Changes between Version 49 and Version 50 of CurationToolMultiGenePhenotypes


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Timestamp:
Mar 18, 2015, 2:28:31 PM (6 years ago)
Author:
mah79
Comment:

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  • CurationToolMultiGenePhenotypes

    v49 v50  
    4242=== New thoughts from testing 2014-10-24 (Val) ===
    4343
    44   * 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and would happily go with any better suggestions (THIS ONE NEED CURATOR DISCUSSION) - MAH 2014-10-28: this 'might' be superseded by ideas from today's call; see below and have a think
     44  * 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and would happily go with any better suggestions (THIS ONE NEED CURATOR DISCUSSION) - MAH 2014-10-28: this ''might'' be superseded by ideas from today's call; see below and have a think
    4545
    4646  * ~~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.~~ - DONE KMR 2015-01-13
     
    6464
    6565=== New thoughts from testing 2014-10-24 (Midori) ===
    66  * 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
     66 * 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 - mah 2015-03-18: also see https://sourceforge.net/p/pombase/curation-tool/771/
    6767 * ~~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).~~ - DONE KMR 2014-11-10
    6868 * ~~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"?~~ - DONE KMR 2014-11-10
     
    113113  * KMR 2014-11-10 - there is now a "Genotypes management" page but the formatting is very basic and the bullet points above aren't done
    114114
    115  * "Find a genotype" behavior:
     115 * "Find a genotype" behavior: - Update: this stuff is sort of implemented but buggy. Can probably follow the whole thing on tracker tickets from now on. (mah 2015-03-18)
    116116  * Use the "choose genes" interface here -- user selects the combination of genes to search for
    117117  * Search retrieves any genotypes that use all of the selected genes
     
    129129
    130130 * Gene page:
    131   * Add list of genotypes involving the gene, with link to genotype page
    132   * Add back "single gene phenotype" curation type
     131  * ~~Add list of genotypes involving the gene, with link to genotype page~~ moved to ticket https://sourceforge.net/p/pombase/curation-tool/781/ (mah 2015-03-18)
     132  * Add back "single gene phenotype" curation type - see https://sourceforge.net/p/pombase/curation-tool/771/ (mah 2015-03-18)
    133133  * ~~Add message "to annotate a multi-gene phenotype involving this gene, go to the genotype page" (or words to that effect), with a link~~ - DONE KMR 2014-11-12 - let me know if you'd like the wording changed.
    134134
    135135=== Ideas from 2014-11-25 call ===
    136136
    137  * Search for genotypes by name as well as by genes
     137 * ~~Search for genotypes by name as well as by genes~~ moved to ticket https://sourceforge.net/p/pombase/curation-tool/779/ (mah 2015-03-18)
    138138 * ~~"Add more genes from PMID:???" is missing from the new evidence selection page~~ - FIXED KMR 2015-03-12
    139139
    140140=== Thought 2014-11-26 ===
    141 I think it was part of the original multi-gene phenotype spec that for genotypes that have both a wild-type copy and a mutant copy of the same gene, either or both can be at the endogenous expression level (if not, it should've been). So we need this change in the interface:
    142  * Allow a wild type allele at endogenous or "not specified" expression as part of a genotype. The single gene phenotype version should not change -- that should still only offer overexpression and knockdown for wild type. If possible, it would be nice to have a warning if a genotype only has wild type, endogenous expression (and no other alleles) for any one gene.
     141~~I think it was part of the original multi-gene phenotype spec that for genotypes that have both a wild-type copy and a mutant copy of the same gene, either or both can be at the endogenous expression level (if not, it should've been). So we need this change in the interface:~~
     142~~ * Allow a wild type allele at endogenous or "not specified" expression as part of a genotype. The single gene phenotype version should not change -- that should still only offer overexpression and knockdown for wild type. If possible, it would be nice to have a warning if a genotype only has wild type, endogenous expression (and no other alleles) for any one gene.~~
    143143
    144 (prompted by an email exchange among curators)
     144~~(prompted by an email exchange among curators)~~
     145moved to ticket https://sourceforge.net/p/pombase/curation-tool/780/ (mah 2015-03-18)
    145146
    146147=== 2015-01-12 ===