Review wiki documentation for existing MF-MF relations

[vanaukenk]

• [x] causally upstream of - Documentation now says not to use
• [x] causally upstream of, positive effect
• [ ] causally upstream of, negative effect - STILL NEEDS AN EXAMPLE
• [x] provides input for
• [x] directly negatively regulates
• [x] directly positively regulates

Link to proposal: https://docs.google.com/document/d/171G2vCVlMPmoeFJE1rNvpzAwEv_IXncW4OJNaoJQ3bo Link to new template: https://docs.google.com/document/d/1H9_VLRFIMPkNSOJB9tKavRBhL7AGSJIRTl_z9zD7q2I

To do:

1. Review what's currently on the existing wiki page
2. On each page, include an Overview, Usage Examples, Link to RO, Date Last Reviewed
3. Quality Control will include a link to the ShEx and any relevant GO rules

[ukemi]

Causally upstream of: https://wiki.geneontology.org/Annotation_Extension_Relation:causally_upstream_of Last reviewed 2020-12-11

1. This is currently under the annotation extension section of the documentation. Do we want to have one central location for all of these on the wiki? Yes, this will be a new project proposal.
2. The page is not of the format specified above. Do we want to edit this page or just start a new one? We will edit this page and move it.
3. Do we want to keep the conventional annotation examples? a. They are both process examples. So in any case, we need to add MF to MF examples. If we keep these examples, we should turn them into GO-CAMs.
4. Do we need to reorganize the relations documentation on the wiki as a whole? We will start a new project for this.

Changing to new template. DONE

[ukemi]

Causally upstream of negative effect- https://wiki.geneontology.org/Causally_upstream_of_negative_effect This is just a placeholder. We should mover this over to the write documentation ticket. Done

[ukemi]

causally upstream of, positive effect - https://wiki.geneontology.org/Causally_upstream_of,_positive_effect

1. I edited this entry to make it better fit with the new definition.
2. I only have one example.
3. I added an abbreviated form of the Shex to the QC section.
4. I left in the children section for now.

Changing to new template.

[vanaukenk]

Regulates - https://wiki.geneontology.org/Regulates

Updated with:

1. Overview
2. Examples of usage - here only referred to the more specific children
3. Quality control - linked to ShEx with a very general description

[ukemi]

directly provides input for - https://wiki.geneontology.org/Directly_provides_input_for

1. I edited this entry to make it better fit with the new definition.
2. I have two examples. One of the ones in the draft doc seems to point to the wrong model.
3. I added an abbreviated form of the Shex to the QC section.

Changing to new template.

[ukemi]

'removes input for' is a new relation Moved to #794

DONE

[vanaukenk]

Positively regulates - https://wiki.geneontology.org/Positively_regulates

To start:

1. This is another old page that will need completely new content.

[vanaukenk]

Negatively regulates - https://wiki.geneontology.org/Negatively_regulates

To start:

1. This page has three words "See positively_regulates"

[vanaukenk]

Directly positively regulates - https://wiki.geneontology.org/Directly_positively_regulates

First draft done - 2022-11-22.

[vanaukenk]

Directly negatively regulates - https://wiki.geneontology.org/Directly_negatively_regulates

To start:

1. This page has text but also a message at the top that the relation has been deprecated.

[vanaukenk]

Made a separate ticket for the example for causally upstream of, negative effect:

https://github.com/geneontology/noctua/issues/820