Creating computable definitions for clades using the Web Ontology Language (OWL)

Ef10e56567f5d6e20bc3f7f4ab4e3254?s=47 Gaurav Vaidya
December 06, 2016

Creating computable definitions for clades using the Web Ontology Language (OWL)

Presented at TDWG 2016 as part of a symposium on semantics

Ef10e56567f5d6e20bc3f7f4ab4e3254?s=128

Gaurav Vaidya

December 06, 2016
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  1. December 6, 2016 Computable definitions for clades Gaurav Vaidya, Hilmar

    Lapp, Nico Cellinese
  2. Campanula latifolia Lobelia cardinalis

  3. Campanula latifolia Lobelia cardinalis

  4. None
  5. None
  6. Campanula latifolia Campanula rotundifolia Lobelia coronopifolia Lobelia cardinalis Cyphocarpus rigescens

    Chrysanthemum
  7. Campanula latifolia Campanula rotundifolia Lobelia coronopifolia Lobelia cardinalis Cyphocarpus rigescens

    Chrysanthemum
  8. Hinchliff et al. (2016) www.opentreeoflife.org

  9. The Solution: Phyloreferences ✤ Explicit definitions for clades. www.phyloref.org

  10. The Solution: Phyloreferences ✤ Explicit definitions for clades. ✤ Built

    around ancestral relationships, so they always match monophyletic groups. www.phyloref.org
  11. The Solution: Phyloreferences ✤ Explicit definitions for clades. ✤ Built

    around ancestral relationships, so they always match monophyletic groups. ✤ But the group’s composition may change from tree to tree! www.phyloref.org
  12. Campanula latifolia Campanula rotundifolia Lobelia coronopifolia Lobelia cardinalis Cyphocarpus rigescens

    Chrysanthemum
  13. Campanula latifolia Campanula rotundifolia Lobelia coronopifolia Lobelia cardinalis Cyphocarpus rigescens

    Chrysanthemum
  14. Campanula latifolia Campanula rotundifolia Lobelia coronopifolia Lobelia cardinalis Cyphocarpus rigescens

    Chrysanthemum Descendants of the ancestors of Campanula latifolia that exclude the ancestors of Lobelia cardinalis
  15. Campanula latifolia Campanula rotundifolia Lobelia coronopifolia Lobelia cardinalis Cyphocarpus rigescens

    Chrysanthemum Descendants of the ancestors of Campanula latifolia that exclude the ancestors of Lobelia cardinalis
  16. Campanula latifolia Campanula rotundifolia Lobelia coronopifolia Lobelia cardinalis Cyphocarpus rigescens

    Chrysanthemum Descendants of the ancestors of Campanula latifolia that exclude the ancestors of Lobelia cardinalis
  17. Campanula latifolia Campanula rotundifolia Lobelia coronopifolia Lobelia cardinalis Cyphocarpus rigescens

    Chrysanthemum Descendants of the ancestors of Campanula latifolia that exclude the ancestors of Lobelia cardinalis
  18. Campanula latifolia Campanula rotundifolia Lobelia coronopifolia Lobelia cardinalis Cyphocarpus rigescens

    Chrysanthemum Descendants of the ancestors of Campanula latifolia that exclude the ancestors of Lobelia cardinalis
  19. Implementing phyloreferences

  20. Implementing phyloreferences ✤ Could we use off-the-shelf open source tools

    to find clades on phylogenetic trees?
  21. Implementing phyloreferences ✤ Could we use off-the-shelf open source tools

    to find clades on phylogenetic trees? ✤ Could we design a system flexible enough to match many different kinds of phyloreferences?
  22. Implementing phyloreferences ✤ Could we use off-the-shelf open source tools

    to find clades on phylogenetic trees? ✤ Could we design a system flexible enough to match many different kinds of phyloreferences? ✤ Could we create a test set of phyloreferences and their expected matches for testing our software and others?
  23. Web Ontology Language (OWL) ✤ Designed to classify individuals and

    classes based on definitions.
  24. Web Ontology Language (OWL) ✤ Designed to classify individuals and

    classes based on definitions. ✤ e.g. A Maharashtrian is a Person who was born in the Indian state of Maharashtra.
  25. Web Ontology Language (OWL) ✤ Designed to classify individuals and

    classes based on definitions. ✤ e.g. A Maharashtrian is a Person who was born in the Indian state of Maharashtra. ✤ Uses OWL Reasoners to infer unknown facts from known facts.
  26. Reasoning over facts ✤ :Gaurav a :Person

