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Cdao Utep10


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A brief introduction to the comparative data analysis ontology given at a UTEP meeting in early 2010

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Cdao Utep10

  1. 1. Comparative Data Analysis Ontology
  2. 2. Presentation Outline <ul><li>Terminology </li></ul><ul><li>Basic Structure </li></ul><ul><li>Design Decisions </li></ul>
  3. 3. Termonology <ul><li>Taxon </li></ul><ul><ul><li>Refers to an organism identifier </li></ul></ul><ul><ul><li>Names are controlled by external vocabularies such as NCBI </li></ul></ul><ul><li>Trait </li></ul><ul><ul><li>Some attribute of a set of organisms being studied </li></ul></ul><ul><li>Tree </li></ul><ul><ul><li>A graph specifying the inferred relationship between taxa in a study </li></ul></ul><ul><li>Matrix </li></ul><ul><ul><li>A matrix is defined as a set of taxa and traits and their associated states. </li></ul></ul>
  4. 4. Basic Structure <ul><li>Network/Tree </li></ul><ul><ul><li>Specifies all classes related to defining cdao trees. </li></ul></ul><ul><ul><li>Includes notions of node and branch </li></ul></ul><ul><ul><li>The actual relationship between nodes is specified in terms of properties such as child and parent </li></ul></ul><ul><li>Matrix </li></ul><ul><ul><li>Contains a set of traits and taxa. </li></ul></ul><ul><ul><li>Traits and taxa are connected to observed state data through the “has” property. </li></ul></ul>
  5. 5. Design Decisions <ul><li>Data were categorized generally as: </li></ul><ul><ul><li>Categorical </li></ul></ul><ul><ul><ul><li>Molecular </li></ul></ul></ul><ul><ul><ul><ul><li>DNA, RNA, or Protein data </li></ul></ul></ul></ul><ul><ul><ul><li>Standard </li></ul></ul></ul><ul><ul><ul><ul><li>Other discrete data such as color </li></ul></ul></ul></ul><ul><ul><li>Continuous </li></ul></ul><ul><ul><ul><li>Continuous data such as beak-length </li></ul></ul></ul><ul><li>Class vs Individual </li></ul><ul><ul><li>We made the decision to treat specific amino acids or nucleotide bases as individuals rather than classes. </li></ul></ul>
  6. 6. Additional Questions