search

geneontology / go-ontology

Source ontology files for the Gene Ontology
http://geneontology.org/page/download-ontology
Creative Commons Attribution 4.0 International
223 stars 40 forks source link

GO:0015563 uptake transmembrane transporter activity vs. GO:0098663 transmembrane transporter activity involved in import into cell #14322

Closed pgaudet closed 7 years ago

pgaudet commented 7 years ago

moved from #14278

Please note the term: GO:0015563 uptake transmembrane transporter activity Definition: Enables the transfer of a specific substance or related group of substances from the outside of a cell to the inside across a membrane. seems to be equivalent to: GO:0098663 transmembrane transporter activity involved in import into cell But GO:0015563 does not have the parent term: GO:0098657 import into cell It looks to me like it should. And then the phrase 'transmembrane transporter activity involved in import into cell' should be added as a synonym to GO:0015563 uptake transmembrane transporter activity

Ruth

pgaudet commented 7 years ago

Hi all,

1) I will propose to obsolete 'GO:0098663 transmembrane transporter activity involved in import into cell'; there are no annotations, and I dont think the specific location of the transport is relevant in the MF.

2) Does anyone know about 'uptake transmembrane transporter activity'? I am tempted to rename the terms with this string to remove the "uptake". It seems like the terms were created to also capture the process of import into cell, but really that needs to be a BP annotation to be consistent across all types of transporters.

pgaudet commented 7 years ago

Moreover about point 2 above: the textual definitions and the logical definition of children of 'uptake transmembrane transporter activity' is not consistent with the 'uptake' textual definition "Enables the transfer of a specific substance or related group of substances from the outside of a cell to the inside across a membrane."

For example:

allantoin uptake transmembrane transporter activity textual definition: Enables the transfer of a specific substance or related group of substances from the outside of a cell to the inside across a membrane. logical definition: 'uptake transmembrane transporter activity' and ('transports or maintains localization of' some allantoin)

So I will make the 'uptake' terms synonyms.

pgaudet commented 7 years ago

For reference: EXP annotations:

GENE PRODUCT DB GENE PRODUCT ID SYMBOL QUALIFIER GO TERM GO NAME ECO_ID GO EVIDENCE CODE REFERENCE WITH/FROM TAXON ID ASSIGNED BY ANNOTATION EXTENSION | 

ValWood commented 7 years ago

Happy for the merge. PomBase annotations have appropriate "x import across plasma membrane" annotation.

ValWood commented 7 years ago

also spotted

high-affinity ferrous iron uptake transmembrane transporter activity high-affinity zinc uptake transmembrane transporter activity used by PomBAse

ValWood commented 7 years ago

need a term for plasma membrane import term for "high-affinity zinc II ion transmembrane import"

There is a similar issue with high and low affinity, it is sometimes doubly encoded in MF and BP I don't think we need it in BP too do we ?

RLovering commented 7 years ago

Can I assume that I don't need to do anything because you will just be renaming? Thanks Ruth

ValWood commented 7 years ago

Hi Ruth. I double checked the pombe ones that the corresponding "import across plasma membrane " term had been used for the process annotation. You might want to do this too?

v

RLovering commented 7 years ago

Good point Processes added, but there is no process term thiamine import (across plasma membrane), but are you going to create new terms for all molecules imported? Or would you be planning on a general term, such as vitamin import? I used AEs to specify extracellular space to cytosol, as extensions to the transmembrane transport term; but not sure this is the best approach to take?

Ruth