Most terms are obsoleted due to flaws such as falling outside the scope of the ontology, faulty definitions, etc. Often, one or more terms in the ontology can be substituted for the obsolete term. OBO-Edit allows users to specify replacements for obsolete terms. These replacements can be used by human annotators as a useful reference, or can be used by software to automatically re-assign database entities that were associated with a term that became obsolete.
Works by: drag and drop
Hot keys: none
Target required?: yes
Source requirements: one or more source terms required
If an obsolete term can be exchanged for another term or terms in all instances of usage (e.g. in annotations or mappings), the new term(s) may be specified as a replacement term. Note that a replacement term should only be specified if the obsolete term can be replaced by exactly this term in every case. If this criterion is not met, use a "consider" term instead.
Replacement terms should be specified when possible, because replacement terms can be used by software agents to do automatic corrections in databases when a term becomes obsolete.
To specify a replacement for an obsolete term, select a source term to act as the replacement. Drag the replacement source onto the target obsolete term. When the term is dropped, a menu will appear:
Choose "Add replacement term" from the menu to assign the replacement term.
Gesture types: drag and drop
Hot keys: none
Target required?: yes
Source requirements: one or more source terms required
Often, there is not a single accurate replacement term for an obsolete term. Usually there are several possible substitutes, and the correct replacement depends on context. In these cases, a user may specify one or more "consider" terms that a human expert would look at.
To specify a "consider" term for an obsolete term, select one or more source terms to consider. Drag the "consider" source onto the target obsolete term. When the terms are dropped, a menu will appear:
Choose "Add consider term" from the menu to assign the replacement terms.
Gesture types: right-click menu, edit menu
Hot keys: none
Target required?: no
Source requirements: one or more source terms required
To remove a replacement or consider term, select the consider or replacement term to remove underneath the obsolete term to which it is assigned. That is, make sure that you have selected the term to remove in the context where it is preceded by the label "replaced by" or "consider":
From the right-click or edit menu, choose either "Remove consider term" or "Remove replacement term".