Changes between Version 637 and Version 638 of CuratorMeeting


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Timestamp:
Jul 8, 2015, 3:23:15 PM (5 years ago)
Author:
mah79
Comment:

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  • CuratorMeeting

    v637 v638  
    88 ==  Curation priorities ==
    99
    10  *  Approval of community sessions
    11  *  Processing phenotype screens
     10 * Approval of community sessions
     11 * Processing phenotype screens
    1212  * Down to one assigned to Jurg (community) and one where I have a couple of questions to discuss (midori 2015-03-25)
    13  *  Identification of stalled community curation sessions and processing of any term requests in these
    14  *  General [http://curation.pombase.org/pombase-trac/wiki/AnnotationPriorities curation priorities]  based on biology
    15  *  Fixing FYPO specificity https://sourceforge.net/p/pombase/chado/419/ (in progress -midori)
    16  *  Fixing GO specificity (I have done most of these)
    17  *  Helpdesk tickets
    18  * logs, antonia 50, midori 51 Val 52 reminder, include the GO terms we don't annotate (canto only)
     13 * Identification of stalled community curation sessions and processing of any term requests in these
     14 * General [http://curation.pombase.org/pombase-trac/wiki/AnnotationPriorities curation priorities]  based on biology
     15 * Fixing GO specificity (I (i.e. Val) have done most of these)
     16 * Helpdesk tickets
     17 * logs - reminder, include the GO terms we don't annotate (canto only)
    1918 
    2019 == In Progress, parked ==
    2120
    22   * which other relations need to be included in Canto? ( so far only has_part, is this in the live tool yet or test only?) All keep a look out for this in the tool, and think about which others we want to see.
     21  * which other relations need to be included in Canto? (so far only has_part, is this in the live tool yet or test only?) All keep a look out for this in the tool, and think about which others we want to see.
    2322
    24   * Discussion about search behavior for phenotypes (alleles, conditions, multigene, and GO extensions
     23  * Discussion about search behavior for phenotypes (alleles, conditions, multigene, and GO extensions)
    2524   Decided:
    26     * For now we will only provide  allele type filter  (ignore conditions, penetance, expressivity) for phenotype, Midiri will do a mock up (null expression/overexpression)
    27    *  Discussion for how to handle searches on GO extensions was postponed, and will be addressed when we go through the relations list and decide what type of queries might be useful
    28    * For multi gene phenotypes so far decided
     25   * For now we will only provide allele type filter (ignore conditions, penetrance, expressivity) for phenotype, Midori will do a mock up (null expression/overexpression) [https://www.ebi.ac.uk/panda/jira/browse/PB-2196 ticket for mockup]
     26    *  Discussion for how to handle searches on GO extensions was postponed, and will be addressed when we go through the relations list and decide what type of queries might be useful
     27    * For multi-gene phenotypes so far decided
    2928     *  will need to be able to search on a phenotype and then filter on one of
    30        i) single gene phenotype. Single gene phenotype only will allow the allele filter option.
    31        II) single or multi gene phenotype
    32        iii) multi gene phenotype only
    33     * we are not currently sure what the results page should show. Two types of output, geneotype list and genes. A summary of the geneotype list and the gene list? discuss this next.
    34        * The gene list will populate the current query history table. but the query history will need an additional table for geneotypes  (what do we want to be able to do with geneotype lists in the history?)
    35        * need the ability to filter results to present genotypes with a specific gene
     29      * single gene phenotype. Single gene phenotype only will allow the allele filter option.
     30      * single or multi-gene phenotype
     31      * multi-gene phenotype only
     32    * we are not currently sure what the results page should show. Two types of output, geneotype list and genes. A summary of the genotype list and the gene list? discuss this next.
     33     * The gene list will populate the current query history table. but the query history will need an additional table for genotypes  (what do we want to be able to do with geneotype lists in the history?)
     34     * need the ability to filter results to present genotypes with a specific gene
    3635
    3736  * creating a DB x-ref for ISS inferences for annotations other than GO
    38     *  will get rid of http://curation.pombase.org/dumps/latest_build/logs/db_xref_problems.txt
     37    * will get rid of http://curation.pombase.org/dumps/latest_build/logs/db_xref_problems.txt
    3938    * https://www.ebi.ac.uk/panda/jira/browse/PB-1916
    4039    * suggestion PB_REF:0000001 "def"
    4140 
    42    *  Do we want to group some phenotypes   (normal?) https://www.ebi.ac.uk/panda/jira/browse/PB-1837 do we have a preferred ordering
     41   *  Do we want to group some phenotypes (normal?) https://www.ebi.ac.uk/panda/jira/browse/PB-1837 do we have a preferred ordering
