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geneontology / noctua-form-legacy

Simple annoton editor workbench for Noctua.
BSD 3-Clause "New" or "Revised" License
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Specifications for BP only implementation of SAE #27

Open vanaukenk opened 6 years ago

vanaukenk commented 6 years ago

The form should allow curators to choose from a drop-down list (above the BP line) to specify the relation between the gene product and the Biological Process term.

The relations to include are (in order from top-to-bottom in the drop-down list):

acts upstream of or within (RO:0002264) -acts upstream of or within, positive effect (RO:new) -acts upstream of or within, negative effect (RO:new) -acts upstream of (RO:0002263) --acts upstream of, positive effect (RO:new) --acts upstream of, negative effect (RO:new)

RO:new = pending a new relation in the Relations Ontology

@tmushayahama - you can wait on implementing this until we have unique ids for each of the RO:new entries.

cmungall commented 6 years ago

https://github.com/oborel/obo-relations/pull/225

tmushayahama commented 6 years ago

@vanaukenk what is the status of the new RO ids?

thomaspd commented 6 years ago

@cmungall - do we have the new RO ids for these terms, and their cognate process-process relations?

cmungall commented 6 years ago

Yes, these are in RO,

Note: the URLs above resolve to ontobee which lags behind the release, so don't be worried if the new ones do not resolve. For browsing I recommend OLS, from this node: https://www.ebi.ac.uk/ols/ontologies/ro/properties?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FRO_0002264

(It looks like OLS isn't displaying property chains, I'll check what the status of that is: https://github.com/EBISPOT/OLS/issues/197)

We also sync this with a list on our wiki, in this category:

http://wiki.geneontology.org/index.php/Category:Gene_Product_to_Term_Relations

tmushayahama commented 6 years ago

@thomaspd I am assuming acts upstream of or within, positive effect will map to directly positively regulates on BP Only?

thomaspd commented 6 years ago

I think RO is still missing: causally upstream of or within, positive effect causally upstream of or within, negative effect

Also, since we've got positive and negative effect for all of these, for completeness (so we don't lose the effect direction when we increase the specificity) do we also want: part of, negative effect part of, positive effect

cmungall commented 6 years ago

I think RO is still missing: causally upstream of or within, positive effect causally upstream of or within, negative effect

we have these:

https://www.ebi.ac.uk/ols/ontologies/ro/properties?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FRO_0002304 https://www.ebi.ac.uk/ols/ontologies/ro/properties?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FRO_0002305

note these are occurrent-occurrent relations

we do not have these:

part of, negative effect part of, positive effect

vanaukenk commented 6 years ago

@thomaspd

part of, negative effect part of, positive effect

is the intent that these would be available for curators to use in their models? If so, do you have examples in mind that we could add to the documentation?

And yes, for the graphical editor, we will still need:

causally upstream of or within, positive effect causally upstream of or within, negative effect

vanaukenk commented 6 years ago

The BP only version of the form is currently not allowing me to save a BP annotation and the error message says: Molecular Function: No evidence for 'Molecular Function'

vanaukenk commented 6 years ago

@tmushayahama - we still need to add the acts upstream of or within, negative effect and acts upstream of or within, positive effect relations to the BP only dropdown.

In the graph editor they will have causally upstream of or within, negative effect and causally upstream of or within, positive effect relations to the MF term. Thx.

vanaukenk commented 6 years ago

@tmushayahama

I've also tested all of the BP only relations and everything looks good here, too.