  27. Reasoning over facts ✤ :Gaurav a :Person ✤ :Gaurav :bornIn

    :Mumbai
  28. Reasoning over facts ✤ :Gaurav a :Person ✤ :Gaurav :bornIn

    :Mumbai ✤ :Mumbai :partOf :Maharashtra
  29. Reasoning over facts ✤ :Gaurav a :Person ✤ :Gaurav :bornIn

    :Mumbai ✤ :Mumbai :partOf :Maharashtra ✤ => :Gaurav :bornIn :Maharashtra
  30. Reasoning over facts ✤ :Gaurav a :Person ✤ :Gaurav :bornIn

    :Mumbai ✤ :Mumbai :partOf :Maharashtra ✤ => :Gaurav :bornIn :Maharashtra ✤ Only if :bornIn o :partOf => :bornIn!
  31. Reasoning over facts ✤ :Gaurav a :Person ✤ :Gaurav :bornIn

    :Mumbai ✤ :Mumbai :partOf :Maharashtra ✤ => :Gaurav :bornIn :Maharashtra ✤ Only if :bornIn o :partOf => :bornIn! ✤ => :Gaurav a :Maharashtrian
  32. Campanula latifolia Campanula rotundifolia Lobelia coronopifolia Lobelia cardinalis Cyphocarpus rigescens

    Chrysanthemum
  33. Campanula latifolia Campanula rotundifolia Lobelia coronopifolia Lobelia cardinalis Cyphocarpus rigescens

    Chrysanthemum ✤ :Campanula_latifolia :has_Sibling 
 :Campanula_rotundifolia
  34. Campanula latifolia Campanula rotundifolia Lobelia coronopifolia Lobelia cardinalis Cyphocarpus rigescens

    Chrysanthemum ✤ :Campanula_latifolia :has_Sibling 
 :Campanula_rotundifolia ✤ :Lobelia_coronopifolia :has_Sibling 
 :Lobelia_cardinalis
  35. Campanula latifolia Campanula rotundifolia Lobelia coronopifolia Lobelia cardinalis Cyphocarpus rigescens

    Chrysanthemum ✤ :Campanula_latifolia :has_Sibling 
 :Campanula_rotundifolia ✤ :Lobelia_coronopifolia :has_Sibling 
 :Lobelia_cardinalis
  36. Campanula latifolia Campanula rotundifolia Lobelia coronopifolia Lobelia cardinalis Cyphocarpus rigescens

    Chrysanthemum ✤ :Campanula_latifolia :has_Sibling 
 :Campanula_rotundifolia ✤ :Lobelia_coronopifolia :has_Sibling 
 :Lobelia_cardinalis ✤ :Node_1 a :Node
  37. Campanula latifolia Campanula rotundifolia Lobelia coronopifolia Lobelia cardinalis Cyphocarpus rigescens

    Chrysanthemum ✤ :Campanula_latifolia :has_Sibling 
 :Campanula_rotundifolia ✤ :Lobelia_coronopifolia :has_Sibling 
 :Lobelia_cardinalis ✤ :Node_1 a :Node ✤ :has_Child :Campanula_latifolia
  38. Campanula latifolia Campanula rotundifolia Lobelia coronopifolia Lobelia cardinalis Cyphocarpus rigescens

    Chrysanthemum ✤ :Campanula_latifolia :has_Sibling 
 :Campanula_rotundifolia ✤ :Lobelia_coronopifolia :has_Sibling 
 :Lobelia_cardinalis ✤ :Node_1 a :Node ✤ :has_Child :Campanula_latifolia ✤ :has_Child :Campanula_rotundifolia
  39. Campanula latifolia Campanula rotundifolia Lobelia coronopifolia Lobelia cardinalis Cyphocarpus rigescens

