Conversation
gouttegd
left a comment
gouttegd
left a comment
There was a problem hiding this comment.
Looks good to me.
As suggested in the inline comments you may want to replace the “adult dorsal vessel” and “embryonic/larval dorsal vessel” FBbt synonyms by a single “dorsal vessel” synonym (now that such a term exists in FBbt).
src/ontology/uberon-edit.obo
Outdated
| synonym: "adult dorsal vessel" NARROW SENSU [FBbt:00003152, NCBITaxon:50557] | ||
| synonym: "adult dorsal vessel" NARROW [FBbt:00003152] | ||
| synonym: "dorsal vessel" EXACT [] | ||
| synonym: "embryonic/larval dorsal vessel" NARROW SENSU [FBbt:00001673, NCBITaxon:50557] |
There was a problem hiding this comment.
Now that FBbt has a stage-neutral term for that structure, I am not sure we need the narrow synonyms pointing to the adult and larval variants. I’d suggest replacing those by a single
synonym: "dorsal vessel" NARROW SENSU [FBbt:00058291, NCBITaxon:50557]
| name: dorsal trunk of insect trachea | ||
| def: "Longitudinal tracheal branch of the insect tracheal system, dorsal to the lateral trunk." [FBbt:00005043] | ||
| synonym: "dorsal trunk" BROAD SENSU [NCBITaxon:50557] | ||
| xref: FBbt:00003039 |
There was a problem hiding this comment.
Please note that mappings to FBbt are now managed on the FBbt side. They are transferred to Uberon as a SSSOM file, from which cross-references are derived during the build process and inserted into the released ontology.
I’ll add this mapping to FBbt, you may remove the cross-reference from here (otherwise it will be removed next time the mappings are updated in Uberon).
| name: insect trachea | ||
| def: "Cuticle-lined epithelial tube that forms part of the insect tracheal system." [FBbt:00005043] | ||
| synonym: "trachea" BROAD SENSU [NCBITaxon:50557] | ||
| xref: FBbt:00005043 |
There was a problem hiding this comment.
On second thought, shouldn’t insect trachea be made a subclass of open tracheal system trachea (UBERON:0003127)?
|
@cmungall : If you agree with the suggestions above (i.e., replace stage-specific synonyms with stage-neutral ones, and more importantly re-classify |
|
Yes, if you can update the PR that would be great!
…On Mon, Feb 7, 2022 at 2:54 AM Damien Goutte-Gattat < ***@***.***> wrote:
@cmungall <https://github.com/cmungall> : If you agree with the
suggestions above (i.e., replace stage-specific synonyms with stage-neutral
ones, and more importantly re-classify insect trachea as a open tracheal
system trachea instead of a epithelial tube), I can take care of updating
the PR if you want.
—
Reply to this email directly, view it on GitHub
<#2272 (comment)>,
or unsubscribe
<https://github.com/notifications/unsubscribe-auth/AAAMMOMDUPDF7NCG36474C3UZ6QHZANCNFSM5NHFWL2A>
.
Triage notifications on the go with GitHub Mobile for iOS
<https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675>
or Android
<https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>.
You are receiving this because you were mentioned.Message ID:
***@***.***>
|
FBbt has a stage-neutral term to represent the dorsal vessel, so we don’t need the synonyms to point to the stage-specific terms.
Update mappings to reflect newly added terms in Uberon (see obophenotype/uberon#2272).
|
@cmungall The agreed upon changes are done, so I’ll go ahead and merge. |
2 participants
No description provided.