new children for protein complexes? transmembrane transporters / drug exporters

geneontology / go-ontology

Source ontology files for the Gene Ontology

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new children for protein complexes? transmembrane transporters / drug exporters #10615

Closed gocentral closed 9 years ago

gocentral commented 11 years ago

Hi,

I am tempted to create new children of GO:0023432 protein complex for complexes associated with

GO:0055085 transmembrane transport (BP) & GO:0022857 transmembrane transporter activity (MF)
(as child of 1.) GO:0006855 drug transmembrane transport (BP) & GO:0015238 drug transmembrane transporter activity (MF)
possibly further child of 2. related to GO:0046618 drug export (BP) & GO:0015307 drug:hydrogen antiporter activity (MF)

Recently curated examples are: GO:1990191, GO:1990196, GO:1990197, GO:1990199, GO:1990200, GO:1990201, GO:1990202, GO:1990203, GO:1990207

Regards, Birgit

Reported by: bmeldal

Original Ticket: geneontology/ontology-requests/10420

gocentral commented 11 years ago

Hi Birgit - surprised we don't already have the terms in 1. The issue will be that we'll have to manually classify all existing transporters under the new term.

I'll bring this up on our call tomorrow. It probably makes sense to add logical defs while we're doing the classification. That way we'll be able to make you a template for [MF]-[protein-complex].

Jane

Original comment by: jl242

gocentral commented 11 years ago

labels: New term request --> New term request, protein complex
assigned_to: Jane Lomax

Original comment by: jl242

gocentral commented 11 years ago

I can see the pain of manually reclassifying them all! I shall wait for the call outcome. Birgit

Original comment by: bmeldal

gocentral commented 11 years ago

Is there a precedent for grouping complexes by process? (at present it appears to be a flat list, with some exceptions like "chromatin remodelling complex"). Is this something we plan to do ? ...I would avoid any classification using "drug" because the def is wooly

a drug, a substance used in the diagnosis, treatment or prevention of a disease; as used here antibiotic substances (see antibiotic metabolism) are considered to be drugs, even if not used in medical or veterinary practice.

in fact, we don't use the same def throughout GO....

Original comment by: ValWood

gocentral commented 11 years ago

Hi Valerie,

I'm curating complexes in IntAct and in the process I'm creating GO terms to link everything together. One of the objectives of my project is to add more of a logical hierarchy to GO:0023432 protein complex. So, 'no', there is no systematic precedent for grouping complexes by process but I'm trying to group them together by logic, which may be by MF or BP. Additionally, the editors create logical definitions to link the complex terms to relevant MFs or BPs.

I agree, the definition of 'drug' is bound to be tricky!

Birgit

Original comment by: bmeldal

gocentral commented 11 years ago

Val - we'll be using the CHEBI role for drug in GO xps:

http://www.ebi.ac.uk/chebi/advancedSearchFT.do?searchString=CHEBI%3A23888&submit=Search+ChEBI&queryBean.stars=2

and we've made the decision to classify protein complexes primarily by function i.e. function X protein complex = protein complex X capable_of function Y

This will allow us to have some structure in the protein complex hierarchy which is, as you say, pretty flat right now.

Original comment by: jl242

gocentral commented 11 years ago

Except for those complexes where the function is not known (or not clearly defined) but the associated process is know, we can link it to process (I'd have to dig to see if we have already linked one to process...)

Did ChEBI think long hard about their 'drug' definition? I can think of many therapeutic substances that are also abused substances... ;-)

Original comment by: bmeldal

gocentral commented 10 years ago

Do we have a solution for this? What came out of the call a few weeks ago? Shall I just create the transmembrane transport complex?

Original comment by: bmeldal

gocentral commented 10 years ago

Yesterday, I created GO:1902495 transmembrane transporter complex using the new TG template and added a SF ticket to move all of 'my' transporter terms over (which is on Becky's list). It would be nice to create a script that looks for all appropriate terms to bind them.

Birgit

Original comment by: bmeldal

gocentral commented 10 years ago

Okay, I'll close this then.

If we add 'capable_of' transmembrane transporter activity relations to the child terms to the appropriate complex terms, they will be automatically classified. This will have to be done by hand though.

Original comment by: jl242

gocentral commented 10 years ago

status: open --> closed-works-for-me

Original comment by: jl242

gocentral commented 10 years ago

Once I have the field in TG FF I will add the capable_of immediately :) I think going back through the legacy terms is not a priority as - I assume - there are 1000s of terms that could have a capable_of or intersection annotation curated retrospectively!

Original comment by: bmeldal

gocentral commented 10 years ago

There certainly are! Maybe we could arrange a jamboree with you for a day or two at some point and work through them.

Original comment by: jl242

gocentral commented 10 years ago

We could do that! It would require lost of brain-food though!

Original comment by: bmeldal