Duplication of synonym type information
tberardini opened this issue · 4 comments
Synonym types are stated twice in the stanzas, once in parenthesis within the synonym name and again as a separate type.
One example:
synonym: "bush (narrow)" NARROW []
Are there plans to clean this up or remove the redundancy?
More below:
[Term]
id: PO:0000003
name: whole plant
namespace: plant_anatomy
def: "A plant structure (PO:0005679) which is a whole organism." [POC:curators]
comment: Examples include plant embryo (PO:0009009), megagametophyte (PO:0025279) and microgametophyte (PO:0025280).
subset: reference
subset: TraitNet
synonym: "bush (narrow)" NARROW []
synonym: "clonal colony (related)" RELATED []
synonym: "colony (related)" RELATED []
synonym: "frutex (narrow)" NARROW [FNA:e4dde193-57f7-4ab9-9d25-96b4ca0088ba]
synonym: "frutices (narrow)" NARROW Plural [FNA:ec8c2064-2a67-43d7-8e14-aecfef5cf33b]
synonym: "gametophyte (narrow)" NARROW []
synonym: "genet (broad)" BROAD []
synonym: "herb (narrow)" NARROW []
synonym: "liana (narrow)" NARROW []
synonym: "planta entera (Spanish, exact)" EXACT Spanish [POC:Maria_Alejandra_Gandolfo]
synonym: "prothalli (narrow)" NARROW Plural [FNA:4b610104-1bb0-4c6b-9bb9-e3cc61d11ac0]
synonym: "prothallium (narrow)" NARROW []
synonym: "prothallus (narrow)" NARROW [FNA:f8f31520-e4bc-4430-9274-8dd3cee7ffd8]
synonym: "ramet (broad)" BROAD []
synonym: "seedling (narrow)" NARROW []
synonym: "shrub (narrow)" NARROW []
synonym: "sporophyte (narrow)" NARROW []
synonym: "suffrutex (narrow)" NARROW [FNA:99508f62-7116-4e2b-90c0-19ff55ebd967]
synonym: "suffrutices (narrow)" NARROW Plural [FNA:ba1b1bd5-75bd-4195-b11c-3aba08da08c2]
synonym: "tree (narrow)" NARROW []
synonym: "vine (narrow)" NARROW []
synonym: "woody clump (narrow)" NARROW [FNA:c1ccca7d-2a98-4a9d-8603-c34b551935e0]
synonym: "植物体全体 (Japanese, exact)" EXACT Japanese [NIG:Yukiko_Yamazaki]
The reason for having the synonym scopes in parentheses is that otherwise the scope is not displayed on the AmiGO browser. For example, see http://browser.planteome.org/amigo/term/PO:0000003 and compare with the stanza above. On the AmiGO browser, only the scope in parentheses is displayed.
This was discussed here; Planteome/amigo#23
Found this
geneontology/amigo#290
Assuming GO does something with AmiGO to display the synonym type/scope information, would you then drop the 'extra' text in the synonym name? I'm going to add myself as a watcher on the geneontology/amigo#290 issue. @cooperl09 : I'll close this and look for your answer to my question.
@lreiser - While trying to track down why the string '(exact)' was showing up in some of the synonym names, I opened this issue. We'll have to deal with the downstream effects for now as it looks like the situation is not going to change anytime soon.