NTR: [Chloride Ion Import into cell]

geneontology / go-ontology

Source ontology files for the Gene Ontology

http://geneontology.org/page/download-ontology

Creative Commons Attribution 4.0 International

220 stars 40 forks source link

NTR: [Chloride Ion Import into cell] #24993

Closed sharan-gh closed 1 year ago

sharan-gh commented 1 year ago

Please provide as much information as you can:

Suggested term label: Chloride Ion Import into cell
Definition (free text) The directed movement of chloride ions into a cell.
Reference, in format PMID:####### PMID: 24431435
Gene product name and ID to be annotated to this term clh-3 (WBGene00000530)
Parent term(s) has parent import into cell [GO:0098657] has parent chloride transport [GO:0006821]
Children terms (if applicable) Should any existing terms that should be moved underneath this new proposed term?
Synonyms (please specify, EXACT, BROAD, NARROW or RELATED)
Cross-references
For enzymes, please provide RHEA and/or EC numbers.
Can also provide MetaCyc, KEGG, Wikipedia, and other links.
Any other information

raymond91125 commented 1 year ago

clh-3 has already been annotated with the MF GO:0005247 voltage-gated chloride channel activity. Do we want to

Create a BP for what appears to be a single step process?
To specify the direction of flow in the term? Or should the direction information be specified during annotation?

Note that we do have a term GO:0098719 sodium ion import across plasma membrane.

sharan-gh commented 1 year ago

My thought was that it would be nice to have the direction specified in the term (an MF term), since there are other terms that explicitly say import vs. export. Also, it seems there are cases where voltage-gated chloride efflux is involved in depolarizing a neuron (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5811518/).

raymond91125 commented 1 year ago

In PMID: 24431435, I see that clh-3 is involved in [GO:1904180 negative regulation of membrane depolarization] in [GO:0005886 plasma membrane] of [WBbt:0006830 HSN]. I don't think "Chloride Ion Import into cell" is a biological process being studied per se. In GO, a single-step biological process is a molecular function. Thus the chloride channel activity of clh-3 is annotated with a MF.

sharan-gh commented 1 year ago

Right, I see GO:0098718 is a BP. I think if this is not convenient from a GO point of view, it's not hugely consequential for our project to leave it as is. Thank you...

raymond91125 commented 1 year ago

GO's current guideline is that NTR is assessed by specific use cases; we are reluctant to create terms that may be useful. Thanks for your suggestion.