Guidelines for creating a Regulation Term: Difference between revisions

From GO Wiki
Jump to navigation Jump to search
mNo edit summary
mNo edit summary
(12 intermediate revisions by 2 users not shown)
Line 1: Line 1:
''See [[Ontology_Editors_Daily_Workflow]] for creating branches and basic Protégé instructions.''
  See [[Ontology_Editors_Daily_Workflow]] for creating branches and basic Protégé instructions.


* To create a ‘positive regulation of x’ or ‘negative regulation of x’ term, the parent ‘regulation of x’ term must first be created.  
* To create a ‘positive regulation of x’ or ‘negative regulation of x’ term, the parent ‘regulation of x’ term must first be created.  
# To create a '''parent regulation term''', make sure the ‘Asserted view’ is active (not the ‘Inferred view’).
# To create a new term, here, the '''parent <code>regulation</code> term''', make sure the ‘Asserted view’ is active (not the ‘Inferred view’).
# In the 'Protege classes view', navigate to ‘biological regulation’.
# In the <code>Protege classes view</code>, navigate to <code>biological regulation</code>.
# Click on the add subclass button at the top left corner.
# Click on the add subclass button at the top left corner.
# In the pop-up window add the name of the new regulation term ‘regulation of target process’. The identifier should auto-populate. Click the button to add the term.
# In the pop-up window add the name of the new regulation term <code>regulation of target process</code>. The identifier should auto-populate. Click the button to add the term.
# Enter the appropriate information for namespace, definition, synonyms, etc. in the obo editing view as described in the ‘Creating a New Ontology Term’ Section.
# Enter the appropriate information for namespace, definition, synonyms, etc. in the obo editing view as described in the ‘Creating a New Ontology Term’ Section.
# Standard definitions for regulation terms:
# Standard definitions for regulation terms:
        Regulation Any process that modulates the frequency, rate or extent of [process]
#* <code>Regulation: Any process that modulates the frequency, rate or extent of [process]</code>
        Positive regulation: Any process that activates or increases the frequency, rate or extent of [process]
#* <code>Positive regulation: Any process that activates or increases the frequency, rate or extent of [process]</code>
        Negative regulation: Any process that stops, prevents or reduces the frequency, rate or extent of [process]
#*  <code>Negative regulation: Any process that stops, prevents or reduces the frequency, rate or extent of [process]</code>
# Create a logical definition for the term: biological regulation and regulates some target process.
# Create a logical definition for the term: <code>biological regulation and (negatively/positively)regulates some target process</code>.
# Remove the asserted ‘biological regulation’ parent.
# Remove the asserted <code>biological regulation</code> parent.
# Run the reasoner to be sure that reasoning results in the correct inferred parents.
# Run the reasoner to be sure that reasoning results in the correct inferred parents.
# Save changes.
# Save changes.


''See [[Ontology_Editors_Daily_Workflow]] for commit, push and merge instructions.''
  See [[Ontology_Editors_Daily_Workflow]] for commit, push and merge instructions.


== Review Status ==
Last reviewed: May 24, 2017
[[Ontology_Development#Editing_the_Ontology |Back to: Editing the Ontology]]


[[Category:GO Editors]][[Category:Ontology]][[Category:Editor_Guide_2018]]
[[Category:GO Editors]][[Category:Ontology]][[Category:Editor_Guide_2018]]

Revision as of 10:31, 5 April 2019

 See Ontology_Editors_Daily_Workflow for creating branches and basic Protégé instructions.
  • To create a ‘positive regulation of x’ or ‘negative regulation of x’ term, the parent ‘regulation of x’ term must first be created.
  1. To create a new term, here, the parent regulation term, make sure the ‘Asserted view’ is active (not the ‘Inferred view’).
  2. In the Protege classes view, navigate to biological regulation.
  3. Click on the add subclass button at the top left corner.
  4. In the pop-up window add the name of the new regulation term regulation of target process. The identifier should auto-populate. Click the button to add the term.
  5. Enter the appropriate information for namespace, definition, synonyms, etc. in the obo editing view as described in the ‘Creating a New Ontology Term’ Section.
  6. Standard definitions for regulation terms:
    • Regulation: Any process that modulates the frequency, rate or extent of [process]
    • Positive regulation: Any process that activates or increases the frequency, rate or extent of [process]
    • Negative regulation: Any process that stops, prevents or reduces the frequency, rate or extent of [process]
  7. Create a logical definition for the term: biological regulation and (negatively/positively)regulates some target process.
  8. Remove the asserted biological regulation parent.
  9. Run the reasoner to be sure that reasoning results in the correct inferred parents.
  10. Save changes.
 See Ontology_Editors_Daily_Workflow for commit, push and merge instructions.

Review Status

Last reviewed: May 24, 2017

Back to: Editing the Ontology