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PMID:31501141 Trichophyton rubrum Azole Resistance Mediated by a New ABC Transporter, TruMDR3. #53

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CuzickA opened this issue Nov 5, 2019 · 13 comments

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@CuzickA
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CuzickA commented Nov 5, 2019

Link to curation session
https://canto.phi-base.org/curs/b06680e815f64df0

Suggest by author 'Marc Feuermann' from Swiss-prot

@CuzickA
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CuzickA commented Nov 5, 2019

help #175908] [uuw] UniProtKB/TrEMBL F2SG60 entry update request
requested MDR3 added as the gene name.
used email address [email protected]

Now done by Marc Feuermann 18/11/2019

@CuzickA
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CuzickA commented Nov 5, 2019

Hi @ValWood Please could you check this very short chemistry curation session.

I'm not sure the best way of capturing the phenotype here as its not clear what to use as the control

  • the clinical isolate TIMM20092 shows increased resistance to VRC and ITC compared to other clinical isolates (CHUV1845)
  • In the paper I can't see a comparison between TIMM20092 with the isolate used by UniProt as the reference proteome.
  • When MDR3 is disrupted in TIMM20092 authors report increased sensitivity to VRC and ITC
    would the phenotype be 'sensitive to VRC'?
    OR a new type of term such as 'increased sensitivity of a VRC resistant strain?

What should we use as the control?
The last chemistry paper we curated was simpler as the resistant strain was compared to the reference strain.

Also to note: UniProt appears to have 2 refernce strains here but I assume we focus on the top entry strain as this matches the UniProt id obtained from the gene id provided in the paper (TERG_02186).
image

@ValWood
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ValWood commented Nov 6, 2019

my assumption is that any mutant is compared to WT of the same strsain.

So here I think "sensitive to x" is OK.
I don't think it matters that they don't show the WT for the strain because we kown that it is resistant from the history

I guess more annotation could be made for this paper if we had a better way to do the ectopic expression ....

@ValWood ValWood removed their assignment Nov 6, 2019
@ValWood
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ValWood commented Nov 29, 2019

+id: GO:0140394
+name: ATPase-coupled azole transmembrane transporter activity
should be available tomorrow

@CuzickA
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CuzickA commented Dec 19, 2019

I have used the new above term to replace the previously used GO term in the session.

@CuzickA
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CuzickA commented Dec 19, 2019

Looks like this basic Tier 1 level curation session is complete.
The gene name has been added by UniProt.

@CuzickA
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CuzickA commented Mar 13, 2020

Session approved, closing ticket.

@CuzickA
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CuzickA commented Dec 7, 2020

Check new 'chemistry phenotype' terms. may need NTR: normal growth chemical X

@CuzickA CuzickA reopened this Dec 7, 2020
@CuzickA CuzickA self-assigned this Dec 7, 2020
@CuzickA CuzickA added next and removed next labels Dec 7, 2020
@CuzickA
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CuzickA commented Dec 8, 2020

Check new 'chemistry phenotype' terms. may need NTR: normal growth chemical X

No need. Closing ticket.

@CuzickA
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CuzickA commented May 23, 2023

Title of publication calls gene TruMDR3
image

UniProt gene name MDR3 and so the GO annotations use MDR3
image

Genotype named as TruMDR3
image

Hi @ValWood, do you think we need the species prefix at the beginning of the gene name in the genotype? Should the genotype also just be MDR3::nptII+(disruption) in stead of TruMDR3::nptII+(disruption)?

@CuzickA CuzickA reopened this May 23, 2023
@ValWood
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ValWood commented May 23, 2023

It is OK to put the genotype name as the authors named it, as long as the description is standardized (i.e disruption), and it is linked to the official gene name.

@CuzickA
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CuzickA commented May 23, 2023

Thanks for confirming this :-).

@CuzickA CuzickA closed this as completed May 23, 2023
@CuzickA
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CuzickA commented Sep 13, 2023

no archetype information found

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