CV Search at Population Data Workbench
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CV Search at Population Data Workbench

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Controlled Vocabulary Search for population data workbench (VectorBase)

Controlled Vocabulary Search for population data workbench (VectorBase)

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CV Search at Population Data Workbench CV Search at Population Data Workbench Presentation Transcript

  • Tutorial: Controlled Vocabulary (CV) Search on population data Workbench This CV Search is designed to help researchers for completing data input file using common terms for population data Workbench.
  • CV Search site
    • Direct link: https://grassi2.ucdavis.edu/Workbench/Docs/Ontology/CVSearch
    From Workbench main page, click ‘ Controlled Vocabulary Search ’ page link
  • Example: find term id for larvae collection method using dipper.
    • On a Collection data table, researchers need to fill in a collection method using a controlled vocabulary. These are under active development.
    • Since genotyping ontology is currently unavailable, we are borrowing terms from mosquito insecticide resistance ontology (MIRO) for species and assay methods for now.
  • 1. Select ontology to search
    • Two ontologies are available.
      • MIRO for assay methods and species_id.
      • Gaz for geographic locations.
    • For a larvae collection method, the select MIRO .
  • 2. Type in a phrase Type in a word or phrase of which CV id you are looking for. For example, type ‘ larvae ’ and a drop box will display all terms that include ‘larvae’.
  • 3. Select a term for detailed info. Among the list, ‘ collection of larvae from dippers ’ is showing in a drop box. Click with left mouse button and the right panel will display detailed information regarding the selected term. Term id is shown in green starting with ‘MIRO:’ which indicates the ontology set it belong to. Use this id to fill in Workbench data input form. Definition describes the term in detail and sometimes list the reference where the protocol is explained.
  • Note : Gaz ontology
    • On a Collection_site table, researchers are asked to fill in a gaz_id for a site.
    • Gaz ontology was originally intended for site_id but many collection sites especially in Africa is not available in this ontology or listed in unintuitive categories.
    • Thus this is optional but later could be used to link other databases that uses Gaz ontology.