    Chrysanthemum ✤ :Campanula_latifolia :has_Sibling 
 :Campanula_rotundifolia ✤ :Lobelia_coronopifolia :has_Sibling 
 :Lobelia_cardinalis ✤ :Node_1 a :Node ✤ :has_Child :Campanula_latifolia ✤ :has_Child :Campanula_rotundifolia
  40. Campanula latifolia Campanula rotundifolia Lobelia coronopifolia Lobelia cardinalis Cyphocarpus rigescens

    Chrysanthemum ✤ :Campanula_latifolia :has_Sibling 
 :Campanula_rotundifolia ✤ :Lobelia_coronopifolia :has_Sibling 
 :Lobelia_cardinalis ✤ :Node_1 a :Node ✤ :has_Child :Campanula_latifolia ✤ :has_Child :Campanula_rotundifolia
  41. Campanula latifolia Campanula rotundifolia Lobelia coronopifolia Lobelia cardinalis Cyphocarpus rigescens

    Chrysanthemum ✤ :Campanula_latifolia :has_Sibling 
 :Campanula_rotundifolia ✤ :Lobelia_coronopifolia :has_Sibling 
 :Lobelia_cardinalis ✤ :Node_1 a :Node ✤ :has_Child :Campanula_latifolia ✤ :has_Child :Campanula_rotundifolia
  42. Phyloreferences in OWL Descendants of the ancestors of Campanula latifolia

    that exclude the ancestors of Lobelia cardinalis
  43. Phyloreferences in OWL ✤ We’re looking for all the descendants

    of a Node that: Descendants of the ancestors of Campanula latifolia that exclude the ancestors of Lobelia cardinalis
  44. Phyloreferences in OWL ✤ We’re looking for all the descendants

    of a Node that: ✤ :has_Descendant :Campanula_latifolia Descendants of the ancestors of Campanula latifolia that exclude the ancestors of Lobelia cardinalis
  45. Phyloreferences in OWL ✤ We’re looking for all the descendants

    of a Node that: ✤ :has_Descendant :Campanula_latifolia ✤ :excludes_lineage_to :Lobelia_cardinalis Descendants of the ancestors of Campanula latifolia that exclude the ancestors of Lobelia cardinalis
  46. Phyloreferences in OWL ✤ We’re looking for all the descendants

    of a Node that: ✤ :has_Descendant :Campanula_latifolia ✤ :has_Child :Campanula_latifolia ✤ :excludes_lineage_to :Lobelia_cardinalis Descendants of the ancestors of Campanula latifolia that exclude the ancestors of Lobelia cardinalis
  47. Phyloreferences in OWL ✤ We’re looking for all the descendants

    of a Node that: ✤ :has_Descendant :Campanula_latifolia ✤ :has_Child :Campanula_latifolia ✤ :has_Child [:has_Child :Campanula_latifolia] ✤ :excludes_lineage_to :Lobelia_cardinalis Descendants of the ancestors of Campanula latifolia that exclude the ancestors of Lobelia cardinalis
  48. Phyloreferences in OWL ✤ We’re looking for all the descendants

    of a Node that: ✤ :has_Descendant :Campanula_latifolia ✤ :has_Child :Campanula_latifolia ✤ :has_Child [:has_Child :Campanula_latifolia] ✤ :has_Child [:has_Child [:has_Child :Campanula_latifolia]] ✤ :excludes_lineage_to :Lobelia_cardinalis Descendants of the ancestors of Campanula latifolia that exclude the ancestors of Lobelia cardinalis
  49. Phyloreferences in OWL ✤ We’re looking for all the descendants

    of a Node that: ✤ :has_Descendant :Campanula_latifolia ✤ :has_Child :Campanula_latifolia ✤ :has_Child [:has_Child :Campanula_latifolia] ✤ :has_Child [:has_Child [:has_Child :Campanula_latifolia]] ✤ … ✤ :excludes_lineage_to :Lobelia_cardinalis Descendants of the ancestors of Campanula latifolia that exclude the ancestors of Lobelia cardinalis
  50. Phyloreferences in OWL ✤ We’re looking for all the descendants

