Changes between Version 11 and Version 12 of CurationToolMultiGenePhenotypes


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Timestamp:
Oct 28, 2014, 4:08:11 PM (6 years ago)
Author:
mah79
Comment:

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  • CurationToolMultiGenePhenotypes

    v11 v12  
    1717=== New thoughts from testing 2014-10-24 (Val) ===
    1818
    19   *  The Genotype list  has instruction s "Add a Genotype" I think that for single gene mutant alleles this might be a bit opaque what the user needs to do. I think it might be more obvious if this was called “Genotype and allele list” and the instruction “Add an allele, or a genotype” ...although I am not welded to this and would happily go with any better suggestions (THIS ONE NEED CURATOR DISCUSSION)
     19  * The Genotype list has instructions "Add a Genotype" I think that for single gene mutant alleles this might be a bit opaque what the user needs to do. I think it might be more obvious if this was called “Genotype and allele list” and the instruction “Add an allele, or a genotype” ...although I am not welded to this and would happily go with any better suggestions (THIS ONE NEED CURATOR DISCUSSION) - MAH 2014-10-28: this 'might' be superseded by ideas from today's call; see below and have a think
    2020
    21   * I think most users won't have a clue what to add for a name. We don't want them typing in the entire plo14-123,cdc2delta,cdc3-345 etc, but we need to make it clearer what to add. So, we need to say (succinctly) something  to convey  this “This is a optional “short name”, the lab strain name will do, or , another published label to enable to you to find this genotype quickly) “ A ‘formal’ description of the form(plo14-123,cdc2delta,cdc3-345) will be constructed from the individual alleles  in the database so you do not need to type that in here"  (THIS ONE NEED CURATOR DISCUSSION) - KMR 2014-10-25: It has improved slightly - it doesn't say "click to add genotype name"
     21  * I think most users won't have a clue what to add for a name. We don't want them typing in the entire plo14-123,cdc2delta,cdc3-345 etc, but we need to make it clearer what to add. So, we need to say (succinctly) something  to convey  this “This is a optional “short name”, the lab strain name will do, or , another published label to enable to you to find this genotype quickly) “ A ‘formal’ description of the form(plo14-123,cdc2delta,cdc3-345) will be constructed from the individual alleles  in the database so you do not need to type that in here"  (THIS ONE NEED CURATOR DISCUSSION) - KMR 2014-10-25: It has improved slightly - it doesn't say "click to add genotype name" - MAH 2014-10-28: On today's call we decided changing the wording to "short genotype name (optional)" would do. The documentation we're gonna write any day now will also help.
    2222
    2323  * It would be nice if it were clearer when an allele had been added from the genes in your list. Maybe oce you have selected your gens for a specific genotype, once you added the allele the "add allle box" changed in some way (this might not be good if you have 2 allleles of the same gene) (IGNORE THIS ONE FOR NOW)
     
    2626 
    2727  * Choose evidence for annotating x with y -Make it clearer that here we are doing evidence AND condition
    28      * 1.  Suggest Select evidence  and add conditions(for x with y)
    29      * 2. Put a bit of separation between the evidence box and the conditions
    30      * 3. Previously used conditions do not get added to the list when you click on them
     28   * 1.  Suggest Select evidence  and add conditions(for x with y)
     29   * 2. Put a bit of separation between the evidence box and the conditions
     30   * 3. Previously used conditions do not get added to the list when you click on them
    3131
    3232  * Duplicating a row, Small bug: When I duplicate a row I can change things,  ( change evidence, add conditions) The evidence changed OK, but the new condition I selected did not appear
    3333
    34   * At some point (after adding a single gene phenotype) the only button available was “change genotype” I hit this and it took me back to the summary page (unexpectedly, but that was where I wanted to go!).  When you curate a “single gene phenotype” like this, the allele name (genotype) does not appear. I think this was because I didn’t name it, but the name should be derived from the allele designation(not from the user) see above.
     34  * At some point (after adding a single gene phenotype) the only button available was “change genotype” I hit this and it took me back to the summary page (unexpectedly, but that was where I wanted to go!).  When you curate a “single gene phenotype” like this, the allele name (genotype) does not appear. I think this was because I didn’t name it, but the name should be derived from the allele designation(not from the user) see above. - MAH 2014-10-28: see below for item from today's call relevant to going to the summary page. Other entries may address more of this, but we'll see what needs further discussion or work.
    3535
    3636 * Bug, when I tried to create a genotype wth 3 deletion alleles I was not allowed to "finish". I had to "cancel" it instead - KMR 2014-10-25: I can't reproduce this
     
    3838
    3939
    40 
    41 
    42 
    43 
    4440=== New thoughts from testing 2014-10-24 (Midori) ===
    45  * The gene page needs a route back to phenotype curation (in addition to "change gene").
     41 * The gene page needs a route back to phenotype curation (in addition to "change gene"). - MAH 2014-10-28: agreed; see ideas from today's call below
    4642 * The ontology term page needs route back to term search (at the moment the only option is the paper summary page, and the "back" button does nothing).
    4743 * The "duplicate" popup has the same header as the "edit" popup ("Edit $annotation for $gene"). Could it say something more helpful, such as "Edit fields to create a new annotation for $gene"?
     
