NTRs: Hormone Transport

[ShirinSaverimuttu]

I’d like to request 3 new terms 'hormone transmembrane transporter activity' + 'hormone import' + 'hormone import across plasma membrane'

Reference PMID: 27053689

Figure 1D: High estrone sulfate uptake into HEK-293 cells following transfection of organic anion transporter 3 (OAT3).

Currently 'GO:0009914 hormone transport' exists.

Suggestions:

1. NTR: 'Hormone transmembrane transporter activity' Parentage: part_of 'GO:0009914 hormone transport' Definition: Enables the transfer of hormones from one side of a membrane to the other. DbxREF: GOC:aruk DbxREF: GOC:sccs (do I need to record anywhere that this is my initials and that I have requested this term?)

2. NTR: 'Hormone import' Parentage: is_a 'GO:0009914 hormone transport' Definition: The directed movement of hormones into a cell by means of some agent such as a transporter or pore. DbxREF: GOC:aruk , GOC:sccs

3. NTR: 'Hormone import across plasma membrane Parentage: is_a 'hormone import' Definition: The directed movement of hormones from outside of a cell, across the plasma membrane and into the cytosol. DbxREF: GOC:aruk , GOC:sccs

cc @RLovering

[krchristie]

Hi @ShirinSaverimuttu & @RLovering

Based on conversation with the ontology editor's group on Monday (3/20/20) about the drug & xenobiotic MF terms, I do not want to make a function term for "hormone transmembrane transporter activity". It is not meaningful to describe a MF term with respect to the role of the substance it acts on. Please find a MF term that describes the chemical type of molecule that is being acted on.

Could you please comment on the level of urgency you feel about the BP terms for import. I haven't finalized a plan for the hormone terms so if I put these in now, they may need to change when I get to the hormone role. But if you need them now, I can put the BP terms in. I recommend that you annotate in some way where you are indicating the specific compound acting as a hormone in some way, whether using an extension, GO-CAM, or double annotation.

Thanks,

-Karen

[RLovering]

Hi Karen

I understand the problem about annotating twice, both to the 'functional' role of the transported target, as well as the chemical make up of the target and therefore why the GO editors are planning to remove this aspect. For now Shirin will create the annotations required to both the hormone and 'chemical' terms that are available.

I have several comments I would like to make about this, listed these below:

1. estrone is a steroid and there are insufficient terms to describe steroid processes, although there are many sterol terms. According to ChEBI sterols are a type of steroid, https://www.ebi.ac.uk/chebi/chebiOntology.do?chebiId=CHEBI:15889 therefore please could the following terms be created:

   NTR: steroid transporter activity Definition: Enables the directed movement of steroids into, out of or within a cell, or between cells.

   With the child term> GO:0015248 sterol transporter activity Definition: Enables the directed movement of sterols into, out of or within a cell, or between cells. Sterol are steroids with one or more hydroxyl groups and a hydrocarbon side-chain in the molecule.

NTR: steroid transport Definition: The directed movement of steroids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.

with the child term> GO:0015918 sterol transport Definition The directed movement of sterols into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Sterols are steroids with one or more hydroxyl groups and a hydrocarbon side-chain in the molecule.

NTR: steroid transmembrane transport Definition: The process in which a steroid is transported across a membrane.

with the child term> GO:0035382 sterol transmembrane transport Definition: The process in which a sterol is transported across a membrane. Sterols are steroids with one or more hydroxyl groups and a hydrocarbon side-chain in the molecule.

2. I think that the value for researchers to have terms which relate to the role of the entity being transported justifies the requirement of curators to create two annotations (or more) to ensure that both the chemical type of molecule which is the target of the process as well as the role of the chemical type of molecule.

In addition, how far would this approach take. Will this be applied to all of the following (obviously not a complete list): hormone transport cytokine transport neurotransmitter transport (SynGO will want to be involved in this discussion, as well as other groups) growth factor transport toxin transport vitamin transport eye pigment precursor transport xenobiotic transport

3. Will this also apply to all of the terms that describe other processes which mention these types of molecules eg: xx metabolic process (biosynthesis and catabolism and recycling) xx signaling pathway detection of xx stimulus
   regulation of xx levels

4. Please would you confirm what research has been conducted to support these suggested revisions wrt to the impact it will have on the user community and whether the current or future uses of these terms have been considered. The problem with removing terms like hormone transport is that the tools are not currently available for researchers to query the GO annotations to find all the transporters that may transport a hormone that a researcher might be interested in, this is also confounded by the lack of tools to use the ChEBI ontology within the annotation extension (or GO-CAM) so that not all possible related compounds have to be included in the search of the 'target' molecule. Plus estrone 3-sulfate and estrone are not related in ChEBI therefore in this case both ChEBI IDs would need to be included in the target search.

Many thanks

Ruth

[ValWood]

out of date?