Curator Guide: Cross Products
From GO Public
Adding cross-product definitions for regulation and cellular component terms
For questions about this procedure, please contact Tanya, David or Jane.
Summary:
Contents |
Step 1
In this example we will illustrate the creation of the term regulation of cartilage condensation. The same principles apply to creating cross-products for cellular component terms, see part II of step 4 for more detailed instructions.
Begin with the REASONER OFF. Create the new term as a child of the term that is being regulated. (Edit -> Create new child)
Step 2
Name the term and commit. Change its relationship to cartilage condensation from is_a to the appropriate relationship, in this case regulates. (Edit -> Change relationship type -> regulates).
Step 3
Add the textual definition for your term in the text editor. Thinking about the textual definition will help you decide what the intersection genus and the discriminating relations are in the cross-product generation. Add your definition dbxrefs.
Step 4
Step 4, Part I
Open the cross-products tab in the text editor. Choose biological regulation as the intersection genus. Add regulates cartilage condensation as the discriminating relation. You may add more than one regulates relationship if this is appropriate.
Step 4, Part II
Adding a cross-product definition for a cellular component term works pretty much the same as for the regulation terms. At present, cross-product definitions are only made for cellular component terms where the discriminating relationship is part_of.
For example a nuclear chromosome is a chromosome that is part_of the nucleus, so we would add the cross-product:
[Term] id: GO:0000228 ! nuclear chromosome intersection_of: GO:0005694 ! chromosome intersection_of: part_of GO:0005634 ! nucleus
Nuclear membrane has a more complex relationship to nucleus (boundary_part_of) so we wouldn't add this cross-product at present.
To add the cross-product definition for nuclear chromosome in OBO-Edit, the intersection genus would be chromosome, the discriminating relationship would be part_of nucleus.
Step 5
Commit your term changes. Add any other terms that you plan to add during your editing session.
Step 6
Run the rule-based reasoner. (Reasoner -> Reasoner Manager -> RuleBasedReasoner (experimental))
The reasoner will run.
Step 7
Under the Edit menu choose: Edit -> Assert implied links. Review the suggested is_a links that pertain to the term you just added. You should ignore any other implied links, these are taken care of during regular QC by David and Tanya.
Step 8
Check the boxes beside the ones that you think are appropriate. If some look strange, review the ontology and see if the parent terms are related to each other properly. You may need to do some editing to fix things that are wrong.
If you do end up editing anything, you should save your file and reload. This is because OBO-Edit 2.0 tends to crash if the reasoner is run twice in one session. Once the file is reloaded, go to step 6.
Step 9
Click on Finish. Wait. The program will freeze for a while as the links are added and the calculations are done. The time will vary depending on how many links you accepted. Turn off the reasoner. Check your work using the Graphviz viewer to make sure the is_a links that you added are indeed there and that the regulates links are also in place. Don’t worry about the dashed lines.
Step 10
Save out file. Commit as usual.
