Discourage "Submit to curators" if there is no annotation

[pombase-admin]

Currently there are users who click "Submit to curators" without trying to make any annotation. In some cases that makes sense - the paper might be a review. Sometimes it's just because the interface scares them and they just want out.

Perhaps we need to grey-out the Submit button if there is no annotation and have a checkbox underneath labelled something like: "No gene specific annotations to curate"

On mouseover we could show: "Select this if you can provide a list of genes mentioned in the paper, but you cannot make gene-specific annotations based on experiments in the paper"

If they tick the box they would need to choose a reason why there is no annotation. Then the submit button would become active / not grey.

As soon as any annotation is added to the session we should hide the checkbox.

Original comment by: kimrutherford

[pombase-admin]

I've started to implement this but I think we might need to revisit the gene upload page functionality at the same time.

The idea with this ticket is to get the users to put in the gene names when there are some, then later click a checkboix on the publication page to say they have genes but no annotation.

If we do that I think this message by the checkbox on the gene upload page needs changing: "This paper is not suitable for gene-specific curation in Canto"

We need to make it clear that listing the gene names count as gene-specific curation.

Any thoughts?

I'll get on with changing the publication page as described in the ticket while we think about it.

Original comment by: kimrutherford

[pombase-admin]

I don't quite understand... Midori?

Do you mean we need to day something along the lines.

"This paper contains NO EXPERIMENTAL INFORMATION to add to the specific genes uploaded" ?

A clear declarative statement.

Original comment by: ValWood

[pombase-admin]

Kim is saying that with the new step in place, the tickbox message at the PREVIOUS step (i.e. the page where you enter gene list, not after the list is already uploaded) doesn't make as much sense as before.

Suggestion: on the gene list entry page, change "This paper is not suitable for gene-specific curation in Canto" to "This paper does not contain any gene-specific information".

Original comment by: mah11

[pombase-admin]

OK yes I see. Change the text to that.

Original comment by: ValWood

[pombase-admin]

In the test tool, I've made to the text on the upload page and I've added the "no annotation" checkbox to the publication page.

Here's an example upload page: http://curation.pombase.org/test/curs/749bb0643165efcb

Here's an example publication page with no annotation: http://curation.pombase.org/test/curs/1f2d24c55c2d2b93

The list of possible reasons on the publication page is just "Review" at the moment. Could someone review the list of reasons on both pages and let me know what is appropriate where. Also please let me know if the labels and text is OK on both pages. The changes aren't in the main tool yet.

If there is no annotation, the reason is shown on the finished publication page and is show as a message when you're reviewing.

It looks like: Reason given for no annotation: Review

but it's currently not very obvious.

(The finished annotation page is a bit un-formatted currently. If anyone has any suggestions for improvement, please let me know.)

Original comment by: kimrutherford

[pombase-admin]

I think this all looks good.

1. Please list the genes studied in this paper using the systematic identifier (eg. SPCC1739.10) or standard name (eg. cdc11) separated by commas, spaces, tabs or one per line. remove 2nd line: The list of gene identifiers can be separated by commas, spaces, tabs or there can be one per line.

1. No annotation for these genes change to No experimental results to add?

we only have one reason, review, what were the others ? add i) Review iii) Opinion or Comment ii) Experimental data, not of available types iv) Method (we need to repeat method here, because it may be a method, but they could have added a gene (if it was an expression vector for example)

1. I wonder if it would be nice if, the very first time the user gets to the curation type selection page, they get a notice

"If you do not know which annotation type to use to describe your experiment, please contact the helpdesk"

but this link disappears after they have managed to add on piece of data

Original comment by: ValWood

[pombase-admin]

I've made those changes. Could you have a look when you get a chance?

Original comment by: kimrutherford

[pombase-admin]

Testing now.

For the test tool I have the following URLs on the wiki https://sourceforge.net/apps/trac/pombase/wiki/UsefulLinks

Test tool, generic front page http://curation.pombase.org/test/docs/canto_front Test Tool, Admin http://curation.pombase.org/test/ Test Tool, Public front page http://curation.pombase.org/test/local/pombase_front_page "Throwaway" session for testing without genes http://curation.pombase.org/test/test_curs/ "Throwaway" session for testing with genes http://curation.pombase.org/test/test_curs/2

The generic front page test links to the live tool, is that OK?

this link: Test Tool, Public front page http://curation.pombase.org/test/local/pombase_front_page does not work should I just delete?

"Throwaway" session for testing without genes http://curation.pombase.org/test/test_curs/ "Throwaway" session for testing with genes http://curation.pombase.org/test/test_curs/2 no longer work

Original comment by: ValWood

[pombase-admin]

If the session is submittted, and no genes have been added becusae there is not gene specific information this message is a little confusing:

If there is any information in your paper which you could not capture in the curation tool, please describe the data briefly, as the 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 (whether the pombe gene complements a homologue in a different organism or vice versa; complementation may be full, partial or absent)
gene product name updates
human or budding yeast orthologs 

Most of these annotation-types will be handled in future releases of the curation tool.

I think only this is required here If there is any information in your paper which you could not capture in the curation tool, please describe the data briefly, as the curators may be able to include it in the database.

but not the examples, which are gene specific.

Original comment by: ValWood

[pombase-admin]

For this message,

If you do not know which annotation type to use to describe your experiment, please contact the helpdesk

I think this will work, but it needs to move forward one page so it appears when you first select a gene product. I have a 'hunch' people were clicking on the gene name (which is not so scary), being scared by the available list of annotation types, and then bailing by hitting 'back' and then hitting 'submit'.

So we need to let them no we can help them, when they are first on the 'scary' page.

Original comment by: ValWood

[pombase-admin]

but not the examples, which are gene specific.

continued from above. The current text box is absolutely fine for the situation when genes are added but no curation is made. But not when no genes are added. Does that make sense.

Other than the above, this is all looking like a well set trap to entice them in.....

Original comment by: ValWood

[pombase-admin]

A few text changes are still needed for this ticket. I'll do them today so hopefully it will be ready to go tomorrow.

Original comment by: kimrutherford

[pombase-admin]

I think this will work, but it needs to move forward one page so it appears when you first select a gene product.

That makes sense. I've moved the message to the gene page.

Do you think we need a friendly one-off message on the publication like: "To start annotating, choose a gene from the list"? Or is it obvious enough?

Original comment by: kimrutherford

[pombase-admin]

For the test tool I have the following URLs on the wiki https://sourceforge.net/apps/trac/pombase/wiki/UsefulLinks

I've just removed a bunch of links that don't work anymore. The /test_curs/ links have been "retired" as you can now just put any old pubmed ID into the test tool to get a test session.

Original comment by: kimrutherford

[pombase-admin]

The current text box is absolutely fine for the situation when genes are added but no curation is made. But not when no genes are added. Does that make sense.

Yep, that makes sense. They now only see the examples of other information if they added some genes to the session.

Original comment by: kimrutherford

[pombase-admin]

• status: open --> closed
• Group: -->

Original comment by: kimrutherford

[pombase-admin]

Do you think we need a friendly one-off message on the publication like: "To start annotating, choose a gene from the list"? Or is it obvious enough?

Apart from this, I think we're finished. I'm closing the ticket. Please re-open if you'd like this message added.

Original comment by: kimrutherford