    Label Detail Type Character Detail Character 79 Similarity Index 1st Conceptual graph based model
  70. Our approach OTU Type OTU Label Detail Character-State Type State

    Label Detail Type Character Detail Character 1st Conceptual graph based model 80 Similarity Index 2nd Conceptual graph based model OTU Type OTU Label Detail Character Type Character Label Detail Character-State Type Character-State ! Label Detail
  71. Our approach OTU Type OTU Label Detail Character-State Type State

    Label Detail Type Character Detail Character 81 Similarity Index 1st Conceptual graph based model 2nd Conceptual graph based model OTU Type OTU Label Detail Character Type Character Label Detail Character-State Type Character-State ! Label Detail
  72. Our approach OTU Type OTU Label Detail Character-State Type State

    Label Detail Type Character Detail Character 82 Similarity Index 1st Conceptual graph based model 2nd Conceptual graph based model OTU Type OTU Label Detail Character Type Character Label Detail Character-State Type Character-State ! Label Detail
  73. Our approach OTU Type OTU Label Detail Character-State Type State

    Label Detail Type Character Detail Character 83 Similarity Index 1st Conceptual graph based model 2nd Conceptual graph based model OTU Type OTU Label Detail Character Type Character Label Detail Character-State Type Character-State ! Label Detail
  74. Our approach TreeEdge OTU Type OTU Label Detail Character Type

    Character Label Detail HTU Type HTU Type TreeEdge Character-State Type Character-State Label Detail Character-State Type Character-State OTU Type OTU Label Detail Character-State Type State Label Detail Type Character Detail Character 84 Similarity Index 1st Conceptual graph based model 2nd Conceptual graph based model
  75. Our approach 89 Marattia Pseudosporochnus Zygopteris Equisetum Ophioglossum Webbing within

    the LBS Webbing of the terminal units Branchiness of the LBS 0 1
  76. Our approach 90 unbranched Marattia Pseudosporochnus Zygopteris Equisetum Ophioglossum Webbing

    within the LBS Webbing of the terminal units Branchiness of the LBS 0 1
  77. Our approach 91 unbranched Marattia Pseudosporochnus Zygopteris Equisetum Ophioglossum Webbing

    within the LBS Webbing of the terminal units Branchiness of the LBS 0 1
  78. Our approach 92 Present (leaflets) unbranched Marattia Pseudosporochnus Zygopteris Equisetum

    Ophioglossum Webbing within the LBS Webbing of the terminal units Branchiness of the LBS 0 1
  79. Our approach 93 Present (leaflets) unbranched Marattia Pseudosporochnus Zygopteris Equisetum

    Ophioglossum Webbing within the LBS Webbing of the terminal units Branchiness of the LBS 0 1
  80. Our approach 94 absent Present (leaflets) unbranched Marattia Pseudosporochnus Zygopteris

    Equisetum Ophioglossum Webbing within the LBS Webbing of the terminal units Branchiness of the LBS 0 1
  81. Our approach 95 Similarity Index Computes the similarity degree between

    two morphological character descriptions which will represent how close related they are.
  82. Our approach 96 Similarity Index Scenario 1 Extent of the

    planated parts within the LBS Pseudosporochnus restricted to the extremities Author A Planation Pseudosporochnus restricted to the extremities Author B
  83. Our approach 97 Similarity Index Scenario 1 Extent of the

    planated parts within the LBS Pseudosporochnus restricted to the extremities Author A Planation Pseudosporochnus restricted to the extremities Author B Scenario 2 Planation of vegetative leaves Pseudosporochnus inapplicable     Author C Planation of vegetative leaves Pseudosporochnus restricted to the extremities Author D
  84. Our approach 102 Similarity Index – Part I 1 2

    3 4 5 A B NA = { 1, 3, 5 } Taxon Character
  85. Our approach 103 1 2 3 4 5 A B

    NA = { 1, 3, 5 } Similarity Index – Part I Taxon Character
  86. Our approach 104 1 2 3 4 5 A B

    NA = { 1, 3, 5 } NB = { 2, 4, 5 } Similarity Index – Part I Taxon Character
  87. Our approach 105 1 2 3 4 5 A B

    NA = { 1, 3, 5 } NB = { 2, 4, 5 } Similarity Index – Part I Taxon Character
  88. Our approach 106 1 2 3 4 5 A B

    circular rounded Similarity Index – Part II round Taxon Character
  89. Our approach 107 1 2 3 4 5 B circular

    rounded Similarity Index – Part II round A Taxon Character
  90. Our approach 108 1 2 3 4 5 B circular

    rounded Similarity Index – Part II round A LA = { circular, rounded, round } Taxon Character
  91. Our approach 109 1 2 3 4 5 A circular

    rounded Similarity Index – Part II round LA = { circular, rounded, round } B Taxon Character
  92. Our approach 110 1 2 3 4 5 A circular

    rounded Similarity Index – Part II round LA = { circular, rounded, round } LB = { circular, triangular, ovate } B Taxon Character
  93. Our approach 111 1 2 3 4 5 A circular

    rounded Similarity Index – Part II round LA = { circular, rounded, round } LB = { circular, triangular, ovate } B Taxon Character
  94. Our approach 112 Practical Experiment of the Similarity Measure Author