    5147  * Maybe a bit more border, too, although there's a risk that would look naff.
    5248  * It'll also help to mention conditions in the header ("Choose evidence and conditions for annotating ...").
    53  * It would be nice to have a way to edit a genotype, in case we make a mistake entering details.
     49 * It would be nice to have a way to edit a genotype, in case we make a mistake entering details. - MAH 2014-10-28: agreed; see ideas from today's call below
    5450  * Ooh, and maybe also a duplicate-and-edit option analogous to "duplicate annotation"? If I have two genotypes, each with six alleles of which five are the same .. (was Antonia asking for something like this on the last call?)
    5551  * Another thing that might be handy is a list of all the genotypes and their descriptions. It might be too much to put in the genotype box on the paper summary page (some genotypes will be complicated), so maybe a new page or popup, with a "see genotype descriptions" link.
    56  * Question for curators: should we have a way to delete an unused genotype from a session? We don't want to delete a genotype from the database, but maybe one that gets added in a session but not used could safely be deleted to declutter the interface.
     52 * Question for curators: should we have a way to delete an unused genotype from a session? We don't want to delete a genotype from the database, but maybe one that gets added in a session but not used could safely be deleted to declutter the interface. - MAH 2014-10-28: see ideas from today's call; see below
    5753
    5854=== Suggested changes from Val ===
     
    6258 * Add conditions to evidence page
    6359 * ~~on publication page "Add a genotype" -> "Select a genotype"~~ - DONE kmr 2014-06-06
    64  * on the "Select a genotype" page
     60 * ~~on the "Select a genotype" page~~ - MAH 2014-10-28: superseded by ideas from today's call; see below
    6561   * ~~first choose the genes for the genotype - checkboxes~~ - DONE kmr 2014-06-06
    6662   * ~~then "Continue"~~ - DONE kmr 2014-06-06
    67    * then "choose an existing genotype" from a list, if any
    68    * otherwise, add alleles ...
    69  * Add auto suggest existing geneotypes based on the collection of genes selected from the list of available genes (BEFORE alleles are added, you only need to do this if your genetype does not already exist)
     63   * ~~then "choose an existing genotype" from a list, if any~~
     64   * ~~otherwise, add alleles ...~~
     65 * ~~Add auto suggest existing geneotypes based on the collection of genes selected from the list of available genes (BEFORE alleles are added, you only need to do this if your genetype does not already exist)~~
    7066
    7167=== To-do items / bugs ===
     
    7672 * It quite happily let me add a duplicate genotype. I think we want to disallow that -- cough up a message such as "That genotype already exists [with the name $genotype_name]", don't we? (mah 2014-10-24)
    7773 * Is the definition getting lost for a term suggestion? I can see the name but not the def for suggestions I put in. (mah 2014-10-24)
     74
     75=== Ideas from 2014-10-28 call ===
     76 * General: any button that goes back to the paper summary page should be labeled (wait for it) "Back to summary".
     77  * we'll also think about what other links might be useful, and where hyperlinks or buttons should go
     78
     79 * Create a separate page for genotype details:
     80  * Name & description for each genotype used for the paper
     81  * "Find a genotype" link
     82  * "Add a genotype" link
     83  * For any genotypes, add a "duplicate" link that behaves like the duplicate-annotation link (to speed up & simplify adding new ones)
     84  * For genotypes added in this session, add an "edit" link (spout a warning if you try to edit a genotype that has phenotypes annotated to it)
     85  * For genotypes added in this session, and NOT used for any annotations, add a "delete this genotype" option
     86
     87 * "Find a genotype" behavior:
     88  * Use the "choose genes" interface here -- user selects the combination of genes to search for
     89  * Search retrieves any genotypes that use all of the selected genes
     90   * each offers an "add a phenotype to this genotype" link
     91  * Also offer link to "Add a new genotype for these genes"
     92   * show the interface with "add allele" just for the selected genes
     93
     94 * "Add a genotype" behavior:
     95  * Remove the "choose genes" step from the current interface; go straight to the gene list with "add allele" buttons for each
     96   * also make sure a genotype can be finished if there isn't an allele for each gene in the list
     97
     98 * On the paper summary page, replace the "Genotype list" box with a briefer summary such as "n genotypes" and link to new Genotypes page. Might need further discussion to get appearance and wording nice.
     99
     100 * Gene page:
     101  * Add list of genotypes involving the gene, with link to genotype page
     102  * Add back "single gene phenotype" curation type
     103  * Add message "to annotate a multi-gene phenotype involving this gene, go to the genotype page" (or words to that effect), with a link