obophenotype / obophenotype/uberon

untangle forebrain bundles

Open
#1,280 5 comments 0 reactions 0 assignees View on GitHub

Nobody has claimed this yet.

Dominant language
Emacs Lisp
Stars
163
Forks
43
Avg merge
1d 17h
Merged PRs (30d)
5

Description

vis @ChrisOchs see https://github.com/obophenotype/uberon/issues/1277#issuecomment-253952186

There are many structures called forebrain bundles (lateral, basal, medial) in many species. We need to untangle synonymy vs homology vs same structure/connections etc

cc @cerivs @mellybelly @ANiknejad

reptiles/birds

There is also a lateral/basal forebrain bundle in reptiles and birds http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=2465

teleost

ZFA:0007012 ! lateral forebrain bundle

(no def)

lungfish

There is also a structure with this name in lungfish

xenopus

XAO:0004559 ! lateral forebrain bundle A fiber system that is formed by pallial and subpallial components that join in the caudal telencephalon. It proceeds caudally, piercing the optic tract, to the ventral part of the hypothalamus

lamprey

https://sites.google.com/site/subcorticalbrain/home/lamprey-lateral-forebrain-bundle

mammals

Exists in mammals,

UBERON:0001910 ! medial forebrain bundle

See also BAMS https://bams2.bams1.org/brain_parts/Lateral-forebrain-bundle-system-2/

Contributor guide

Open the contributing guide

First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Start with the linked discussion in UBERON issue 1277 and review the species-specific sections here, including UBERON:0001910, ZFA:0007012, and XAO:0004559. Compare the cited BAMS and anatomical references to determine which forebrain bundle concepts are synonymous, homologous, or distinct; done means the relationships and definitions are resolved across the listed species.

Written by the indexing model from the issue text.

Assessment

Domain
bioinformatics
Issue type
Refactor
Difficulty
5/5
Estimated time
Over a week
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
25/100

Get new issues in your inbox

A short digest of beginner-friendly GitHub issues.