Changes between Version 49 and Version 50 of CurationToolMultiGenePhenotypes

Timestamp:

Mar 18, 2015, 2:28:31 PM (6 years ago)

Author:

mah79

Comment:

--

CurationToolMultiGenePhenotypes

@@ -42 +42 @@
 === New thoughts from testing 2014-10-24 (Val) ===
 
-  * 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and would happily go with any better suggestions (THIS ONE NEED CURATOR DISCUSSION) - MAH 2014-10-28: this 'might' be superseded by ideas from today's call; see below and have a think
+  * 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and would happily go with any better suggestions (THIS ONE NEED CURATOR DISCUSSION) - MAH 2014-10-28: this ''might'' be superseded by ideas from today's call; see below and have a think
 
   * ~~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
@@ -64 +64 @@
 
 === New thoughts from testing 2014-10-24 (Midori) ===
- * 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
+ * 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/
  * ~~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
  * ~~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
@@ -113 +113 @@
   * 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
 
- * "Find a genotype" behavior:
+ * "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)
   * Use the "choose genes" interface here -- user selects the combination of genes to search for
   * Search retrieves any genotypes that use all of the selected genes
@@ -129 +129 @@
 
  * Gene page:
-  * Add list of genotypes involving the gene, with link to genotype page
-  * Add back "single gene phenotype" curation type
+  * ~~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)
+  * Add back "single gene phenotype" curation type - see https://sourceforge.net/p/pombase/curation-tool/771/ (mah 2015-03-18)
   * ~~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.
 
 === Ideas from 2014-11-25 call ===
 
- * Search for genotypes by name as well as by genes
+ * ~~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)
  * ~~"Add more genes from PMID:???" is missing from the new evidence selection page~~ - FIXED KMR 2015-03-12
 
 === Thought 2014-11-26 ===
-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:
- * 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.
+~~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:~~
+~~ * 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.~~
 
-(prompted by an email exchange among curators)
+~~(prompted by an email exchange among curators)~~
+moved to ticket https://sourceforge.net/p/pombase/curation-tool/780/ (mah 2015-03-18)
 
 === 2015-01-12 ===