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. 4.
  2. 5.
  3. 10.

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

    around ancestral relationships, so they always match monophyletic groups. www.phyloref.org
  4. 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
  5. 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
  6. 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
  7. 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
  8. 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
  9. 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
  10. 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?
  11. 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?
  12. 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.
  13. 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.
  14. 28.

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

    :Mumbai ✤ :Mumbai :partOf :Maharashtra
  15. 29.

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

    :Mumbai ✤ :Mumbai :partOf :Maharashtra ✤ => :Gaurav :bornIn :Maharashtra
  16. 30.

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

    :Mumbai ✤ :Mumbai :partOf :Maharashtra ✤ => :Gaurav :bornIn :Maharashtra ✤ Only if :bornIn o :partOf => :bornIn!
  17. 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
  18. 33.

    Campanula latifolia Campanula rotundifolia Lobelia coronopifolia Lobelia cardinalis Cyphocarpus rigescens

    Chrysanthemum ✤ :Campanula_latifolia :has_Sibling 
 :Campanula_rotundifolia
  19. 34.

    Campanula latifolia Campanula rotundifolia Lobelia coronopifolia Lobelia cardinalis Cyphocarpus rigescens

    Chrysanthemum ✤ :Campanula_latifolia :has_Sibling 
 :Campanula_rotundifolia ✤ :Lobelia_coronopifolia :has_Sibling 
 :Lobelia_cardinalis
  20. 35.

    Campanula latifolia Campanula rotundifolia Lobelia coronopifolia Lobelia cardinalis Cyphocarpus rigescens

    Chrysanthemum ✤ :Campanula_latifolia :has_Sibling 
 :Campanula_rotundifolia ✤ :Lobelia_coronopifolia :has_Sibling 
 :Lobelia_cardinalis
  21. 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
  22. 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
  23. 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
  24. 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
  25. 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
  26. 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
  27. 42.

    Phyloreferences in OWL Descendants of the ancestors of Campanula latifolia

    that exclude the ancestors of Lobelia cardinalis
  28. 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
  29. 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
  30. 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
  31. 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
  32. 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
  33. 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
  34. 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
  35. 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
  36. 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
  37. 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
  38. 53.
  39. 54.

    What are we building? ✤ Software tools and standards for

    converting phylogenies to logical statements.
  40. 55.

    What are we building? ✤ Software tools and standards for

    converting phylogenies to logical statements. ✤ Ontologies to make these relationships simple and clear.
  41. 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.
  42. 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.
  43. 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.
  44. 59.
  45. 60.
  46. 61.
  47. 62.
  48. 63.
  49. 64.
  50. 65.
  51. 66.
  52. 68.

    Conclusions ✤ OWL reasoners can identify parts of a phylogenetic

    tree based on phyloreferences expressed in OWL.
  53. 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?
  54. 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.
  55. 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.
  56. 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/
  57. 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
  58. 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.
  59. 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
  60. 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
  61. 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
  62. 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
  63. 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
  64. 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:
  65. 84.

    A SEMANTIC CLADE Node-based A B C Last common ancestor

    of B and C The clade originating with:
  66. 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:
  67. 86.