    of a Node that: ✤ :has_Descendant :Campanula_latifolia ✤ :excludes_lineage_to :Lobelia_cardinalis ✤ Either :has_Sibling :Lobelia_cardinalis Descendants of the ancestors of Campanula latifolia that exclude the ancestors of Lobelia cardinalis
  51. Phyloreferences in OWL ✤ We’re looking for all the descendants

    of a Node that: ✤ :has_Descendant :Campanula_latifolia ✤ :excludes_lineage_to :Lobelia_cardinalis ✤ Either :has_Sibling :Lobelia_cardinalis ✤ Or :has_Sibling that :has_Descendent :Lobelia_cardinalis Descendants of the ancestors of Campanula latifolia that exclude the ancestors of Lobelia cardinalis
  52. Phyloreferences in OWL ✤ We’re looking for all the descendants

    of a Node that: ✤ :has_Descendant :Campanula_latifolia ✤ :excludes_lineage_to :Lobelia_cardinalis Descendants of the ancestors of Campanula latifolia that exclude the ancestors of Lobelia cardinalis
  53. None
  54. What are we building? ✤ Software tools and standards for

    converting phylogenies to logical statements.
  55. What are we building? ✤ Software tools and standards for

    converting phylogenies to logical statements. ✤ Ontologies to make these relationships simple and clear.
  56. What are we building? ✤ Software tools and standards for

    converting phylogenies to logical statements. ✤ Ontologies to make these relationships simple and clear. ✤ Defining terms like excludes_lineage_to so you don’t have to.
  57. What are we building? ✤ Software tools and standards for

    converting phylogenies to logical statements. ✤ Ontologies to make these relationships simple and clear. ✤ Defining terms like excludes_lineage_to so you don’t have to. ✤ Web application and web service to make phyloreferences quick and easy to use.
  58. What are we building? ✤ Software tools and standards for

    converting phylogenies to logical statements. ✤ Ontologies to make these relationships simple and clear. ✤ Defining terms like excludes_lineage_to so you don’t have to. ✤ Web application and web service to make phyloreferences quick and easy to use. ✤ Testing to ensure that phyloreferences match the correct nodes on the tree.
  59. None
  60. None
  61. None
  62. None
  63. None
  64. None
  65. None
  66. None
  67. Conclusions

  68. Conclusions ✤ OWL reasoners can identify parts of a phylogenetic

    tree based on phyloreferences expressed in OWL.
  69. Conclusions ✤ OWL reasoners can identify parts of a phylogenetic

    tree based on phyloreferences expressed in OWL. ✤ But can we make them work fast, through easy-to-use websites and over web services?
  70. Conclusions ✤ OWL reasoners can identify parts of a phylogenetic

    tree based on phyloreferences expressed in OWL. ✤ But can we make them work fast, through easy-to-use websites and over web services? ✤ Continuous testing will make sure that all existing phyloreferences continue to work in the future.
  71. Conclusions ✤ OWL reasoners can identify parts of a phylogenetic

    tree based on phyloreferences expressed in OWL. ✤ But can we make them work fast, through easy-to-use websites and over web services? ✤ Continuous testing will make sure that all existing phyloreferences continue to work in the future. ✤ We need you to submit useful phyloreferences and tricky phylogenies, to complain about phyloreferences that don’t make sense to you, and to use our infrastructure to identify clades in your datasets.
  72. We need a postdoc! ✤ “Specifically, you will work with

    other projects funded by NSF’s GoLife program to obtain large phylogenies, gather sources for meaningful phyloreferences, and develop phyloreferencing proof-of-concept applications for these. These applications will include aggregating trait and other domain-relevant data.” ✤ “Strong background in Systematic Biology required. You should be well versed in all aspects of theoretical phylogenetics and related topics.” ✤ http://www.phyloref.org/blog/2016/10/postdoc2-ad/
  73. Acknowledgements ✤ NSF: “An Ontology-Based System for Querying Life in

    a Post-Taxonomic Age” (NSF-DBI 1458604) ✤ Available on FigShare: http://dx.doi.org/10.6084/ m9.figshare.1401984.v1
  74. Questions? phyloref.org @phyloref

