Relations are not being recognized and displayed in AmiGO 2.0

[cooperl09]

Currently, there are a limited number of relations being recognized by AmiGO 2.0: is_a part_of occurs_in In the Plant Ontology file, we have a number of important relations that are missing in the browser view:

Relations with examples:

[Typedef] id: adjacent_to name: adjacent_to xref: RO:0002220

e.g. _id: PO:0025382! name: substomatal cavity relationship: adjacentto PO:0008032 ! stomatal pore

[Typedef] id: derives_by_manipulation_from name: derives_by_manipulation_from

e.g. _id: PO:0000007 leaf-derived cultured plant cell relationship: derives_by_manipulationfrom PO:0025034 ! leaf

[Typedef] id: develops_from name: develops_from xref: RO:0002202 is_transitive: true

e.g. _id: PO:0000015 name: cotyledon primordium relationship: developsfrom PO:0025432 ! cotyledon anlagen

[Typedef] id: has_part name: has_part xref: BFO:0000051 is_transitive: true

e.g. _id: PO:0009049 name: inflorescence relationship: haspart PO:0009046 ! flower

[Typedef] id: has_participant name: has_participant xref: BFO:0000057

e.g. _id: PO:0007033 name: whole plant development stage relationship: hasparticipant PO:0000003 ! whole plant

[Typedef] id: located_in name: located_in xref: RO:0001025

e.g. _id: PO:0025281 name: pollen; relationship: locatedin PO:0025277 ! pollen sac

[Typedef] id: participates_in name: participates_in xref: BFO:0000056

e.g. _id: PO:0000423 name: plant zygote relationship: participatesin PO:0001097 ! plant zygote stage

[Typedef] id: preceded_by name: preceded_by xref: BFO:0000062 is_transitive: true

e.g. _id: PO:0001040 name: dry seed stage relationship: precededby PO:0007632 ! seed maturation stage

[Typedef] id: precedes name: precedes xref: BFO:0000063

e.g. _id: PO:0001078 name: plant embryo cotyledonary stage relationship: precededby PO:0004507 ! plant embryo bilateral stage relationship: precedes PO:0001081 ! mature plant embryo stage

[cmungall]

@kltm @hditeze I can't find the ticket on the main tracker right now but I know we've discussed this a few times. We only want to filter relationships for ancestry. For direct relationships it's very useful to see and traverse over any relationship types. We really need this in the main amigo. I think this should be relatively straightforward to handle on the owltools end with no changes required on the amigo app or configurations itself

[cmungall]

Here: https://github.com/geneontology/amigo/issues/220

[marieALaporte]

The CO properties method_of, scale_of and variable_of don't show up neither on the browser.

[cmungall]

This is already covered in the main amigo ticket, but if we want a test case that is plant specific, see how anther looks in OLS:

http://www.ebi.ac.uk/ols/beta/ontologies/po/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FPO_0009066

I think this gets it right (never mind details about whether a denormalized tree view is the best way of showing things, or if the 'visualize' link gives you a headache). The crucial points are:

• Some kind of relationship lineage display that operates over a subset of the relations (for OLS, isa and part-of; we can include develops-from for amigo if we like)
  • Display of direct incoming and outgoing edges, unrestricted by relationship type

The details of how this would look in amigo would be different. We may have the inferredtreeview as default for the lineage, and we may show what OLS calls 'class relations' in the TermInfo panel, or a new tab. But the information would be the same.

[cooperl09]

This issue was moved to Planteome/amigo#20

[cooperl09]

This issue was moved to Planteome/amigo#21