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I am trying to insert data manually on all tables on the back end. I am facing a problem while inserting data to wp_terms. I can successfully insert category into wp_terms and define relationships in wp_term_relationships and wp_term_taxonomy. How does WordPress differentiate between category and tags ?

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take a look at wp_term_taxonomy table you will see a column called taxonomy, categories has "category" taxonomy in the field for each category and tags has "post_tag" taxonomy, custom defined taxonomies are also working this way.

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