Changes between Version 134 and Version 135 of PombasePlanningMeetingAgendaNext


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Timestamp:
Dec 17, 2012, 8:05:10 PM (9 years ago)
Author:
gomidori
Comment:

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  • PombasePlanningMeetingAgendaNext

    v134 v135  
    11October 2012
    22
    3  == Outstanding Action items from July ==
     3 == Outstanding Action items from previous meeting ==
    44
    5     * Action: Documentation task for curators; in progress
     5    * Action:
    66
    7  == New Action items from July ==
     7 == New Action items ==
    88
    9     * Action: Curators look into acquiring data from strain collection in Japan
    10     * Action: Curators to monitor web site for problems (ongoing)
    11     * Action: Functional genomics views demo at next meeting (EBI)
    12     * Action: Val to circulate non-redundant list of genome browser requests & feedback from community
    13     * Action: PK et al. to create Jira tracker for Ensembl genome browser issues; PK to triage tickets
    14     * Action: Diagnose the cause of the not synching of the update (Mark)
    15 
    16  == Ensembl Functional Genomics Module Demo ==
     9    * Action:
    1710
    1811
    1912 == General ==
    2013
    21  * Usage stats http://tinyurl.com/7qs2zap
     14 * Usage stats
    2215
    2316= Updates from various Areas =
     
    2518== Curation Update ==
    2619 
    27  * All papers are triaged (upto ~August?)
    28  * Of 9510 papers 4602 are "curatable" with gene product specific information
    29  * 3550 annotations in curation tool
    30  * 591 curation session (papers) in progress
    31  * 299 approved
    32  * 47 needing approval
    33  * 153 newer have been identified as community curatable, not sure how many in progress/ sent out but 19 have been completed and approved by community (5 from Ryoko Mandeville, Nurse lab)
     20 * triage
     21 * sessions
     22 * etc.
    3423
    3524 == Phenotype Ontology ==
    36  * 1625  phenotype terms
    37  * Reasoner deployed to check logical consistency
    38  * Midori has written a paper describing the ontology which will be submitted to Genome biology shortly
     25 * n  phenotype terms
     26 * anything else
    3927 
    4028
    4129 == Chado loading ==
    42  * allele names, allele description, conditions now loaded into Chado
    43  * GO and BioGrid export format nearly complete
     30 * anything
    4431 
    4532 == Curation tool ==
    46  * Curtion tool individual data items are now "editable"
    47  * Curation tool deployed for pichia
    48  * Curation tool deployed for Ruth Loverings GO curation workshop at UCL
    49  * speed improvements
    50  * lucene search improvements
    51  * Interface for curating allele/description/expression/conditions (single genes phenotypes)
    52  * Lots of small fixes
     33 * anything
    5334
    54  == Review "Post-preview" and "GeneDB decommissioning" criteria & progress ==
     35 == Review priorities & progress ==
    5536
    56  Current jira status: Open 161 Closed/Resolved  808  (was 150/655 last meeting, July)
     37 Current jira status:
    5738
    58  === Next priorities  (Pombase website) ===
    59 
    60 1. Host new dataset with curation tool annotations (2000? check annotations)
    61 
    62   * This is now on stage/dev with a few tickets which still need to be cleared to get the new data hosted       
    63    
    64 
    65 The next dataset (nG 28) si the first one to include display of
    66      * All annotation from  completed sessions curated in the curation tool
    67      * phenotype data with alleles
    68      * annotation extensions on GO data
    69      * manual human orthologs (final in  Chado load 29)
    70 
    71 Once this is done, curators can announce phenotypes, annotation extensions and new annotation from curation tool (and promote community curation) via pombelist. Once NG v29 is hosted, human ortholog data can be announced.
    72 
    73 
    74 2. GeneDB decommissioning tasks
    75      * Next prioities for Mark, 15 jira items
    76 
    77 3. Post GeneDB decommissioning tasks 16 items
    78    These are features which are provided by GeneDB, and used, but are not as critical. Provided they are replaced fairly quickly people can probably survive for a while if the old site is taken down
    79 
    80 4. Hosting genome wide datasets
    81 
    82 5. Unscheduled items (103)
    83 
    84 
    85  == Problems reported ==
    86    
    87  * wildcard search issue, lucene cannot accept wildcard at the front of search. Can we work around this somehow?
    8839
    8940== Meetings Attended/ Upcoming ==
    9041
    91  * GO meeting next week (Pasadena). Curators will attend remotely
    92  * proposed Workshop for 2013 (International meeting) straw poll?
    93  * Proposed Pombase 1-2 hour workshop at CRUK, with 1-2 hour curation tool demo and or jamboree
    94  
     42 * item
    9543
    9644 == AOB ==
    9745
    98  * incentives for community curation, amazon voucher 'curator of the month'
    99  * Some issues from Jurg
    100  * Next meeting  (doodle)
    101 
     46 * item
    10247
    10348 == PI's meeting ==