Changes between Version 37 and Version 38 of PreviousCurationMeetings


Ignore:
Timestamp:
Apr 22, 2013, 10:14:31 PM (8 years ago)
Author:
val_wood
Comment:

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  • PreviousCurationMeetings

    v37 v38  
    314314   * Val will make poster/slides/text
    315315 
     316
     317
     318 == Monday 22 April ==
     319
     320
     321 * follow up from below: Antonia will paste in her "protein glycosylation" so far (DONE)
     322
     323 * check that the qualitative/quantitative expression stuff is all documented and working OK (need list of allowed qualifiers etc)
     324 (DONE OR IN PROGRESS)
     325
     326 * Call with Kim to chat about Curation tool :
     327   * request to curate a paper e-mail, revisions (IN PROGRESS WE 3 VW,MH,AL, will do thorough testing once next batch of changes are made to test)
     328
     329
     330 * PomBase User Documentation Drafts (see wiki, mainly done, we should check these through  for details (i.e where TMHMMs from) and move onto jira for mark to link to  page sections, and announce)
     331 (IN PROGRESS, MOST POMBASE USER DOCUMENTATION IS IN PLACE, NEED TO LINK FROM SPECIFIC PAGE SECTIONS TO HELP, and ANNOUNCE)
     332
     333
     334 * make some FYPO terms unavailable for direct annotation. There are  lots of terms where it should be possible to make a more specific phenotype annotation (i.e swollen, elongated, multinucleate, aseptate etc), where it is possible that we did not know this when we made the original annotation. We should slowly look through these and move down. An example but not a great one: https://sourceforge.net/p/pombase/curation-tasks/181/...we we should make the curation tool force people to annotate more specifically for these. For example they should never be able to annotate to a term which does not specify vegetative/ vs G0/ meiotic etc....
     335 (DISCUSSED, AS WE NOTICE TERMS WE CAN ADD THIS SUBSET, AND "DO NOT ANNOTATE" COMMENT. ASKED KIM TO ADD A WARNING TO LOGS)
     336 
     337
     338 * "response to" phenotype only?
     339   * Antonia: when to use cellular response to terms (I know they should not be used for expression data and not to use 'toxin' or 'drug'. But what if there is a sensitivity/growth assay? they are sort of informative are they not - I just want a reminder).
     340   * It seems odd that sty1 will only be annotated to "response to oxidative stress" via 'regulation....'
     341its almost as if we need a term "signalling in response to oxidative stress"
     342
     343 (DISCUSSED, WE WILL NOT USUALLY USE "RESPONSE TO" Terms for GO TERM ANNOTATIONS ANY MORE, BUT WE WILL USE TO  MAKE PHENOTYPE ANNOTATIONS AND USE "IN RESPONSE TO" IN EXTENSIONS)
     344
     345
     346 * How to alert users to scope of terms with 'during vegetative growth' in synonyms and xps, but not the term names? Could rename all, or add to defs, or add comments. (IN PROGRESS)
     347    * i) Midori will add "vegetative growth to definitions"
     348    * ii) We will ask Kim if it is possible to have a "group"  to use a different synonym_type_def and if we did this  would it be possible to display this term name as a default for these terms in the curation tool
     349    * iii) if not we will add to term names (will be a bit clunky on gene pages)
     350   (example processes localisation to centromere/ spindle pole body duplication)
     351( DISCUSSED THIS SHOULD BE FINE AS SYNONYMS ARE NOW ADDED, AND EXACT SYNONYMS WILL BE DISPLAYED BY DEFAULT FOR PHENOTYPE)
     352
     353
     354== Discussed the following "Reminders" ==
     355
     356 *  keep a look out for these:
     357 http://curation.pombase.org/pombe/curs/cc872132c252909e look for others in response waiting file
     358 I changed the evidence for the IGI annotations to ISO because it wasn't really shown in this paper that it is   involved in those processes, it only rescued a growth defect in cerevisiae ortholog mutant
     359
     360 * check all community curation flags set on approved papers
     361For any papers you have sent out, can you check that the "community curatable" flag is set in the triag (also that they have triage status "curatable", some appear to have had the papers added, but the status wasn't set  (probably because it was added directly rather than by the automated paper load).
     362
     363 * Val: I might have put some things through to abnormal chromosome/chromatin organization that should probably be morphology...could you have a look out for them?
     364(we should do queries on this for V 34 and V35 to check)
     365https://sourceforge.net/p/pombase/fission-yeast-phenotype/647/
     366
     367 * localization dependency (many should move to phenotype only during reannotation)
     368
     369