Changes between Version 404 and Version 405 of CuratorMeeting


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Timestamp:
Apr 22, 2013, 10:11:07 PM (9 years ago)
Author:
val_wood
Comment:

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  • CuratorMeeting

    v404 v405  
    1111 * follow up from below: Antonia will paste in her "protein glycosylation" so far (DONE)
    1212
    13  * check that the qualative/quantitve expression stuff is all documented and working OK (need list of allowed qualifiers etc)
     13 * check that the qualitative/quantitative expression stuff is all documented and working OK (need list of allowed qualifiers etc)
    1414 (DONE OR IN PROGRESS)
    1515
     
    1919
    2020 * 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)
    21  (IN PROGRESS, MODT POMBASE USER DOCUMENTATION IS IN PLACE, NEED TO LINK FROM SPECIFIC PAGE SECTIONS TO HELP, and ANNOUNCE)
    22 
    23 
    24  * make some FYPO terms unavaiable 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....
     21 (IN PROGRESS, MOST POMBASE USER DOCUMENTATION IS IN PLACE, NEED TO LINK FROM SPECIFIC PAGE SECTIONS TO HELP, and ANNOUNCE)
     22
     23
     24 * 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....
    2525 (DISCUSSED, AS WE NOTICE TERMS WE CAN ADD THIS SUBSET, AND "DO NOT ANNOTATE" COMMENT. ASKED KIM TO ADD A WARNING TO LOGS)
    2626 
     
    3434
    3535
    36  == Group call ==
    37 
    38 General issues:
    39 
    40    * ISB/ GO meeting (GMOD (canto/ chado), curation rules (function prediction people)
    41    * nextPomBase build
    42    
    43     Individual Updates & Priorities
    44    * Val priorities: cell cycle report and related annotation updates, import of deletion project morphology phenotypes (~5000 annotations), curation session approval, curation, off work 2 weeks, tidy wiki, curation tool video (Val will look at S/ware and or contact Gulietta), more consistency rules, community curation launch preparation
    45  
    46    * Midori (FYPO, queries for Val, now in progress)
    47    * Antonia (RT, more curation)
    48    * Kim  (Community curation release items )
    49      * V 35 build, is ready for curators for checking
    50    * MArk (version 34 tickets, will check open RT tickets)
    51      * V34 will be  hopefully be live for 29th
    52      * Sam's data, seems to be some discreapancy in the amount of data but should be between 2-4 annotatiosn per gene?
    53 
    54 
    55 
    56  * If time go through curation tracker, and see what con be done quickly
    57 
    58  == Tuesday 23rd April  ==
    59 
    60 A.M 11.00 Group call
    61 
    62   General
    63   Val ISB/ GO meeting (GMOD (canto/ chado), curation rules (function prediction people) curation session approval, curation, off work 2 weeks, tidy wiki), curation tool video
    64    * nextPomBase build
    65   Individual Updates & Priorities
    66    * Val (cell cycle report & annotation updates, import of morphology phenotypes, consistency rules)
    67    * Midori (FYPO)
    68    * Antonia (RT)
    69    * Kim  ( Community curation release)
    70    * MArk (version 34 tickets)
    71 
    72 
    73  == Monday 6 May ==
    74 
    75 Go ahead or cancel?
    76 
    77  == Tue 22 May ==
    78 
    79 Go ahead or cancel?
    80 
    81  == Next  plan dates, no room booked ==
    82 
    83  * Galaxy demo, pombe specific example (would the bent cells work?)
    84 
    85  
    86  == Reminders ==
    87 
    88  *  keep a look out for these:
    89  http://curation.pombase.org/pombe/curs/cc872132c252909e look for others in response waiting file
    90  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
    91 
    92  * check all community curation flags set on approved papers
    93 For 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).
    94 
    95  * 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?
    96 (we should do queries on this for V 34 and V35 to check)
    97 https://sourceforge.net/p/pombase/fission-yeast-phenotype/647/
    98 
    99  * localization dependency
    100 
    101 
    102  == Next ==
    103 
    104  * Use of inhibited by...used for "biological inhibition" (i.e regulation)  and exogenous inhibition...discuss?
    105 
    106 
    107  * discuss what should be the default text for searching terms etc (see e-mail with subject "default text")
    108 
    109   * 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)
     36 * 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)
    11037    * i) Midori will add "vegetative growth to definitions"
    11138    * 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
    11239    * iii) if not we will add to term names (will be a bit clunky on gene pages)
    11340   (example processes localisation to centromere/ spindle pole body duplication)
     41( DISCUSSED THIS SHOULD BE FINE AS SYNONYMS ARE NOW ADDED, AND EXACT SYNONYMS WILL BE DISPLAYED BY DEFAULT FOR PHENOTYPE)
     42
     43
     44== Discussed the following "Reminders" ==
     45
     46 *  keep a look out for these:
     47 http://curation.pombase.org/pombe/curs/cc872132c252909e look for others in response waiting file
     48 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
     49
     50 * check all community curation flags set on approved papers
     51For 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).
     52
     53 * 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?
     54(we should do queries on this for V 34 and V35 to check)
     55https://sourceforge.net/p/pombase/fission-yeast-phenotype/647/
     56
     57 * localization dependency (many should move to phenotype only during reannotation)
     58
     59
     60 == Group call ==
     61
     62General issues:
     63
     64   * ISB/ GO meeting (GMOD (canto/ chado), curation rules (function prediction people)
     65   * next PomBase build
     66   
     67Individual Updates & Priorities
     68   * Val priorities: cell cycle report and related annotation updates, import of deletion project morphology phenotypes (~5000 annotations), curation session approval, curation, off work 2 weeks, tidy wiki, curation tool video (Val will look at S/ware and or contact Gulietta), more consistency rules, community curation launch preparation
     69 
     70   * Midori (FYPO, queries for Val, now in progress, Documentation)
     71   * Antonia (RT, more curation)
     72   * Kim  (Community curation release items )
     73     * V 35 build, is ready for curators for checking
     74   * Mark (version 34 tickets, will check open RT tickets)
     75     * many outstanding issues related to ftp site and file download, mark is still working on this pipeline
     76
     77     * V34 will be  hopefully be live for 29th
     78     * Sam's data, seems to be some discrepancy in the amount of data but should be between 2-4 annotations per gene?
     79
     80
     81
     82 * If time go through curation tracker, and see what con be done quickly
     83
     84 == Tuesday 23rd April  ==
     85
     86 == Monday 6 May ==
     87
     88Go ahead or cancel?
     89
     90 == Tue 22 May ==
     91
     92 Cancelled
     93
     94 == Next  plan dates, no room booked ==
     95
     96 * Galaxy demo, pombe specific example (would the bent cells work?)
     97
     98 
     99 
     100
     101
     102 == Next ==
     103
     104 * Use of inhibited by...used for "biological inhibition" (i.e regulation)  and exogenous inhibition...discuss?
     105
     106
     107 * discuss what should be the default text for searching terms etc (see e-mail with subject "default text")
     108
     109 
    114110
    115111 * GO regulation of process discuss, make guidelines