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statonlab / tripal_ssr

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featureprop cvterms #6

Open bradfordcondon opened 7 years ago

bradfordcondon commented 7 years ago

SSR terms are created as feature prop terms, and therefore do not link to a CV.

For example:


  tripal_insert_cvterm(array(
    'name' => 'tripal_ssr_repeats',
    'def' => 'The number of repeats in an SSR.',
    'cv_name' => 'feature_property',
    'db_name' => 'tripal',
  ));

  tripal_insert_cvterm(array(
    'name' => 'tripal_ssr_start',
    'def' => 'The start of an SSR.',
    'cv_name' => 'feature_property',
    'db_name' => 'tripal',
  ));

Start could be the SIO start term. Repeat number could be http://www.ebi.ac.uk/ols/ontologies/ncit/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FNCIT_C93650 (find a non-NCI term)

Repeat unit: http://www.ebi.ac.uk/ols/ontologies/so/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FSO_0000726

bradfordcondon commented 6 years ago

start/end are deprecated thanks to using featureloc instead.

f/r primer sequence and tm are unlikely since need a forward and reverse term.