    1 •  Cauline cladotaxy •  Protoxylem position within the cauline stele •  Xylem configuration in the rachis •  Xylem configuration in the leaflets •  Development of the LBS •  Organotaxy of the LBS •  Presence of planated parts within the LBS •  Extent of the planation
  95. Our approach 113 Practical Experiment of the Similarity Measure Author

    1 •  Cauline cladotaxy •  Protoxylem position within the cauline stele •  Xylem configuration in the rachis •  Xylem configuration in the leaflets •  Development of the LBS •  Organotaxy of the LBS •  Presence of planated parts within the LBS •  Extent of the planation Author 2 •  Cauline cladotaxy •  Protoxylem position within the cauline stele •  Xylem configuration in the rachis •  Xylem configuration in the leaflets •  Development of the foliar organ •  Phyllotaxy •  Planation
  96. Our approach 114 Cauline cladotaxy Protoxylem position w ithin the

    cauline stele Organotaxy of the LBS Xylem conguration in the leaets Planation Development of the foliar organ Phyllotaxy Xylem conguration in the rachis Extent of the planation Presence of planated parts w ithin the LBS Development of the LBS
  97. Our approach 115 Cauline cladotaxy Protoxylem position w ithin the

    cauline stele Organotaxy of the LBS Xylem conguration in the leaets Planation Development of the foliar organ Phyllotaxy Xylem conguration in the rachis Extent of the planation Presence of planated parts w ithin the LBS Development of the LBS
  98. Our approach 116 Cauline cladotaxy Protoxylem position w ithin the

    cauline stele Organotaxy of the LBS Xylem conguration in the leaets Planation Development of the foliar organ Phyllotaxy Xylem conguration in the rachis Extent of the planation Presence of planated parts w ithin the LBS Development of the LBS
  99. Our approach 117 An algorithm to trace changes in traits

    of phylogenetic trees. absent Present (leaflets) unbranched root Marattia Pseudosporochnus Zygopteris Equisetum Ophioglossum Webbing within the LBS Webbing of the terminal units Branchiness of the LBS 0 1
  100. Our approach 118 An algorithm to trace changes in traits

    of phylogenetic trees. Marattia Webbing within the LBS Webbing of the terminal units Branchiness of the LBS Pseudosporochnus Zygopteris Equisetum Ophioglossum root EvolvedTrait EvolvedTrait 0 1
  101. Conclusions 119 •  The present work explores the availability of

    data that are represented in many standards not often interconnectable and designed and implemented an approach to link and combine these resources. •  Our approach enables us to discover and make explicit the potential semantics raised by linking previously unconnected information.
  102. Contributions 120 •  The design and implementation of a prototype

    to transform phenotype descriptions and phylogenetic trees in graph representations. •  An heuristic similarity measure. •  A visual tool prototype to analyze chaacters correlation . •  An algorithm to trace changes in traits.
  103. Publications 121 •  Unifying phenotypes to support semantic descriptions. In

    Proceedings of the 6th Seminar on Ontology Research in Brazil, volume 1041, pages 154 – 165, September 2013. •  Coupling phenotype descriptions and phylogenetic trees: from SDD to ontologies via graph databases. Talk at TDWG 2013 Annual Conference Florence, Italy, 28th of October – 1st of November 2013.
  104. Extensions 122 •  The incorporation of morphological descriptions stored in

    other knowledge bases. •  Further investigations in the similarity measure. •  Extend the correlations analysis to the relation between character nodes and ontology terms.
  105. Acknowledgments 123 •  Prof. André Santanchè •  Anaïs Grand and

    Régine Vignes Lebbe •  Laboratory of Information Systems (LIS) •  IC infrastructure and staff •  Financial support: •  CNPq (grant 138197/2011-3) •  Microsoft Research FAPESP Virtual Institute (NavScales Project) •  CNPq (MuZOO Project and PRONEX-FAPESP) •  INCT in Web Science (CNPq 557.128/2009-9) •  CAPES •  FAPESP
  106. Linked biology – from phenotypes towards phylogenetic trees Eduardo de

    Paula Miranda Advisor: Prof. Dr. André Santanchè Institute of Computing Unicamp November 22, 2013