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PMID:17107817 MgMfs1, a major facilitator superfamily transporter from the fungal wheat pathogen Mycosphaerella graminicola, is a strong protectant against natural toxic compounds and fungicides #204

Closed jingluodatacurator closed 5 months ago

jingluodatacurator commented 8 months ago

Curated by @jingluodatacurator

https://canto.phi-base.org/curs/49a9994d2b20ee03

Notes: Uniprot ID: F9XG71 Strains: IPO323 Main expt. for curation: see Materials and Methods 2.4 & 2.5, and Results 3.3.

CuzickA commented 5 months ago

Checking UniProt - looks fine 'The nucleotide sequence of MgMfs1 is available at GenBank with Accession No. DQ6619111.'

Nothing found in UniProt or Genbank when search for 'DQ6619111'

search UniProt for 'MgMfs1' gives three entries. The entry for Zt reference IPO323 has correctly been selected https://www.uniprot.org/uniprotkb/F9XG71/entry image

CuzickA commented 5 months ago

Current annotations image

CuzickA commented 5 months ago

Feedback for @jingluodatacurator 1) Please change the genotype to MgMfs1::Hyg cassette (disruption) to be consistent with disruption genotype naming as discussed previously in ticket https://github.com/PHI-base/curation/issues/202 2) Update the phenotypes - I think these should both be 'sensitive to' image image

image

3) As discussed in https://github.com/PHI-base/curation/issues/207 Please check and update the conditions so that they contain the chemical and the conditions used within the phenotype expt rather than the generation of the mutations. image image

4) I think PHI phenotype annotations could be made please image image image image

Thanks @jingluodatacurator, please let me know how you get on and if you have any queries.

CuzickA commented 5 months ago

I think that adding the AE alteration in archetype is N/A as NTSR, MFS transporter.

jingluodatacurator commented 5 months ago

Feedback for @jingluodatacurator

  1. Please change the genotype to MgMfs1::Hyg cassette (disruption) to be consistent with disruption genotype naming as discussed previously in ticket PMID:17379549 MgAtr7, a new type of ABC transporter from Mycosphaerella graminicola involved in iron homeostasis #202
  2. Update the phenotypes - I think these should both be 'sensitive to' image image

image

  1. As discussed in PMID:21933337 Risk assessment studies on succinate dehydrogenase inhibitors, the new weapons in the battle to control Septoria leaf blotch in wheat #207 Please check and update the conditions so that they contain the chemical and the conditions used within the phenotype expt rather than the generation of the mutations. image image
  2. I think PHI phenotype annotations could be made please image image image image

Thanks @jingluodatacurator, please let me know how you get on and if you have any queries.

Hi @CuzickA, I have made the updates as below:

  1. changed the genotype to MgMfs1::Hyg cassette (disruption) to be consistent with disruption genotype naming.
  2. updated the phenotypes of mutants to be 'sensitive to'.
  3. updated conditions and figures according to experiments.
  4. PHI phenotype annotations have been created.

Please check them and let me know any corrections to be made or further actions to be done, thanks.

jingluodatacurator commented 5 months ago

Hi @CuzickA, I have a question regarding the expression of mutant genotype. According to the text in text page 385, section 3.6. Expression of MgMfs1 in disruptants (again, I tried snip tool to copy and paste image of the text but it didn't work. I have contacted James to help me solving this hopefully soon!). Would the expression level be Not assayed or Knockdown in this case? Thanks.

CuzickA commented 5 months ago

Hi @CuzickA, I have a question regarding the expression of mutant genotype. According to the text in text page 385, section 3.6. Expression of MgMfs1 in disruptants (again, I tried snip tool to copy and paste image of the text but it didn't work. I have contacted James to help me solving this hopefully soon!). Would the expression level be Not assayed or Knockdown in this case? Thanks.

Hi @jingluodatacurator, good spot. Yes, I think you use expression level knockdown.

CuzickA commented 5 months ago

Hi @jingluodatacurator, Feedback on 1. The disruption genotype is very close but still not quite right. In the example in #202 it looks like this image image

We currently have image

The extra information that has been added to the description needs to be added into the gene name section please image

CuzickA commented 5 months ago

Hi @jingluodatacurator, Feedback on 2 and 3 image

  1. sensitive to... phenotype annotations look good. We do not curate the wild type controls for the pathogen only phenotype annotations, we only curate them for the pathogen host interaction (metagenotypes) phenotypes. We have a note of this from Maiara, in the Google FAQ document 'Draft Chemistry curation FAQ and tips' under 'Information not to curate in PHI-Canto for Chemistry curation' 'Pathogen phenotype controls.'

  2. conditions and figures look good

CuzickA commented 5 months ago

Hi @jingluodatacurator, Feedback on 5

PHI phenotypes look pretty good. Just a few things to change please a) the AEs have been added to the Wild type control metagenotype instead of the pathogen mutant metagenotype.

b) The condition 'rich media' is not really used for PHI phenotypes it really applies more to the pathogen only phenotypes. Instead the condition 'delivery mechanism: pathogen inoculation' would be better here.

image

jingluodatacurator commented 5 months ago

Hi @CuzickA, our internet has been really slow this morning, but all points above have been updated and corrected. Please check thanks. https://canto.phi-base.org/curs/49a9994d2b20ee03

CuzickA commented 5 months ago

1 and 2. Looks good

image

CuzickA commented 5 months ago
  1. looks good

image

CuzickA commented 5 months ago

I think that adding the AE alteration in archetype is N/A as NTSR, MFS transporter.

Session now approved.

Closing ticket.