  75. References ✤ Hinchliff et al. (2016): http://dx.doi.org/10.1073/ pnas.1423041112

  76. Images ✤ https://commons.wikimedia.org/wiki/ File:Tree_of_life_SVG.svg ✤ https://commons.wikimedia.org/wiki/ File:Lobelia_cardinalis_-_Cardinal_Flower.jpg ✤ https://commons.wikimedia.org/wiki/ File:Campanula_latifolia_(7814338584).jpg

    ✤ https://commons.wikimedia.org/wiki/ File:Unclesamwantyou.jpg
  77. A database of clades: PhyloRegnum Name Definition Campanulaceae The clade

    originating with the most recent common ancestor of Campanula latifolia Linnaeus 1753 and all extant organisms or species that share a more recent common ancestor with Campanula latifolia than with Roussea simplex J. E. Smith 1789, Pentaphragma ellipticum Poulsen 1903, or Stylidium graminifolium Swartz ex Willdenow 1805. Campanuloideae The clade originating with the most recent common ancestor of Campanula latifolia Linnaeus 1753, Wahlenbergia linifolia A. de Candolle 1830, and Platycodon grandiflorus (Jacquin) A. de Candolle 1830.
  78. :Campanula_latifolia :Campanula_rotundifolia ✤ :Campanula_latifolia :has_Sibling 
 :Campanula_rotundifolia ✤ :Lobelia_coronopifolia :has_Sibling

    
 :Lobelia_cardinalis ✤ :Node_1 a :Node ✤ :has_Child :Campanula_latifolia ✤ :has_Child :Campanula_rotundifolia
  79. :Campanula_latifolia :Campanula_rotundifolia has_Sibling ✤ :Campanula_latifolia :has_Sibling 
 :Campanula_rotundifolia ✤ :Lobelia_coronopifolia

    :has_Sibling 
 :Lobelia_cardinalis ✤ :Node_1 a :Node ✤ :has_Child :Campanula_latifolia ✤ :has_Child :Campanula_rotundifolia
  80. :Campanula_latifolia :Campanula_rotundifolia has_Sibling :Node_1 … ✤ :Campanula_latifolia :has_Sibling 
 :Campanula_rotundifolia

    ✤ :Lobelia_coronopifolia :has_Sibling 
 :Lobelia_cardinalis ✤ :Node_1 a :Node ✤ :has_Child :Campanula_latifolia ✤ :has_Child :Campanula_rotundifolia
  81. :Campanula_latifolia :Campanula_rotundifolia has_Sibling :Node_1 has_Child … ✤ :Campanula_latifolia :has_Sibling 


    :Campanula_rotundifolia ✤ :Lobelia_coronopifolia :has_Sibling 
 :Lobelia_cardinalis ✤ :Node_1 a :Node ✤ :has_Child :Campanula_latifolia ✤ :has_Child :Campanula_rotundifolia
  82. :Campanula_latifolia :Campanula_rotundifolia has_Sibling :Node_1 has_Child has_Child … ✤ :Campanula_latifolia :has_Sibling

    
 :Campanula_rotundifolia ✤ :Lobelia_coronopifolia :has_Sibling 
 :Lobelia_cardinalis ✤ :Node_1 a :Node ✤ :has_Child :Campanula_latifolia ✤ :has_Child :Campanula_rotundifolia
  83. A SEMANTIC CLADE Node-based Branch-based Apomorphy-based A A A B

    B B C C C Last common ancestor of B and C X Last ancestor of B that is not an ancestor of A Last ancestor of B that exhibits apomorphy X The clade originating with:
  84. A SEMANTIC CLADE Node-based A B C Last common ancestor

    of B and C The clade originating with:
  85. A SEMANTIC CLADE Node-based Branch-based A A B B C

    C Last common ancestor of B and C Last ancestor of B that is not an ancestor of A The clade originating with:
  86. None