    4342     *  Suggestion:  group by putting all gene expression phenotypes together at the bottom, and possibly normal/abnormal
    4443    * want to avoid terms which are not 'disjoint'
    4544
    46    * describing multinucleate...HOW?  https://github.com/pombase/fypo/issues/1764
    47      Need to find out when a cell is considered separate cells Frist. Asking Jacky and Mohan
     45   * describing multinucleate...HOW? https://github.com/pombase/fypo/issues/1764
     46     Need to find out when a cell is considered separate cells first. Asking Jacky and Mohan
    4847 
    4948   * Did we decide for sure whether 'abolished' means (to the best of our knowledge..) 'does not start at all' or 'may start but never completes' (I tend to use it in the latter sense, but Midori seemed to favour the former?).
    50      * e.g chromosome segregation and  https://sourceforge.net/p/pombase/fission-yeast-phenotype/1726/
     49    * e.g chromosome segregation and  https://github.com/pombase/fypo/issues/1711
    5150     (Midori is asking about the PATO structure)
    52 
    53      * Things to do after multi-gene phenotypes  available ==
    54           * update curation tool documentation
    55           * get some example multigene phenotypes visible on  pomBase pages ( where is display mock-up )
    56           * update pombase web documentation to reflect new in
    57           * announce multi gene phenotype availability
    58           * make  podcasts to demo curation tool (announce on pombelist)
    59           * send out session reminders, and new sessions
    60           * target individual groups who have not participated, or who have stalled sessions
     51    * Things to do after multi-gene phenotypes available
     52     * update curation tool documentation (first draft done; curators to review)
     53     * get some example multigene phenotypes visible on  pomBase pages (q: where is display mock-up? a: [https://www.ebi.ac.uk/panda/jira/browse/PB-1840 compact] [https://www.ebi.ac.uk/panda/jira/browse/PB-1839 full])
     54     * update pombase web documentation to reflect new in
     55     * announce multi-gene phenotype availability
     56     * make podcasts to demo curation tool (announce on pombelist)
     57     * send out session reminders, and new sessions
     58     * target individual groups who have not participated, or who have stalled sessions
    6159 
    6260   * annotate to protein complex ID (can get from PRO)?
    63    * example: PMID:18723846 has direct assays showing ORC binding to origin DNA, but doesn't distinguish subunits; from other work, it's known that some but not all ORC subunits actually make contact with DNA. Annotate all to DNA binding anyway, with or without contributes_to, or annotate to a complex ID? (I'd prefer the latter but will it break anything?)
     61   * example: PMID:18723846 has direct assays showing ORC binding to origin DNA, but doesn't distinguish subunits; from other work, it's known that some but not all ORC subunits actually make contact with DNA. Annotate all to DNA binding anyway, with or without contributes_to, or annotate to a complex ID? (I'd (m) prefer the latter but will it break anything?)
    6462   * same paper: similar issue for annotation extension - cdt1 or cdc18 increase ORC origin binding - put complex ID in has_regulation_target ext?
    65      * Next step here is to request complex IDs for known complexes from PRO
    66         * Then need to discuss what is needed to annotate to complexes (Canto, Complex pages- which data will be propagated to complex pages from gene pages and vice versa)
     63    * Next step here is to request complex IDs for known complexes from PRO
     64     * Then need to discuss what is needed to annotate to complexes (Canto, Complex pages- which data will be propagated to complex pages from gene pages and vice versa)
    6765
    6866 
    6967  == Next Tasks ==
    7068
    71 
    72     * conflicting extensions used for 'binding of promoter' 'binds' and 'at', see cdc10 and res2
    73 
    74 
    75   * dropbox
    76 
    77  
    78 
    79   * multgene phenotype format  input/output (there is one dataset for this....which one?)
    80 
    81  
    82  
    83  
    84  
    85   * should we filter  redundant ISS?  (I think we should, but we would want them to take precedence over IEA, currently filtering is not specific for evidence code)
    86  
    87   * Q when we say ‘arrest’ what do we mean?, should all 'arrest' phenotypes distinguish between normal and abnormal (should cell cycle arrest phenotype, and some children, be not for direct annotation)
     69 * conflicting extensions used for 'binding of promoter' 'binds' and 'at', see cdc10 and res2
     70 * dropbox
     71 * multgene phenotype format  input/output (there is one dataset for this....which one?)
     72 * should we filter  redundant ISS?  (I think we should, but we would want them to take precedence over IEA, currently filtering is not specific for evidence code)
     73 * Q when we say ‘arrest’ what do we mean?, should all 'arrest' phenotypes distinguish between normal and abnormal (should cell cycle arrest phenotype, and some children, be not for direct annotation)
    8874
    8975
     
