Changes between Initial Version and Version 1 of PombasePlanningMeetingAgenda20130121


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Timestamp:
Jan 22, 2013, 11:10:40 AM (8 years ago)
Author:
val_wood
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  • PombasePlanningMeetingAgenda20130121

    v1 v1  
     1(January 21st 2013)
     2
     3 == Outstanding Action items from November ==
     4
     5 * AI Organise a large general "!PomBase" banner
     6 * Demo of curation tool (postponed)
     7 * Send papers to Paul K.
     8 * AI Val/curators  will start to send out a large number of  community  curation sessions (postponed until new session management and documenation is in place. Will continue to send out small numbers of papers)
     9 * AI Sam's data, decided to add "condition" Val will contact Sam, also need to add PMID and chase "quiescence term", then decide where this data should live (decided Kim's ftp directory or pombe-embl svn repository)
     10
     11 ==  New action items from December ==
     12 
     13* '''VW''' chase up pombe community browser feedback as have not responded to recent requests (DONE, not sure if anyone has responsded still)
     14 * ''VW'' Look into WT grant and forward details to Jürg (DONE, Jurg thinks not appropriate. Val has written application for money for catering for poster session at ISB)
     15 * Redesign of the !PomBase front page.
     16   *  VW open new jira item  with mock up (DONE)
     17   * '''VW''': Source some images of cells that could be used.
     18   * '''VW''': Highlight specific papers to display on the front page
     19   * '''MM''': Convert to a multi-column format.
     20 * '''MM''': Load the transcriptome datasets listed on JIRA
     21 * '''MM''': Update xref names before running the update annotation scripts.
     22 * MM takes some time to consider the order of the loading for GO term names and gene names (related to above)
     23 * '''PK/DS/MM''': EMBL submission files.  Work out what is going to happen with these going forward (for this Val will first test how close the current file is )
     24 * Search:
     25   * '''MM''': Auto-regenerate the search indexes and get ES to set up a new domain and index the !PomBase dumps.
     26   * '''MM''': Get the simple search to include the orthologues (DONE)
     27   * '''All curators''': discussion to nail down what search options and behaviour we really want, then update Jira
     28(DONE  see http://www.ebi.ac.uk/panda/jira/browse/PB-1127)
     29   * '''VW''' to chase up motif search code from Sanger (DONE)
     30   * '''VW/MAH''' to look into where UTR.fasta data came from - DONE
     31 * '''KR''': Generate v31 Chado dump (DONE)
     32 * '''DS/MM''': GFF and GTF usage standardisation in ensembl for downloads.   Needs assigning.
     33 * '''KR''': Work on the Session Management for the curation tool.
     34
     35 
     36
     37 == New Agenda Items ==
     38
     39  * speed and page loading
     40  http://www.ebi.ac.uk/panda/jira/browse/PB-1140
     41  (for examples 40,000 new interactions will come from a single paper in next bioGRID update)
     42
     43  * wild card searching "Not being able to search on partial gene names or IDs"
     44
     45  * It is particularly important that the curators know  in advance that a particular dataset will be taken
     46 i)  to be  used in Ensembl and ii) to be hosted as the next version in PomBase.
     47just in case we know of any issues with these datasets that we are in the process of fixing etc.etc.
     48
     49 (we also usually do a run, check the logs, fix warnings and do another run)
     50
     51 *  Turnaround time of < 2 months  is too long once community curation is launched (version 30 is from  12
     52November). We should talk about ways to improve this (most MODs update nightly).
     53
     54
     55 * implement the RNA/protein expression data from Sam's paper
     56    *  The file format is described here and was supplied in this format be Sam https://sourceforge.net/apps/trac/pombase/wiki/CapturingGeneExpression
     57        * put files in /pombe-embl/
     58        * extend the file format documentation to include "condition" (AI Antonia)
     59        * liaise with Sam to include this in his data  using condition ontology terms/IDs (AI ANtonia)
     60        * ensure the PMID column is populated
     61        * update files from other labs formatted by Sam
     62     * need an ontology term for quiescence..... quiescence is a state, not a process...
     63        * In GO "cell cycle quiescence" is currently a related synonym of G1 to G0 transition              https://sourceforge.net/tracker/?func=detail&aid=3577358&group_id=36855&atid=440764
     64        *  history https://sourceforge.net/tracker/?func=detail&aid=3049742&group_id=36855&atid=440764 https://sourceforge.net/tracker/?func=detail&aid=2810209&group_id=36855&atid=440764
     65        *  need some way to describe that this data is from quiescent cells. Maybe we  can just allow the string "quiescence" in this field temporarily?
     66     * Go through the tracker item with Mark http://www.ebi.ac.uk/panda/jira/browse/PB-1002
     67
     68     * phenotype allele display,
     69        * http://www.ebi.ac.uk/panda/jira/browse/PB-1074
     70        * http://www.ebi.ac.uk/panda/jira/browse/PB-1083 (merge)
     71
     72     * Gene name synching (e.g.  why is mre11 still called rad32…was changed in early November?)
     73
     74     * What do we need to tell CRUK lab heads to resolve their fire wall problem ? 
     75 
     76     * Helpdesk Did anyone answer the GFF/GTF query
     77       * General helpdesk procedure. ...answer  within a couple of days
     78       
     79
     80 == General ==
     81
     82 * Usage stats
     83  * Usage stats http://tinyurl.com/7qs2zap
     84
     85= Updates from various Areas =
     86
     87== Curation Update ==
     88 
     89 * triage
     90 * sessions, not much curation 441 approved sessions up from 432
     91 *  A few communiyt curation, but still not sent out bulk
     92   * http://curation.pombase.org/pombe/curs/2306fd737a53d0b4 (Labbe user feedback eg)
     93   * http://curation.pombase.org/pombe/curs/5c30b3bf5c5da95c (Songtao jia new terms)
     94   * http://curation.pombase.org/pombe/curs/7c5a980860f3b18c (Colm, new terms)
     95
     96 == Phenotype Ontology ==
     97 * n  phenotype terms
     98 * anything else
     99 
     100
     101 == Chado loading ==
     102 * anything
     103 
     104 == Curation tool ==
     105 * anything
     106
     107 == Review priorities & progress ==
     108
     109 Current jira status:
     110
     111
     112== Meetings Attended/ Upcoming ==
     113
     114 * 28 Feb/ 1 MArch GO cell cycle ontology contant meeting ( GO and Jacky Hayles)
     115
     116 * March 20-22 BYG 2 posters submitted:  Antonia (community curation), Midori (phenotype ontology)
     117
     118
     119 *  April 7-10 ISB, 4 posters submitted: Val (Annotation QC, general PomBase), Antonia (community curation), Midori (phenotype ontology)
     120   Mark might want to attend, at least poster sessions?
     121   * April 10-13 GO meeting is immediately after this meeting,  Mark should attend the software sessions
     122 
     123 * Pombe meeting, still need to decide what to do about PomBase/GO/curation demo
     124 
     125
     126
     127 == AOB ==
     128
     129 * item
     130
     131 == PI's meeting ==
     132