Changes between Version 3 and Version 4 of CurationToolMultiGenePhenotypes

Oct 24, 2014, 2:00:35 PM (6 years ago)



  • CurationToolMultiGenePhenotypes

    v3 v4  
    1 = Multi gene phenotype support =
     1= Multi-gene phenotype support =
    33== Suggestions from Skype calls ==
    1414   * allow searching by genotype "name" - autocomplete and then fill in the identifiers
     16=== New thoughts from testing 2014-10-24 (Midori) ===
     17 * The gene page needs a route back to phenotype curation (in addition to "change gene").
     18 * 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).
     19 * 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"?
     20 * The "Add ..." link for the phenotype table needs some sort of cleverness for before any genotypes are added. It would probably be simplest just to have it not appear until after there's at least one genotype available in the session (at least for now). Later we could think about having it link to the genotype-adding interface if there are no genotypes yet.
     21 * In the "standard" phenotype curation interface, the box for adding conditions is subtle and kind of easy to overlook.
     22  * It could probably be (a) a bit smaller and (b) not rammed up against the evidence selector (i.e. put a little bit of vertical whitespace between the evidence pulldown and the conditions box).
     23  * Maybe a bit more border, too, although there's a risk that would look naff.
     24  * It'll also help to mention conditions in the header ("Choose evidence and conditions for annotating ...").
     25 * It would be nice to have a way to edit a genotype, in case we make a mistake entering details.
     26  * 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?)
     27  * 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.
     28 * 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.
    1630=== Suggested changes from Val ===
    1731 * ~~have an "edit gene list" on the "Add a genotype" page - call it "add genes" on this page~~ - DONE kmr 2014-06-06
    2539   * then "choose an existing genotype" from a list, if any
    2640   * otherwise, add alleles ...
    27  * Add auto suggest existing geneotypes based on the collection of genes
    28 selected from the list of avaiable genes (BEFORE alleles are added, you
    29 only need to do this if your genetype does not already exist)
     41 * 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)
    3143=== To-do items / bugs ===
    3244 * ~~the same annotation appears on every gene and genotype page~~ - DONE kmr 2014-10-23
     45 * In the "standard" ontology term search, when I go to select an ontology term, it only "takes" the second time I click it. Not sure how else to describe it -- click to select a term, and nothing happens; click again and it's selected. (This feels like the sort of bug that's going to be a nightmare to reproduce and track down, but I get it in both Firefox and Safari. Happy to demo if that'd help.) Term selection in popups ("Add", "Edit", etc) works as expected. (mah 2014-10-24)
     46 * Is the annotation extension box supposed to appear in the "duplicate" and "edit" popups when one is not logged in? It does at the moment ... (mah 2014-10-24)
     47 * I gave my genotypes names, but the "Add" phenotype popup doesn't use them in the genotype pulldown; I get what I presume is the internal ID gibberish instead, and have to guess which is which. (mah 2014-10-24)
     48 * 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)
     49 * 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)