Add all possible annotation and annotation extension relations to Noctua form

[vanaukenk]

Following up from 2022-03-02 manager's call where we discussed adding all possible annotation and annotation extension relations to the Noctua form, i.e. adding all relations currently available to curators in other tools or Noctua workbenches.

@thomaspd below is the list gathered from Protein2GO (note that below is only the subset of relations in Protein2GO that are GO-CAM applicable) and ShEx. Do you have time to review this together? Thx.

BP relations: part of has input has primary input has output has primary output occurs in has target end location has target start location causally upstream of causally upstream of negative effect causally upstream of positive effect regulates negatively regulates positively regulates results in development of results in division of results in formation of results in morphogenesis of results in acquisition of features of results in commitment to results in determination of results in specification of results in assembly of results in disassembly of results in organization of results in maturation of results in growth of results in movement of results in remodeling of transports or maintains localization of

MF relations: part of has part occurs in has input has primary input has output has primary output directly provides input for regulates negatively regulates positively regulates directly regulates directly negatively regulates directly positively regulates causally upstream of or within causally upstream of or within positive effect causally upstream of or within negative effect causally upstream of causally upstream of negative effect causally upstream of positive effect happens during transports of maintains localization of has target start location has target end location

CC relations: part of adjacent to overlaps existence overlaps existence starts and ends during

PCC relations: located in is active in has part part of existence overlaps existence starts and ends during

GP relations: contributes to located in part of colocalizes with

[pgaudet]

I thought we wanted to lint to the relations allowed in ShEx, and remove 'leftover' relations that we haven't been able to fix yet, ie 'directly regulates'. What about the the chained relations?

[vanaukenk]

In GO-CAM, there is an alternative way to model the biology captured by chained relations, so we don't absolutely need them. Conceptually, we won't lose any information, it will just be annotated a bit differently.

For other relations, yes, we have said we would phase some of these out, but this is currently what's in the ShEx and in Protein2GO. We can continue to move forward with our decision to remove some of these (e.g. directly regulates) but I wasn't entirely clear what the relations project status was for dealing with these others. We still need to coordinate the efforts here across tools and other software, so someone needs to be responsible for doing that.

[vanaukenk]

Here's a summary table with AE relations and their current status wrt Noctua and ShEx.

[vanaukenk]

From 2022-12-01 workbenches meeting:

We decided that if a more specific BP term shares a relation with a relation in the root BP shape, we will override displaying the relation and its constraints from the root BP shape and instead display the more relation and constraints from the more specific BP term.

See for example: Metabolic Process