Merging

It is possible to merge two concepts into one. When term A is merged into term B, the following things happen:

• A's ID is assigned as an alternate ID of B
• All of A's synonyms are copied to B
• All of A's dbxrefs are copied to B
• A & B's comments are merged (see Merging Comments & Definitions )
• A & B's definitions are merged (see Merging Comments & Definitions )
• A's name is assigned as an exact synonym of B.
• All of A's parents become parents of B (see Caveats )
• All of A's children become children of B (see Caveats )
• All of A's parent relationships are deleted
• All of A's child relationships are deleted

  It is impossible to create a cycle by merging, because any potentially cyclic links are not copied to the target term. See caveats for potential pitfalls of this behavior.

  To merge two terms, select the source term you would like to merge (if a term appears in the ontology editor panel multiple times because of multiple parentage, it does not matter which one you choose). Indicate the target term by right-clicking or drag and drop.

  Choose "Merge" from the right-click menu or drag and drop popup menu. The terms will be merged.

  Merging Comments & Definitions

  When two terms are merged, the source term's comments are merged with the target term's comments, and the source term's definition is merged with the target term's definition. When merging comments and definitions, the following rules are used:

  • If both the source term & target term have a blank comment or definition, the merged term's comment or definition is left blank.
  • If the source term's comment or definition is blank, the target term's comment or definition is used
  • If the target term's comment or definition is blank, the source term's comment or definition is used
  • If both the source and target term have a comment or definition defined, the comment or definition of both the source and target term are concatenated together. This concatenated comment or definition becomes the comment or definition for the merged term.

  Caveats

  • When two terms are merged, only one "survives". The other term's ID only lives on as a secondary ID. Therefore, it's very important to consider which term should be the source term (the one whose ID becomes secondary) and which is the target term (the one that lives on).
  • Any term can be merged with any other term. However, some merges could result in a horrible mess of cycles, because the merged term gets all the parents and children of the source term (for example, if a term was merged with a grandchild, a cycle is certain). Therefore, OBO-Edit will simply remove any cyclic links when a merge occurs. Since potential cycles can be very hard for humans to detect, you may be surprised that certain relationships from the source term have not carried over to the merged term. Always check to make sure no critical links have disappeared after a merge! (The good news: OBO-Edit will never delete a link from the target term; it will only choose to not copy some links from the source term).

  Diagnosing Disappearing Links

  ---

  You merged two terms, but OBO-Edit keeps refusing to copy a certain link from the source term! You hit Undo, but you can't figure out what's going on! Here's a technique to figure out why OBO-Edit is discarding a link when you merge...

  First, do a search for all the descendants of your target term, and leave the search results on screen. Then, do a search for all the ancestors of your target term, and leave those results on screen too. (Note: you will need to turn on the reasoner in order to be offered the "ancestor" search aspect.) Now look at the parents and children of the source term using the ontology editor panel and the parent editor. If any child of the source term is an ancestor of the target term, that link will be discarded. If any parent of the source term is a descendant of the target term, that link will be discarded.

  Once you've verified that OBO-Edit is right about the potential cycle, use the Tree Viewer to figure out how the potentially cyclic term connects to the source term. There's probably one or two links that you need to delete somewhere to disconnect the source term from the potentially cyclic term before you can merge.

   

  Hotkeys

  Hold down the "Command", "Shift" and "M" keys while dragging to specify the "Merge" operation. The toolbar will show "Current drag and drop behavior: Merge [Command]+Shift+M" and the title above the dragged terms will change from "Dragging..." to "Merge...":

  

  When the term is dropped, the source and target term will be merged automatically.