    11197 
    11298  * Discuss regulation of G1/S in relation to  6ff4c9edff12167b (look at annotation in context of all genes in this session)
    113   * no entry into meiosis and cell cycle phenotype https://sourceforge.net/p/pombase/fission-yeast-phenotype/709/
     99  * no entry into meiosis and cell cycle phenotype https://github.com/pombase/fypo/issues/708
    114100
    115101 === Transcription ===
     
    130116 * Canto documentation required
    131117  * From Scott: provide even one paper and walk the user through entering the paper, the genes and a sample entry.  Then you could also walk through an administrative approval and saving the data to Chado (Kim suggested we start with just a list of bullet points)
    132   * and https://sourceforge.net/p/pombase/curation-tasks/365/
     118  * and https://github.com/pombase/curation/issues/384
    133119 * Tidy wiki, move obsolete pages
    134120
     
    138124  * Val will get UK lab list (done)
    139125  * Midori will draft e-mail (done)
    140   * after BYGa and Toronto, will begin to pin down dates. Antonia will try to set up some whilst at BYG
     126  * after BYG and Toronto, will begin to pin down dates. Antonia will try to set up some whilst at BYG
    141127   
    142128   * Newsletter?
    143129   * Gene naming 3578 genes  primary name assigned (now 3671)
    144130   * annotation complete genes
    145    *  annotation amnestly
     131   * annotation amnesty
    146132   * solicit more HTP datasets 
    147133   * unknowns
     
    173159  * collection of phenotype images
    174160
    175   * Low penetracne check (I think this is about population phenotype-> fully penetrant?)
     161  * Low penetrance check (I think this is about population phenotype-> fully penetrant?)
    176162 
    177163  * Idea for accessing completed curation sessions add review links to paper section for community curated papers
     
    184170    * preparing HTP datasets
    185171    * community curation demo etc
    186     * alignments Draw attention too specifically, Update re improved alignments  and Schizos new 'did you knows'
    187     *  [wiki:CommunityAlerts]
     172    * alignments Draw attention too specifically, Update re improved alignments and Schizos new 'did you knows'
     173    * [wiki:CommunityAlerts]
    188174    etc
    189175
     
    204190
    205191  * Curating alternative transcripts
    206     * https://sourceforge.net/p/pombase/curation-tasks/31/
    207     * related - [https://sourceforge.net/p/pombase/curation-tasks/325/ uvi15 UTRs] 
     192   * https://github.com/pombase/curation/issues/61
     193    * includes notes about uvi15 UTRs (previously in separate ticket)
    208194
    209195  * how to represent the reintegration assays ? (see for example !Alper/Partridge and !Shanker/Partridge