Changes between Initial Version and Version 1 of PombasePlanningMeetingAgenda20121004


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Timestamp:
Dec 17, 2012, 8:00:29 PM (8 years ago)
Author:
gomidori
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  • PombasePlanningMeetingAgenda20121004

    v1 v1  
     1October 2012
     2
     3 == Outstanding Action items from July ==
     4
     5    * Action: Documentation task for curators; in progress
     6
     7 == New Action items from July ==
     8
     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 ==
     17
     18
     19 == General ==
     20
     21 * Usage stats http://tinyurl.com/7qs2zap
     22
     23= Updates from various Areas =
     24
     25== Curation Update ==
     26 
     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)
     34
     35 == 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
     39 
     40
     41 == Chado loading ==
     42 * allele names, allele description, conditions now loaded into Chado
     43 * GO and BioGrid export format nearly complete
     44 
     45 == 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
     53
     54 == Review "Post-preview" and "GeneDB decommissioning" criteria & progress ==
     55
     56 Current jira status: Open 161 Closed/Resolved  808  (was 150/655 last meeting, July)
     57
     58 === Next priorities  (Pombase website) ===
     59
     601. 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
     65The 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
     71Once 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
     742. GeneDB decommissioning tasks
     75     * Next prioities for Mark, 15 jira items
     76
     773. 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
     804. Hosting genome wide datasets
     81
     825. 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?
     88
     89== Meetings Attended/ Upcoming ==
     90
     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 
     95
     96 == AOB ==
     97
     98 * incentives for community curation, amazon voucher 'curator of the month'
     99 * Some issues from Jurg
     100 * Next meeting  (doodle)
     101
     102
     103 == PI's meeting ==