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Planteome / amigo

This repo is the Planteome fork of geneontology.org AmiGO2 project. Issues in this repo should be reported only on AmiGO issues. Issues can be pushed upstream if relevant for GO.
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Synonym dbxrefs are not being displayed #29

Open cooperl09 opened 7 years ago

cooperl09 commented 7 years ago

In the plant structure development stage (PO:0009012) branch of the PO we have a large number of mappings from our stage terms to terms in other ontologies and vocabularies.
The corresponding mappings (eg GRO:ID) do not show up in the browser and you cannot search for them.

For example: [Term] id: PO:0007022 name: seed imbibition stage namespace: plant_structure_development_stage def: "A seed germination stage (PO:0007057) during which there is absorption of water by the seed (PO:0009010)." [Gramene:Anuradha_Pujar, ISBN:0306416875, POC:Laurel_cooper] synonym: "0.1 imbibition in maize (related)" RELATED [MaizeGDB:64054] synonym: "01 Beginning of seed imbibition in soybean (related)" RELATED [SOY:0000090] synonym: "03 Seed imbibition complete in soybean (related)" RELATED [SOY:0000091] synonym: "1.02-start of imbibition in barley (related)" RELATED [GRO:0007053] synonym: "1.02-start of imbibition in oat (related)" RELATED [GRO:0007053] synonym: "1.02-start of imbibition in Triticeae (related)" RELATED [GRO:0007053] synonym: "1.02-start of imbibition in wheat (related)" RELATED [GRO:0007053] synonym: "1.03-imbibition complete in barley (related)" RELATED [GRO:0007054] synonym: "1.03-imbibition complete in oat (related)" RELATED [GRO:0007054] synonym: "1.03-imbibition complete in Tricticeae (related)" RELATED [GRO:0007054] synonym: "1.03-imbibition complete in wheat (related)" RELATED [GRO:0007054] synonym: "BBCH growth stage 01 (related)" RELATED [ISBN:3826331524] synonym: "imbibition in Arabidopsis (related)" RELATED [TAIR:0000394] synonym: "imbibition in Solanaceae (related)" RELATED [SGN:0000004] xref: PO_GIT:366 xref: PO_GIT:595 is_a: PO:0007057 ! seed germination stage

Is there a way to display these in the Planteome browser?

cmungall commented 7 years ago

The solution outlined for synonym scopes/types here:

https://github.com/geneontology/amigo/issues/290#issuecomment-243309763

will also work for xrefs on synonyms