Changes between Version 174 and Version 175 of CuratorMeeting


Ignore:
Timestamp:
Jan 25, 2012, 1:50:55 PM (10 years ago)
Author:
val_wood
Comment:

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  • CuratorMeeting

    v174 v175  
    4242 * Need a list of curation tool features, existing and proposed
    4343
    44  
    45 
    4644
    4745
    4846== Tuesday 24rd a.m. ==
    4947
    50  * Get Antonia's visitor pass
    51 
     48 
    5249== To discuss with Kim ==
    5350
    54   * Get Artemis running for Antonia
    55 
    56  * Next things for Kim to work on (rough order)
    57     * 1. admin related, ,managing session status
    58     * 2. Triage options and refinement of,
    59     * 3. refine phenotype to cope with multiple phenotype
     51
     52 * Next things for Kim to work on (rough order) Curation tool
     53   
    6054      * need to thrash out allele descriptions
    6155      * Val needs to check that the proposal to change the tool fits with the phenotype format/model
     
    6458      * ii) annotation transfer of extensions and qualifier
    6559    * 5. New datatypes, expression (dependent on outcome of discussion below), complementation (probably we will split out complementation as a curation type in the tool), protein sequence features (subset of SO)
    66 
    67 === Curation tool ===
    68 
    69    * GO through high priority SF items  (1 & 2 above)
     60      * GO through high priority SF items  (1 & 2 above)
     61
    7062   
    7163         
     
    7668   * Implications of sequence change for residues and alleles , checks curators need to take, also need to discuss this with Mark
    7769
    78 While Kim and Mark chat curators can get on with some of Antonia's questions below
     70
    7971
    8072== Tuesday 24rd p.m. ==
     
    8375== To discuss with Mark ==
    8476
    85    * val questions for Mark
    86      * see folder, includes GO slim/ convergent genes query (user queries generally)/ chado version/ usage stats
    87 
     77   
    8878   * Usage stats, updates for planning meeting
    8979
    90    * Announcements for updated things/ new features
    91 
    92    * UTRs on gene pages/ in Ensembl (access to db_xref & sequence)
    93      see http://www.ebi.ac.uk/panda/jira/browse/PB-471
    94 
    95    * Query tool  (add relevant SF items)
    96       * Discuss exactly what options can be done in the interface vs. history
    97          * do we need the interface? or just the history  if it was clear that query  manipulation can be done here
    98          *  If we need the interface, how will it be obvious how nesting is done?
    99       * Discuss use of  i) Add ii) AND/OR vs. Intersect/union (pretty much decided by email -m)
    100       * What is being searched by the query tool keyword search? (see http://www.ebi.ac.uk/panda/jira/browse/PB-537 -m)
    101       * Ability to upload user defined list send user defined list to query/ query download options
    102       * ability to send lists from Genedb to query history/download
    103          * Discuss Is evidence required in GO gene list? what happens if more than one evidence? (consistency?) see Genes annotated with GO:2000045 - regulation of G1/S transition of mitotic cell cycle (biological_process)
    104          * lists look different in different places, make gene list look more similar to query builder results list
    105  
    106      * Download file options         
    107         * filenames .html confusing
    108         * can the files render in the browser, or as GeneDB separate options for viewing in browser and download?
    109         * tab delimited file options
    110           * can files be tab delimited rather than comma?
    111           * Gene names list default
    112           * Allow user to select additional column options, other names, product, GO annotations, orthologs (yeast, human-later), interaction
    113          * Sequence download option
    114           * "real" UTRs or upstream downstream regions as a sequence download option
    115           http://www.ebi.ac.uk/panda/jira/browse/PB-444
    116           http://www.ebi.ac.uk/panda/jira/browse/PB-514
    117          
    118 
    119       * Display of sequence features http://www.ebi.ac.uk/panda/jira/browse/PB-510
    120 
    121    * replacing current ftp site and download files (currently links to Sanger and matches GeneDB datasets)
    122       * migration of Sanger ftp site
    123 
    124    * EG release cycle, advance warning for deadline for changes (procedures in place to let us know as soon as you know the dates)
    125 
    126 
    127 
    128    * Future user configuration of gene pages,
     80All items from discussion with mark added to relelvent jira tracker item, other action items
     81
     82   * Download file options  (val to document)       
     83   * replacing current ftp site and download files (val to document)
     84
     85
     86Future tasks
     87   * User configuration of gene pages (discuss in detail in future)
    12988      * Ability to collapse/open sections by default
    13089      * Ability to configure order of sections on gene pages
    13190      * Some sections may become so long that we need to rethink how redundant data is presented (Antonia's examples)
    13291
    133    * Brief discussion about future suppression of redundancy on the gene pages (may depend on avaiability of user configuration)
    134 
    135    * Unlinking names from Ensembl http://www.ebi.ac.uk/panda/jira/browse/PB-555
    136      Names from August onwards are not yet appearing in PomBase so we are very "out of synch"
    137 
    138    * Brief discussion about column 17 display (this might result in a new jira item)
     92   * Discuss column 17 display (this might result in a new jira item)
    13993
    14094   * Where did the annotation_extension data preview go (It was nearly right....)
    141 
    142    * new data associated with phenotypes http://www.ebi.ac.uk/panda/jira/browse/PB-492
    143 
    144    * Compiling new features and sending to the mailing list
    145 
    146    * Demo "assembly re-mapper" to us
    147 
    14895
    14996   * Update planning meeting agenda based on discussions with Mark and any newly completed jira items