small text change to end of session message/ quick

[pombase-admin]

If there is any information in your paper which you could not curate in the curation tool, (for example orthologs, protein domain data, other protein sequence features, missing gene names, transcriptional regulation or complementation data) please describe the type of data briefly. The curators may be able to capture this information.

To If there is any information in your paper which you could not curate in the curation tool, (for example substrates of protein kinases or other gene products with protein substrates, localization dependencies, specific residues modified in annotated protein modifications, orthologs, protein domain data, other protein sequence features, missing gene names, transcriptional regulation or complementation data) please describe the type of data briefly. The curators may be able to capture this information.

(We can revise this text as new features are added)

Original comment by: ValWood

[pombase-admin]

I think the list of possible additional information is now too long to squeeze into the middle of the first sentence. Wouldn't this read better?

"If there is any information in your paper which you could not capture in the curation tool, please describe the data briefly, as the PomBase curators may be able to include it in the database. Examples include substrates of protein kinases or other gene products with protein substrates, localization dependencies, specific residues modified in annotated protein modifications, orthologs, protein domain data, other protein sequence features, missing gene names, transcriptional regulation or complementation data."

m

Original comment by: mah11

[pombase-admin]

One suggestion for change on Midori's text:

Examples include gene products with protein substrates, for instance substrates of protein kinases, localization dependencies, specific residues modified...

Original comment by: Antonialock

[pombase-admin]

Yes thats better, I think its good to make the list fairly comprehensive, just to prompt them, I am guessing most of the info we will get will relate directly to the examples. ...a list might even work better?

val

Original comment by: ValWood

[pombase-admin]

yeah, a bullet point list might be clearer (by the way, won't 'localization dependencies' be captured with extensions?) eg

Examples include:

* substrates of gene products (e.g. protein substrates of kinases)

• localization dependencies
• specific residues modified in annotated protein modifications (e.g. phosphorylated on residue S45)
• orthologs
• protein domain data or other protein sequence features,
• missing gene names (synonyms)
• transcriptional regulation (of the WT allele - transcriptional changes due to mutations can be captured in the tool)
• complementation data (the pombe gene complements a homologue in a different organism or vice versa, complementation may be full, partial or not complementary)

Original comment by: Antonialock

[pombase-admin]

Yes that is better.

everything will be captured eventually, but it is likely to be a couple of months before users can do extensions. I want to start sending out sessions before this is implemeted. We will need to revise the list as new curation types are added

Original comment by: ValWood

[pombase-admin]

ok that should probably have an example too:

* substrates of gene products (e.g. protein substrates of kinases)

• localization dependencies (e.g. localizes to the nucleus during cellular response to osmotic stress, or during mitotic prophase etc)
• specific residues modified in annotated protein modifications (e.g. phosphorylated on residue S45)
• orthologs
• protein domain data or other protein sequence features
• missing gene names (synonyms)
• transcriptional regulation (of the WT allele - transcriptional changes due to mutations can be captured in the tool)
• complementation data (the pombe gene complements a homologue in a different organism or vice versa, complementation may be full, partial or not complementary)

Original comment by: Antonialock

[pombase-admin]

is it intuitively clear that 'localization dependencies' refers to the GO cellular component annotations? (I don't think it is)

Original comment by: Antonialock

[pombase-admin]

localization dependencies is when the localization of one protein is dependent on another. Lots of people use this terminology when they describe localization dependencies (at least in recent papers)...I'm even wondering if, as most of these will no be caprured with phenotypes, a "comment" on these terms suggesting that users supply the assayed_by gene_products in the feedback at the end, should be included in the terms? these could be deleted as soon as annotation extensions are implemented

Original comment by: ValWood

[pombase-admin]

see google "localization dependencies" and pombe lots of papers (160) use this exact phrase......

Original comment by: ValWood

[pombase-admin]

What is the final text for this?

Original comment by: kimrutherford

[pombase-admin]

• assigned_to: nobody --> kim_rutherford

Original comment by: kimrutherford

[pombase-admin]

Go with: ( I suspect it will be tweaked a bit over the next week or 2) v

If there is any information in your paper which you could not capture in the curation tool, please describe the data briefly, as the PomBase curators may be able to include it in the database. Examples include

• multi-gene phenotypes
• substrates of gene products (e.g. protein substrates of kinases or protein transporters)
• "targets" of localization dependencies (e.g. gene A localizes gene B)
• cell cycle phases when a process occurs (during…)
• specific residues modified in annotated protein modifications (e.g. phosphorylated on residue S45)
• protein domain data or other protein sequence features
• missing gene names (synonyms)
• transcriptional regulation (of the WT allele - transcriptional changes due to mutations can be captured in the tool)
• complementation data (the pombe gene complements a homologue in a different organism or vice versa, complementation may be full, partial or not complementary)
• gene product name updates
• human or budding yeast orthologs Most of these annotation-types will be handled in future releases of the curation tool.

Original comment by: ValWood

[pombase-admin]

sorry, just one tiny change to correct punctuation -

this one should be:

• complementation data (whether the pombe gene complements a homologue in a different organism or vice versa; complementation may be full, partial or not complementary)

... and maybe "full, partial or absent" might read a little better than "complementation may be ... not complementary"? but run with Val's as fixed above for now

Original comment by: mah11

[pombase-admin]

yep use both of Midori's suggestions.

Original comment by: ValWood

[pombase-admin]

I've put Midori's suggestion in as: "complementation data (whether the pombe gene complements a homologue in a different organism or vice versa; complementation may be full, partial or absent)"

Yell if wrong.

Original comment by: kimrutherford

[pombase-admin]

• status: open --> closed-fixed

Original comment by: kimrutherford

[pombase-admin]

Just saw it in the flesh ...er, electrons -- looks fine :)

Original comment by: mah11